@article{roberts_spang_sanozky-dawes_nethery_barrangou_2024, title={Characterization of Ligilactobacillus salivarius CRISPR-Cas systems}, url={https://doi.org/10.1128/msphere.00171-24}, DOI={10.1128/msphere.00171-24}, abstractNote={ABSTRACT Ligilactobacillus is a diverse genus among lactobacilli with phenotypes that reflect adaptation to various hosts. CRISPR-Cas systems are highly prevalent within lactobacilli, and Ligilactobacillus salivarius , the most abundant species of Ligilactobacillus , possesses both DNA- and RNA-targeting CRISPR-Cas systems. In this study, we explore the presence and functional properties of I-B, I-C, I-E, II-A, and III-A CRISPR-Cas systems in over 500 Ligilactobacillus genomes, emphasizing systems found in L. salivarius . We examined the I-E, II-A, and III-A CRISPR-Cas systems of two L. salivarius strains and observed occurrences of split cas genes and differences in CRISPR RNA maturation in native hosts. This prompted testing of the single Cas9 and multiprotein Cascade and Csm CRISPR-Cas effector complexes in a cell-free context to demonstrate the functionality of these systems. We also predicted self-targeting spacers within L. salivarius CRISPR-Cas systems and found that nearly a third of L. salivarius genomes possess unique self-targeting spacers that generally target elements other than prophages. With these two L. salivarius strains, we performed prophage induction coupled with RNA sequencing and discovered that the prophages residing within these strains are inducible and likely active elements, despite targeting by CRISPR-Cas systems. These findings deepen our comprehension of CRISPR-Cas systems in L. salivarius , further elucidating their relationship with associated prophages and providing a functional basis for the repurposing of these Cas effectors for bacterial manipulation. IMPORTANCE Ligilactobacillus salivarius is a diverse bacterial species widely used in the food and dietary supplement industries. In this study, we investigate the occurrence and diversity of their adaptive immune systems, CRISPR-Cas, in over 500 genomes. We establish their function and provide insights into their role in the interplay between the bacterial host and the predatory phages that infect them. Such findings expand our knowledge about these important CRISPR-Cas immune systems widespread across the bacterial tree of life and also provide a technical basis for the repurposing of these molecular machines for the development of molecular biology tools and the manipulation and engineering of bacteria and other life forms.}, journal={mSphere}, author={Roberts, Avery and Spang, Daniel and Sanozky-Dawes, Rosemary and Nethery, Matthew A. and Barrangou, Rodolphe}, editor={Ellermeier, Craig D.Editor}, year={2024}, month={Jul} }
 @article{barrangou_2024, title={Surveying the State of CRISPR and Gene Editing}, volume={7}, ISSN={["2573-1602"]}, url={https://doi.org/10.1089/crispr.2024.0045}, DOI={10.1089/crispr.2024.0045}, number={3}, journal={CRISPR JOURNAL}, author={Barrangou, Rodolphe}, year={2024}, month={Jun}, pages={133–134} }
 @article{gilfillan_vilander_pan_goh_o'flaherty_feng_fox_lang_greenberg_abdo_et al._2023, title={<i>Lactobacillus acidophilus</i> Expressing Murine Rotavirus VP8 and Mucosal Adjuvants Induce Virus-Specific Immune Responses}, volume={11}, ISSN={["2076-393X"]}, url={https://www.mdpi.com/2076-393X/11/12/1774}, DOI={10.3390/vaccines11121774}, abstractNote={Rotavirus diarrhea-associated illness remains a major cause of global death in children under five, attributable in part to discrepancies in vaccine performance between high- and low-middle-income countries. Next-generation probiotic vaccines could help bridge this efficacy gap. We developed a novel recombinant Lactobacillus acidophilus (rLA) vaccine expressing rotavirus antigens of the VP8* domain from the rotavirus EDIM VP4 capsid protein along with the adjuvants FimH and FliC. The upp-based counterselective gene-replacement system was used to chromosomally integrate FimH, VP8Pep (10 amino acid epitope), and VP8-1 (206 amino acid protein) into the L. acidophilus genome, with FliC expressed from a plasmid. VP8 antigen and adjuvant expression were confirmed by flow cytometry and Western blot. Rotavirus naïve adult BALB/cJ mice were orally immunized followed by murine rotavirus strain ECWT viral challenge. Antirotavirus serum IgG and antigen-specific antibody-secreting cell responses were detected in rLA-vaccinated mice. A day after the oral rotavirus challenge, fecal antigen shedding was significantly decreased in the rLA group. These results indicate that novel rLA constructs expressing VP8 can be successfully constructed and used to generate modest homotypic protection from rotavirus challenge in an adult murine model, indicating the potential for a probiotic next-generation vaccine construct against human rotavirus.}, number={12}, journal={VACCINES}, author={Gilfillan, Darby and Vilander, Allison C. and Pan, Meichen and Goh, Yong Jun and O'Flaherty, Sarah and Feng, Ningguo and Fox, Bridget E. and Lang, Callie and Greenberg, Harry B. and Abdo, Zaid and et al.}, year={2023}, month={Dec} }
 @article{foley_walker_stewart_o'flaherty_gentry_patel_beaty_allen_pan_simpson_et al._2023, title={Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut}, volume={3}, ISSN={["2058-5276"]}, DOI={10.1038/s41564-023-01337-7}, abstractNote={Abstract}, journal={NATURE MICROBIOLOGY}, author={Foley, Matthew H. and Walker, Morgan E. and Stewart, Allison K. and O'Flaherty, Sarah and Gentry, Emily C. and Patel, Shakshi and Beaty, Violet V. and Allen, Garrison and Pan, Meichen and Simpson, Joshua B. and et al.}, year={2023}, month={Mar} }
 @article{barrangou_2023, title={CRISPR Technology and its Many Applications with Select Examples Related to Animal Agriculture}, volume={101}, ISSN={["1525-3163"]}, DOI={10.1093/jas/skad068.001}, abstractNote={Abstract}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Barrangou, Rodolphe}, year={2023}, month={May} }
 @article{adler_trinidad_bellieny-rabelo_zhang_karp_skopintsev_thornton_weissman_yoon_chen_et al._2023, title={CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes}, volume={10}, ISSN={["1362-4962"]}, url={https://doi.org/10.1093/nar/gkad890}, DOI={10.1093/nar/gkad890}, abstractNote={Abstract}, journal={NUCLEIC ACIDS RESEARCH}, author={Adler, Benjamin A. and Trinidad, Marena I and Bellieny-Rabelo, Daniel and Zhang, Elaine and Karp, Hannah M. and Skopintsev, Petr and Thornton, Brittney W. and Weissman, Rachel F. and Yoon, Peter H. and Chen, Linxing and et al.}, year={2023}, month={Oct} }
 @article{page_perez-diaz_pan_barrangou_2023, title={Genome-Wide Comparative Analysis of Lactiplantibacillus pentosus Isolates Autochthonous to Cucumber Fermentation Reveals Subclades of Divergent Ancestry}, volume={12}, ISSN={["2304-8158"]}, url={https://doi.org/10.3390/foods12132455}, DOI={10.3390/foods12132455}, abstractNote={Lactiplantibacillus pentosus, commonly isolated from commercial cucumber fermentation, is a promising candidate for starter culture formulation due to its ability to achieve complete sugar utilization to an end pH of 3.3. In this study, we conducted a comparative genomic analysis encompassing 24 L. pentosus and 3 Lactiplantibacillus plantarum isolates autochthonous to commercial cucumber fermentation and 47 lactobacillales reference genomes to determine species specificity and provide insights into niche adaptation. Results showed that metrics such as average nucleotide identity score, emulated Rep-PCR-(GTG)5, computed multi-locus sequence typing (MLST), and multiple open reading frame (ORF)-based phylogenetic trees can robustly and consistently distinguish the two closely related species. Phylogenetic trees based on the alignment of 587 common ORFs separated the L. pentosus autochthonous cucumber isolates from olive fermentation isolates into clade A and B, respectively. The L. pentosus autochthonous clade partitions into subclades A.I, A.II, and A.III, suggesting substantial intraspecies diversity in the cucumber fermentation habitat. The hypervariable sequences within CRISPR arrays revealed recent evolutionary history, which aligns with the L. pentosus subclades identified in the phylogenetic trees constructed. While L. plantarum autochthonous to cucumber fermentation only encode for Type II-A CRISPR arrays, autochthonous L. pentosus clade B codes for Type I-E and L. pentosus clade A hosts both types of arrays. L. pentosus 7.8.2, for which phylogeny could not be defined using the varied methods employed, was found to uniquely encode for four distinct Type I-E CRISPR arrays and a Type II-A array. Prophage sequences in varied isolates evidence the presence of adaptive immunity in the candidate starter cultures isolated from vegetable fermentation as observed in dairy counterparts. This study provides insight into the genomic features of industrial Lactiplantibacillus species, the level of species differentiation in a vegetable fermentation habitat, and diversity profile of relevance in the selection of functional starter cultures.}, number={13}, journal={FOODS}, author={Page, Clinton A. and Perez-Diaz, Ilenys M. and Pan, Meichen and Barrangou, Rodolphe}, year={2023}, month={Jul} }
 @article{o'flaherty_cobian_barrangou_2023, title={Impact of Pomegranate on Probiotic Growth, Viability, Transcriptome and Metabolism}, volume={11}, ISSN={["2076-2607"]}, url={https://doi.org/10.3390/microorganisms11020404}, DOI={10.3390/microorganisms11020404}, abstractNote={Despite rising interest in understanding intestinal bacterial survival in situ, relatively little attention has been devoted to deciphering the interaction between bacteria and functional food ingredients. Here, we examined the interplay between diverse beneficial Lactobacillaceae species and a pomegranate (POM) extract and determined the impact of this functional ingredient on bacterial growth, cell survival, transcription and target metabolite genesis. Three commercially available probiotic strains (Lactobacillus acidophilus NCFM, Lacticaseibacillus rhamnosus GG and Lactiplantibacillus plantarum Lp-115) were used in growth assays and flow cytometry analysis, indicating differential responses to the presence of POM extract across the three strains. The inclusion of POM extract in the growth medium had the greatest impact on L. acidophilus cell counts. LIVE/DEAD staining determined significantly fewer dead cells when L. acidophilus was grown with POM extract compared to the control with no POM (1.23% versus 7.23%). Whole-transcriptome analysis following exposure to POM extract showed markedly different global transcriptome responses, with 15.88% of the L. acidophilus transcriptome, 19.32% of the L. rhamnosus transcriptome and only 2.37% of the L. plantarum transcriptome differentially expressed. We also noted strain-dependent metabolite concentrations in the medium with POM extract compared to the control medium for punicalagin, ellagic acid and gallic acid. Overall, the results show that POM extract triggers species-specific responses by probiotic strains and substantiates the rising interest in using POM as a prebiotic compound.}, number={2}, journal={MICROORGANISMS}, author={O'Flaherty, Sarah and Cobian, Natalia and Barrangou, Rodolphe}, year={2023}, month={Feb} }
 @article{raftopoulou_barrangou_2023, title={Mining microbial organisms to discover and characterize novel CRISPR-Cas systems}, volume={27}, ISSN={["2468-4511"]}, url={https://doi.org/10.1016/j.cobme.2023.100469}, DOI={10.1016/j.cobme.2023.100469}, abstractNote={The need for new genome manipulation tools is leading the way for the continued discovery of novel clustered regularly interspaced short palindromic repeats— CRISPR associated sequences (CRISPR-Cas) systems. Researchers have been analyzing the genomes of prokaryotes and more recently metagenomic sequencing data to find novel and diverse CRISPR-Cas systems and their associated genome editing effectors. In this review, we provide an overview of in silico, in vitro, and in vivo analyses performed to characterize key elements of CRISPR-Cas systems, encompassing the CRISPR array, Cas proteins, guide ribonucleic acid (RNAs), and protospacer-adjacent motif (PAM) which defines targeting. We also highlight subsequent in vitro and in vivo assays employed to validate CRISPR function and Cas effector activity in the context of genome editing in various cellular contexts.}, journal={CURRENT OPINION IN BIOMEDICAL ENGINEERING}, author={Raftopoulou, Ourania and Barrangou, Rodolphe}, year={2023}, month={Sep} }
 @article{sulis_jiang_yang_marques_matthews_miller_lan_cofre-vega_liu_sun_et al._2023, title={Multiplex CRISPR editing of wood for sustainable fiber production}, volume={381}, ISSN={["1095-9203"]}, url={http://europepmc.org/abstract/med/37440632}, DOI={10.1126/science.add4514}, abstractNote={The domestication of forest trees for a more sustainable fiber bioeconomy has long been hindered by the complexity and plasticity of lignin, a biopolymer in wood that is recalcitrant to chemical and enzymatic degradation. Here, we show that multiplex CRISPR editing enables precise woody feedstock design for combinatorial improvement of lignin composition and wood properties. By assessing every possible combination of 69,123 multigenic editing strategies for 21 lignin biosynthesis genes, we deduced seven different genome editing strategies targeting the concurrent alteration of up to six genes and produced 174 edited poplar variants. CRISPR editing increased the wood carbohydrate-to-lignin ratio up to 228% that of wild type, leading to more-efficient fiber pulping. The edited wood alleviates a major fiber-production bottleneck regardless of changes in tree growth rate and could bring unprecedented operational efficiencies, bioeconomic opportunities, and environmental benefits.}, number={6654}, journal={SCIENCE}, author={Sulis, Daniel B. and Jiang, Xiao and Yang, Chenmin and Marques, Barbara M. and Matthews, Megan L. and Miller, Zachary and Lan, Kai and Cofre-Vega, Carlos and Liu, Baoguang and Sun, Runkun and et al.}, year={2023}, month={Jul}, pages={216-+} }
 @article{pyhtila_kasowitz_leeson_barrangou_2023, title={The Expanding Dissemination and Distribution Patterns of Diverse CRISPR Plasmids by Addgene}, volume={11}, ISSN={["2573-1602"]}, url={https://doi.org/10.1089/crispr.2023.0059}, DOI={10.1089/crispr.2023.0059}, abstractNote={CRISPR-based technologies have rapidly enabled the democratization of genome editing in academic institutions through distribution by Addgene over the past decade. Recently, several distribution milestones have been reached, with a collection of >15,000 plasmids deposited by >1,000 laboratories spanning ∼40 countries now shipped 300,000 times to ∼5,000 organizations traversing ∼100 countries. Yet, both deposits of and requests for CRISPR plasmids continue to rise for this disruptive technology. Distribution patterns revealed robust demand for three distinct classes of CRISPR effectors, namely nucleases (e.g., Cas9 and Cas12), modulators (deactivated CRISPR nucleases fused to transcriptional regulators and epigenome modifiers), and chimeric effectors (Cas proteins fused to enzymes carrying out other activities such as deamination, reverse transcription, transposition, and integration). Yearly deposits over the past decade are requested in near-even proportions, reflecting continuous technological development and requests for novel constructs. Though it is unclear whether the slowing rate of requests is inherent to a pandemic operational lag or a transition from emerging to mature technology, it is noteworthy that the relative proportion of requests from plasmids deposited in the previous year remains stable, suggesting robust development of novel tools concurrent with continued adoption of editing, base editing, prime editing, and more. Predictably, most requested plasmids are designed for mammalian genome manipulation, presumably for medical research and human health pursuits, reflecting investments in therapeutic applications. Concurrently, requests for plant and microbial constructs are on the rise, especially in regions of the world more reliant on local agricultural inputs and focused on food and feed applications, illustrating continued diversification of genome editing applications.}, journal={CRISPR JOURNAL}, author={Pyhtila, Brook and Kasowitz, Seth and Leeson, Rachel and Barrangou, Rodolphe}, year={2023}, month={Nov} }
 @article{adler_hessler_cress_lahiri_mutalik_barrangou_banfield_doudna_2022, title={Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing}, volume={10}, ISSN={["2058-5276"]}, url={https://doi.org/10.1038/s41564-022-01258-x}, DOI={10.1038/s41564-022-01258-x}, abstractNote={Abstract}, journal={NATURE MICROBIOLOGY}, author={Adler, Benjamin A. and Hessler, Tomas and Cress, Brady F. and Lahiri, Arushi and Mutalik, Vivek K. and Barrangou, Rodolphe and Banfield, Jillian and Doudna, Jennifer A.}, year={2022}, month={Oct} }
 @article{nethery_hidalgo-cantabrana_roberts_barrangou_2022, title={CRISPR-based engineering of phages for in situ bacterial base editing}, volume={119}, ISSN={["1091-6490"]}, url={https://doi.org/10.1073/pnas.2206744119}, DOI={10.1073/pnas.2206744119}, abstractNote={
            Investigation of microbial gene function is essential to the elucidation of ecological roles and complex genetic interactions that take place in microbial communities. While microbiome studies have increased in prevalence, the lack of viable in situ editing strategies impedes experimental progress, rendering genetic knowledge and manipulation of microbial communities largely inaccessible. Here, we demonstrate the utility of phage-delivered CRISPR-Cas payloads to perform targeted genetic manipulation within a community context, deploying a fabricated ecosystem (EcoFAB) as an analog for the soil microbiome. First, we detail the engineering of two classical phages for community editing using recombination to replace nonessential genes through Cas9-based selection. We show efficient engineering of T7, then demonstrate the expression of antibiotic resistance and fluorescent genes from an engineered λ prophage within an
            Escherichia coli
            host. Next, we modify λ to express an APOBEC-1-based cytosine base editor (CBE), which we leverage to perform C-to-T point mutations guided by a modified Cas9 containing only a single active nucleolytic domain (nCas9). We strategically introduce these base substitutions to create premature stop codons in-frame, inactivating both chromosomal (
            lacZ
            ) and plasmid-encoded genes (mCherry and ampicillin resistance) without perturbation of the surrounding genomic regions. Furthermore, using a multigenera synthetic soil community, we employ phage-assisted base editing to induce host-specific phenotypic alterations in a community context both in vitro and within the EcoFAB, observing editing efficiencies from 10 to 28% across the bacterial population. The concurrent use of a synthetic microbial community, soil matrix, and EcoFAB device provides a controlled and reproducible model to more closely approximate in situ editing of the soil microbiome.
          }, number={46}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Nethery, Matthew A. and Hidalgo-Cantabrana, Claudio and Roberts, Avery and Barrangou, Rodolphe}, year={2022}, month={Nov} }
 @article{monte_nethery_berman_keelara_lincopan_fedorka-cray_barrangou_landgraf_2022, title={Clustered Regularly Interspaced Short Palindromic Repeats Genotyping of Multidrug-Resistant Salmonella Heidelberg Strains Isolated From the Poultry Production Chain Across Brazil}, volume={13}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2022.867278}, abstractNote={Salmonella enterica subsp. enterica serovar Heidelberg has been associated with a broad host range, such as poultry, dairy calves, swine, wild birds, environment, and humans. The continuous evolution of S. Heidelberg raises a public health concern since there is a global dispersal of lineages harboring a wide resistome and virulome on a global scale. Here, we characterized the resistome, phylogenetic structure and clustered regularly interspaced short palindromic repeats (CRISPR) array composition of 81 S. Heidelberg strains isolated from broiler farms (n = 16), transport and lairage (n = 5), slaughterhouse (n = 22), and retail market (n = 38) of the poultry production chain in Brazil, between 2015 and 2016 using high-resolution approaches including whole-genome sequencing (WGS) and WGS-derived CRISPR genotyping. More than 91% of the S. Heidelberg strains were multidrug-resistant. The total antimicrobial resistance (AMR) gene abundances did not vary significantly across regions and sources suggesting the widespread distribution of antibiotic-resistant strains from farm to market. The highest AMR gene abundance was observed for fosA7, aac(6′)-Iaa, sul2, tet(A), gyrA, and parC for 100% of the isolates, followed by 88.8% for blaCMY–2. The β-lactam resistance was essentially driven by the presence of the plasmid-mediated AmpC (pAmpC) blaCMY–2 gene, given the isolates which did not carry this gene were susceptible to cefoxitin (FOX). Most S. Heidelberg strains were classified within international lineages, which were phylogenetically nested with Salmonella strains from European countries; while CRISPR genotyping analysis revealed that the spacer content was overall highly conserved, but distributed into 13 distinct groups. In summary, our findings underscore the potential role of S. Heidelberg as a key pathogen disseminated from farm to fork in Brazil and reinforce the importance of CRISPR-based genotyping for salmonellae. Hence, we emphasized the need for continuous mitigation programs to monitor the dissemination of this high-priority pathogen.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Monte, Daniel F. M. and Nethery, Matthew A. and Berman, Hanna and Keelara, Shivaramu and Lincopan, Nilton and Fedorka-Cray, Paula J. and Barrangou, Rodolphe and Landgraf, Mariza}, year={2022}, month={Jun} }
 @article{roberts_nethery_barrangou_2022, title={Functional characterization of diverse type I-F CRISPR-associated transposons}, volume={11}, ISSN={["1362-4962"]}, url={https://doi.org/10.1093/nar/gkac985}, DOI={10.1093/nar/gkac985}, abstractNote={Abstract}, journal={NUCLEIC ACIDS RESEARCH}, author={Roberts, Avery and Nethery, Matthew A. and Barrangou, Rodolphe}, year={2022}, month={Nov} }
 @article{pan_morovic_hidalgo-cantabrana_roberts_walden_goh_barrangou_2022, title={Genomic and epigenetic landscapes drive CRISPR-based genome editing in Bifidobacterium}, volume={119}, ISSN={["1091-6490"]}, url={https://doi.org/10.1073/pnas.2205068119}, DOI={10.1073/pnas.2205068119}, abstractNote={Bifidobacteriumis a commensal bacterial genus ubiquitous in the human gastrointestinal tract, which is associated with a range of health benefits. The advent of CRISPR-based genome editing technologies provides opportunities to investigate the genetics of important bacteria and transcend the lack of genetic tools in bifidobacteria to study the basis for their health-promoting attributes. Here, we repurpose the endogenous type I-G CRISPR-Cas system and adopt an exogenous CRISPR base editor for genome engineering inB. animalissubsp.lactis,demonstrating that both genomic and epigenetic contexts drive editing outcomes across strains. We reprogrammed the endogenous type I-G system to screen for naturally occurring large deletions up to 27 kb and to generate a 500-bp deletion intetWto abolish tetracycline resistance. A CRISPR-cytosine base editor was optimized to install C•G-to-T•A amber mutations to resensitize multipleB. lactisstrains to tetracycline. Remarkably, we uncovered epigenetic patterns that are distributed unevenly amongB. lactisstrains, despite their genomic homogeneity, that may contribute to editing efficiency variability. Insights were also expanded toBifidobacterium longumsubsp.infantisto emphasize the broad relevance of these findings. This study highlights the need to develop individualized CRISPR-based genome engineering approaches for distinct bacterial strains and opens avenues for engineering of next generation probiotics.}, number={30}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Pan, Meichen and Morovic, Wesley and Hidalgo-Cantabrana, Claudio and Roberts, Avery and Walden, Kimberly K. O. and Goh, Yong Jun and Barrangou, Rodolphe}, year={2022}, month={Jul} }
 @article{chamberlain_o'flaherty_cobian_barrangou_2022, title={Metabolomic Analysis of Lactobacillus acidophilus, L. gasseri, L. crispatus, and Lacticaseibacillus rhamnosus Strains in the Presence of Pomegranate Extract}, volume={13}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2022.863228}, abstractNote={Lactobacillus species are prominent inhabitants of the human gastrointestinal tract that contribute to maintaining a balanced microbial environment that positively influences host health. These bacterial populations can be altered through use of probiotic supplements or via dietary changes which in turn affect the host health. Utilizing polyphenolic compounds to selectively stimulate the growth of commensal bacteria can have a positive effect on the host through the production of numerous metabolites that are biologically active. Four Lactobacillus strains were grown in the presence of pomegranate (POM) extract. Two strains, namely, L. acidophilus NCFM and L. rhamnosus GG, are commonly used probiotics, while the other two strains, namely, L. crispatus NCK1351 and L. gasseri NCK1342, exhibit probiotic potential. To compare and contrast the impact of POM on the strains' metabolic capacity, we investigated the growth of the strains with and without the presence of POM and identified their carbohydrate utilization and enzyme activity profiles. To further investigate the differences between strains, an untargeted metabolomic approach was utilized to quantitatively and qualitatively define the metabolite profiles of these strains. Several metabolites were produced significantly and/or exclusively in some of the strains, including mevalonate, glutamine, 5-aminoimidazole-4-carboxamide, phenyllactate, and fumarate. The production of numerous discrete compounds illustrates the unique characteristics of and diversity between strains. Unraveling these differences is essential to understand the probiotic function and help inform strain selection for commercial product formulation.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Chamberlain, MaryClaire and O'Flaherty, Sarah and Cobian, Natalia and Barrangou, Rodolphe}, year={2022}, month={May} }
 @article{barrangou_2022, title={Next-Generation Foods and CRISPR Engineering}, url={https://doi.org/10.52750/106366}, DOI={10.52750/106366}, abstractNote={The advent of CRISPR-based technologies has revolutionized our ability to manipulate the genomes of virtually every entity across the tree of life.Besides the tremendous progress in the medical applications of CRISPR technologies for gene therapies and cell engineering in the clinic, there are tremendous opportunities to exploit genome editing for food and agriculture.Indeed, breeding of crops and livestock can address grand challenges for our food supply chain and revolutionize agriculture at a time when resources are scarce and sustainability is crucial.Rodolphe Barrangou, Ph.D., discusses how genome editing is opening new avenues for a more sustainable agriculture.Barrangou is the T.R. Klaenhammer Distinguished professor at NC State.He is focusing on the characterization of CRISPR-Cas systems, and their applications in bacteria.Barrangou spent nine years in research and development, and mergers and acquisitions at Danisco and DuPont.}, author={Barrangou, Rodolphe}, year={2022}, month={Aug} }
 @article{adler_hessler_cress_mutalik_barrangou_banfield_doudna_2022, title={RNA-targeting CRISPR-Cas13 Provides Broad-spectrum Phage Immunity}, volume={3}, url={https://doi.org/10.1101/2022.03.25.485874}, DOI={10.1101/2022.03.25.485874}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Adler, Benjamin A. and Hessler, Tomas and Cress, Brady F and Mutalik, Vivek K. and Barrangou, Rodolphe and Banfield, Jillian and Doudna, Jennifer A}, year={2022}, month={Mar} }
 @article{barrangou_marraffini_2022, title={Turning CRISPR on with antibiotics}, volume={30}, ISSN={["1934-6069"]}, DOI={10.1016/j.chom.2021.12.013}, abstractNote={CRISPR-Cas systems have the ability to integrate invasive DNA sequences to build adaptive immunity in bacteria. In this issue Dimitriu et al. show bacteriostatic antibiotics prompt CRISPR acquisition events, illustrating how environmental conditions affect complex dynamics between host and virus and the corresponding biological and genetic arms race.}, number={1}, journal={CELL HOST & MICROBE}, author={Barrangou, Rodolphe and Marraffini, Luciano A.}, year={2022}, month={Jan}, pages={12–14} }
 @article{kuiken_barrangou_grieger_2021, title={(Broken) Promises of Sustainable Food and Agriculture through New Biotechnologies: The CRISPR Case}, volume={4}, ISSN={["2573-1602"]}, DOI={10.1089/crispr.2020.0098}, abstractNote={In recent years, the development of diverse CRISPR-based technologies has revolutionized genome manipulation and enabled a broad scientific community in industry, academia, and beyond to redefine research and development for biotechnology products encompassing food, agriculture, and medicine. CRISPR-based genome editing affords tremendous opportunities in agriculture for the breeding of crops and livestock across the food supply chain that could benefit larger portions of the population compared to CRISPR applications in medicine, for example by helping to feed a growing global population, reach sustainability goals, and possibly mitigate the effects of climate change. These promises come alongside concerns of risks and adverse impacts associated with CRISPR-based genome editing and concerns that governance systems that are ill equipped or not well suited to evaluate these risks. The international community will continue to gather, in multiple venues, in the coming years to discuss these concerns. At the same time, responsible research and innovation paradigms also promise to evaluate the risks and benefits better while incorporating broad stakeholder engagement across the research and development process. The CRISPR community therefore must actively engage with these international deliberations, society, and national governance systems that have promised to build better agricultural systems and provide better food products to achieve equitable outcomes while protecting the environment. Without this active engagement, the promises discussed in this paper are sure to be broken.}, number={1}, journal={CRISPR JOURNAL}, author={Kuiken, Todd and Barrangou, Rodolphe and Grieger, Khara}, year={2021}, month={Feb}, pages={25–31} }
 @article{mcclements_barrangou_hill_kokini_lila_meyer_yu_2021, title={Building a Resilient, Sustainable, and Healthier Food Supply Through Innovation and Technology}, volume={12}, ISSN={["1941-1421"]}, DOI={10.1146/annurev-food-092220-030824}, abstractNote={The modern food supply faces many challenges. The global population continues to grow and people are becoming wealthier, so the food production system must respond by creating enough high-quality food to feed everyone with minimal damage to our environment. The number of people suffering or dying from diet-related chronic diseases, such as obesity, diabetes, heart disease, stroke, and cancer, continues to rise, which is partly linked to overconsumption of highly processed foods, especially high-calorie or rapidly digestible foods. After falling for many years, the number of people suffering from starvation or malnutrition is rising, and thishas been exacerbated by the global COVID-19 pandemic. The highly integrated food supply chains that spread around the world are susceptible to disruptions due to policy changes, economic stresses, and natural disasters, as highlighted by the recent pandemic. In this perspective article, written by members of the Editorial Committee of the Annual Review of Food Science and Technology, we highlight some of the major challenges confronting the modern food supply chain as well as how innovations in policy and technology can be used to address them. Pertinent technological innovations include robotics, machine learning, artificial intelligence, advanced diagnostics, nanotechnology, biotechnology, gene editing, vertical farming, and soft matter physics. Many of these technologies are already being employed across the food chain by farmers, distributors, manufacturers, and consumers to improve the quality, nutrition, safety, and sustainability of the food supply. These innovations are required to stimulate the development and implementation of new technologies to ensure a more equitable, resilient, and efficient food production system. Where appropriate, these technologies should be carefully tested before widespread implementation so that proper risk–benefit analyses can be carried out. They can then be employed without causing unforeseen adverse consequences. Finally, it is important to actively engage all stakeholders involved in the food supply chain throughout the development and testing of these new technologies to support their adoption if proven safe and effective.}, journal={ANNUAL REVIEW OF FOOD SCIENCE AND TECHNOLOGY, VOL 12, 2021}, author={McClements, David Julian and Barrangou, Rodolphe and Hill, Colin and Kokini, Jozef L. and Lila, Mary Ann and Meyer, Anne S. and Yu, Liangli}, year={2021}, pages={1–28} }
 @article{nethery_korvink_makarova_wolf_v. koonin_barrangou_2021, title={CRISPRclassify: Repeat-Based Classification of CRISPR Loci}, volume={4}, ISSN={["2573-1602"]}, DOI={10.1089/crispr.2021.0021}, abstractNote={Detection and classification of CRISPR-Cas systems in metagenomic data have become increasingly prevalent in recent years due to their potential for diverse applications in genome editing. Traditionally, CRISPR-Cas systems are classified through reference-based identification of proximate cas genes. Here, we present a machine learning approach for the detection and classification of CRISPR loci using repeat sequences in a cas-independent context, enabling identification of unclassified loci missed by traditional cas-based approaches. Using biological attributes of the CRISPR repeat, the core element in CRISPR arrays, and leveraging methods from natural language processing, we developed a machine learning model capable of accurate classification of CRISPR loci in an extensive set of metagenomes, resulting in an F1 measure of 0.82 across all predictions and an F1 measure of 0.97 when limiting to classifications with probabilities >0.85. Furthermore, assessing performance on novel repeats yielded an F1 measure of 0.96. Although the performance of cas-based identification will exceed that of a repeat-based approach in many cases, CRISPRclassify provides an efficient approach to classification of CRISPR loci for cases in which cas gene information is unavailable, such as metagenomes and fragmented genome assemblies.}, number={4}, journal={CRISPR JOURNAL}, author={Nethery, Matthew A. and Korvink, Michael and Makarova, Kira S. and Wolf, Yuri I. and V. Koonin, Eugene and Barrangou, Rodolphe}, year={2021}, month={Aug}, pages={558–574} }
 @article{cobian_garlet_hidalgo-cantabrana_barrangou_2021, title={Comparative Genomic Analyses and CRISPR-Cas Characterization of Cutibacterium acnes Provide Insights Into Genetic Diversity and Typing Applications}, volume={12}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2021.758749}, abstractNote={Cutibacterium acnes is an important member of the human skin microbiome and plays a critical role in skin health and disease. C. acnes encompasses different phylotypes that have been found to be associated with different skin phenotypes, suggesting a genetic basis for their impact on skin health. Here, we present a comprehensive comparative analysis of 255 C. acnes genomes to provide insights into the species genetic diversity and identify unique features that define various phylotypes. Results revealed a relatively small and open pan genome (6,240 genes) with a large core genome (1,194 genes), and three distinct phylogenetic clades, with multiple robust sub-clades. Furthermore, we identified several unique gene families driving differences between distinct C. acnes clades. Carbohydrate transporters, stress response mechanisms and potential virulence factors, potentially involved in competitive growth and host colonization, were detected in type I strains, which are presumably responsible for acne. Diverse type I-E CRISPR-Cas systems and prophage sequences were detected in select clades, providing insights into strain divergence and adaptive differentiation. Collectively, these results enable to elucidate the fundamental differences among C. acnes phylotypes, characterize genetic elements that potentially contribute to type I-associated dominance and disease, and other key factors that drive the differentiation among clades and sub-clades. These results enable the use of comparative genomics analyses as a robust method to differentiate among the C. acnes genotypes present in the skin microbiome, opening new avenues for the development of biotherapeutics to manipulate the skin microbiota.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Cobian, Natalia and Garlet, Allison and Hidalgo-Cantabrana, Claudio and Barrangou, Rodolphe}, year={2021}, month={Nov} }
 @article{goh_barrangou_klaenhammer_2021, title={In Vivo Transcriptome of Lactobacillus acidophilus and Colonization Impact on Murine Host Intestinal Gene Expression}, volume={12}, ISSN={["2150-7511"]}, url={https://doi.org/10.1128/mBio.03399-20}, DOI={10.1128/mBio.03399-20}, abstractNote={
            To date, our basis for comprehending the probiotic mechanisms of
            Lactobacillus acidophilus
            , one of the most widely consumed probiotic microbes, was largely limited to
            in vitro
            functional genomic studies. Using a germfree murine colonization model,
            in vivo
            -based transcriptional studies provided the first view of how
            L. acidophilus
            survives in the mammalian gut environment, including gene expression patterns linked to survival, efficient nutrient acquisition, stress adaptation, and host interactions.
          }, number={1}, journal={MBIO}, publisher={American Society for Microbiology}, author={Goh, Yong Jun and Barrangou, Rodolphe and Klaenhammer, Todd R.}, editor={Huffnagle, Gary B.Editor}, year={2021} }
 @article{foley_o'flaherty_allen_rivera_stewart_barrangou_theriot_2021, title={Lactobacillus bile salt hydrolase substrate specificity governs bacterial fitness and host colonization}, volume={118}, ISSN={["1091-6490"]}, url={https://doi.org/10.1073/pnas.2017709118}, DOI={10.1073/pnas.2017709118}, abstractNote={Significance}, number={6}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Foley, Matthew H. and O'Flaherty, Sarah and Allen, Garrison and Rivera, Alissa J. and Stewart, Allison K. and Barrangou, Rodolphe and Theriot, Casey M.}, year={2021}, month={Feb} }
 @article{goh_barrangou_2021, title={Portable CRISPR-Cas9(N) System for Flexible Genome Engineering in Lactobacillus acidophilus, Lactobacillus gasseri, and Lactobacillus paracasei}, volume={87}, ISSN={["1098-5336"]}, url={https://doi.org/10.1128/AEM.02669-20}, DOI={10.1128/AEM.02669-20}, abstractNote={
            This work describes the development of a lactobacillus CRISPR-based editing system for genome manipulations in three
            Lactobacillus
            species belonging to the lactic acid bacteria (LAB), which are commonly known for their long history of use in food fermentations and as indigenous members of healthy microbiotas and for their emerging roles in human and animal commercial health-promoting applications. We exploited the established CRISPR-SpyCas9 nickase for flexible and precise genome editing applications in
            Lactobacillus acidophilus
            and further demonstrated the efficacy of this universal system in two distantly related
            Lactobacillus
            species.
          }, number={6}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, publisher={American Society for Microbiology}, author={Goh, Yong Jun and Barrangou, Rodolphe}, editor={Dudley, Edward G.Editor}, year={2021}, month={Mar} }
 @article{rubin_diamond_cress_crits-christoph_lou_borges_shivram_he_xu_zhou_et al._2021, title={Species- and site-specific genome editing in complex bacterial communities}, volume={12}, ISSN={["2058-5276"]}, DOI={10.1038/s41564-021-01014-7}, abstractNote={Understanding microbial gene functions relies on the application of experimental genetics in cultured microorganisms. However, the vast majority of bacteria and archaea remain uncultured, precluding the application of traditional genetic methods to these organisms and their interactions. Here, we characterize and validate a generalizable strategy for editing the genomes of specific organisms in microbial communities. We apply environmental transformation sequencing (ET-seq), in which nontargeted transposon insertions are mapped and quantified following delivery to a microbial community, to identify genetically tractable constituents. Next, DNA-editing all-in-one RNA-guided CRISPR–Cas transposase (DART) systems for targeted DNA insertion into organisms identified as tractable by ET-seq are used to enable organism- and locus-specific genetic manipulation in a community context. Using a combination of ET-seq and DART in soil and infant gut microbiota, we conduct species- and site-specific edits in several bacteria, measure gene fitness in a nonmodel bacterium and enrich targeted species. These tools enable editing of microbial communities for understanding and control. A suite of methods enables programmable species- and locus-specific editing of bacteria in communities.}, journal={NATURE MICROBIOLOGY}, author={Rubin, Benjamin E. and Diamond, Spencer and Cress, Brady F. and Crits-Christoph, Alexander and Lou, Yue Clare and Borges, Adair L. and Shivram, Haridha and He, Christine and Xu, Michael and Zhou, Zeyi and et al.}, year={2021}, month={Dec} }
 @article{barrangou_hill_2021, title={Todd R. Klaenhammer, an inspirational food microbiologist who leaves a lasting legacy}, volume={118}, ISSN={["0027-8424"]}, url={https://doi.org/10.1073/pnas.2107754118}, DOI={10.1073/pnas.2107754118}, abstractNote={Todd R. Klaenhammer (1951–2021) dedicated his professional life to the study of bacteria of importance to food. He conducted his doctorate under the guidance of Larry McKay at the University of Minnesota, who inspired him to apply the newest advances in bacterial genetics to the lactic acid bacteria, responsible for many food fermentations. Todd stood out from his peers at an early age. He was offered a position and started his 40-year academic career in the prestigious Food Science Department at North Carolina State University before he had even defended his doctorate. Todd always had a singular focus. While most food scientists followed the lead of the funding agencies and “better” journals by working on foodborne pathogens responsible for infectious diseases, he preferred to study the beneficial bacteria associated with food. Todd forged his illustrious career by working on commercially important bacteria, such as the dairy starter cultures responsible for cheese fermentations and probiotics that were associated with diverse health benefits. Over his long career, Todd managed to combine fundamental science with commercially relevant research. It is a measure of his accomplishments that you could spend a long time in your university library reading the many influential scientific articles Todd wrote, but if you took a lunch break and went to the dairy section of the canteen you could also choose from a variety of cheeses that were made with phage-resistant starter cultures that he generated, or perhaps enjoy a yogurt formulated with some of the health-promoting probiotics he pioneered. Throughout his career, Todd navigated the food microbiology research landscape with flair and intuition. He was always true to his favored lactic acid bacteria, but he repeatedly and skillfully adjusted the focus of his laboratory group, often leading the field into new areas. Todd was particularly attracted to using the emerging science of molecular biology to unravel the mechanisms by which these diverse bacteria play important roles in food. One of his most noteworthy pursuits included his early studies on bacteriocins that remains his most highly cited work (1). He also developed genetic engineering tools to provide the means of genetically dissecting the previously inaccessible streptococci, lactococci, and lactobacilli. These tools are still widely used in both academia and industry. Bacterial viruses (phage) were a constant source of disruption to the cheese industry, and Todd did some of his most elegant work on defining phage-resistance mechanisms and impressively managed to deploy abortive infection and restriction modification defense systems in commercial starter cultures. In this research, he even conducted some of the earliest bacterial work on RNA interference andCRISPR. He also worked extensively on the genetic basis of health-promoting lactobacilli, widely used as commercial probiotics. Much of this latter work built a foundation for the development of next-generation probiotics and Todd provided the tools used in the first series of experiments that laid the basis for the characterization of CRISPR-Cas as the bacterial adaptive immune system, fittingly in dairy cultures. Todd remained fascinated by the molecular mechanisms underpinning the interplay between bacteria and their environment, whether as hosts in need of evading predatory phages, as fermenting cultures responsible for the organoleptic properties of dairy products, or as health-promoting agents for consumers. Todd R. Klaenhammer. Image credit: North Carolina State University/Marc Hall.}, number={22}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Barrangou, Rodolphe and Hill, Colin}, year={2021}, month={Jun} }
 @article{yu_xue_barrangou_chen_huang_2021, title={Toward inclusive global governance of human genome editing}, volume={118}, ISSN={["1091-6490"]}, url={https://doi.org/10.1073/pnas.2118540118}, DOI={10.1073/pnas.2118540118}, abstractNote={In recent years, many have considered how best to govern increasingly powerful genome editing technologies. Since 2015, more than 60 statements, declarations, and other codes of practice have been published by international organizations and scientific institutions (1). In particular, the 2018 birth of two twins, Lulu and Nana—whose HIV-receptors CCR5 were altered by biophysics researcher He Jiankui—triggered widespread condemnation from the scientific community, the public, and even legal institutions. Eminent organizations that have opined on the matter include the World Health Organization’s Expert Advisory Committee on Developing Global Standards for Governance and Oversight of Human Genome Editing (WHO committee) and the International Commission on the Clinical Use of Human Germline Genome Editing (the international commission).}, number={47}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Yu, Hanzhi and Xue, Lan and Barrangou, Rodolphe and Chen, Shaowei and Huang, Ying}, year={2021}, month={Nov} }
 @article{monte_nethery_barrangou_landgraf_fedorka-cray_2021, title={Whole-genome sequencing analysis and CRISPR genotyping of rare antibiotic-resistant Salmonella enterica serovars isolated from food and related sources}, volume={93}, ISSN={["1095-9998"]}, DOI={10.1016/j.fm.2020.103601}, abstractNote={For decades, Salmonella Typhimurium and Salmonella Enteritidis have prevailed in several countries as agents of salmonellosis outbreaks. In Brazil, the largest exporter of poultry meat, relatively little attention has been paid to infrequent serovars. Here, we report the emergence and characterization of rare serovars isolated from food and related sources collected between 2014 and 2016 in Brazil. Twenty-two Salmonella enterica isolates were analyzed through the use of whole-genome sequencing (WGS) and clustered regularly interspaced short palindromic repeats (CRISPR) genotyping. These isolates were classified into 10 infrequent serovars, including S. Abony, S. Isangi, S. Rochdale, S. Saphra, S. Orion, S. Ouakam, S. Grumpensis, S. Carrau, S. Abaetetuba, and S. Idikan. The presence of six antimicrobial resistance (AMR) genes, qnrB19, blaCMY-2, tetA, aac(6')-Iaa, sul2 and fosA7, which encode resistance to quinolones, third-generation cephalosporin, tetracycline, aminoglycoside, sulfonamide and fosfomycin, respectively, were confirmed by WGS. All S. Isangi harbored qnrB19 with conserved genomic context across strains, while S. Abony harbored blaCMY-2. Twelve (54.5%) strains displayed chromosomal mutations in parC (Thr57→Ser). Most serovars were classified as independent lineages, except S. Abony and S. Abaetetuba, which phylogenetically nested with Salmonella strains from different countries. CRISPR analysis revealed that the spacer content was strongly correlated with serovar and multi-locus sequence type for all strains, independently confirming the observed phylogenetic patterns, and highlighting the value of CRISPR-based genotyping for Salmonella. These findings add valuable information to the epidemiology of S. enterica in Brazil, where the emergency of antibiotic-resistant Salmonella continues to evolve.}, journal={FOOD MICROBIOLOGY}, author={Monte, Daniel F. M. and Nethery, Matthew A. and Barrangou, Rodolphe and Landgraf, Mariza and Fedorka-Cray, Paula J.}, year={2021}, month={Feb} }
 @article{brandt_barrangou_2020, title={Adaptive response to iterative passages of five Lactobacillus species in simulated vaginal fluid}, volume={20}, url={https://doi.org/10.1186/s12866-020-02027-8}, DOI={10.1186/s12866-020-02027-8}, abstractNote={Abstract}, number={1}, journal={BMC Microbiology}, publisher={Springer Science and Business Media LLC}, author={Brandt, Katelyn and Barrangou, Rodolphe}, year={2020}, month={Dec} }
 @article{roberts_barrangou_2020, title={Applications of CRISPR-Cas systems in lactic acid bacteria}, volume={44}, url={https://doi.org/10.1093/femsre/fuaa016}, DOI={10.1093/femsre/fuaa016}, abstractNote={ABSTRACT}, number={5}, journal={FEMS Microbiology Reviews}, publisher={Oxford University Press (OUP)}, author={Roberts, Avery and Barrangou, Rodolphe}, year={2020}, month={Sep}, pages={523–537} }
 @article{barrangou_sontheimer_2020, title={CRISPR Shields: Fending Off Diverse Cas Nucleases with Nucleus-like Structures}, volume={77}, ISSN={["1097-4164"]}, DOI={10.1016/j.molcel.2020.02.015}, abstractNote={Two recent studies have uncovered a novel means by which bacteriophages thwart host immunity. Mendoza et al. (2020) and Malone et al. (2020) demonstrate that a nucleus-like proteinaceous structure shields phage DNA from CRISPR-associated nucleases encompassing Cascade-Cas3, Cas9, and Cas12.}, number={5}, journal={MOLECULAR CELL}, author={Barrangou, Rodolphe and Sontheimer, Erik J.}, year={2020}, month={Mar}, pages={934–936} }
 @article{hidalgo-cantabrana_barrangou_2020, title={Characterization and applications of Type I CRISPR-Cas systems}, volume={48}, url={https://doi.org/10.1042/BST20190119}, DOI={10.1042/BST20190119}, abstractNote={CRISPR-Cas constitutes the adaptive immune system of bacteria and archaea. This RNA-mediated sequence-specific recognition and targeting machinery has been used broadly for diverse applications in a wide range of organisms across the tree of life. The compact class 2 systems, that hinge on a single Cas effector nuclease have been harnessed for genome editing, transcriptional regulation, detection, imaging and other applications, in different research areas. However, most of the CRISPR-Cas systems belong to class 1, and the molecular machinery of the most widespread and diverse Type I systems afford tremendous opportunities for a broad range of applications. These highly abundant systems rely on a multi-protein effector complex, the CRISPR associated complex for antiviral defense (Cascade), which drives DNA targeting and cleavage. The complexity of these systems has somewhat hindered their widespread usage, but the pool of thousands of diverse Type I CRISPR-Cas systems opens new avenues for CRISPR-based applications in bacteria, archaea and eukaryotes. Here, we describe the features and mechanism of action of Type I CRISPR-Cas systems, illustrate how endogenous systems can be reprogrammed to target the host genome and perform genome editing and transcriptional regulation by co-delivering a minimal CRISPR array together with a repair template. Moreover, we discuss how these systems can also be used in eukaryotes. This review provides a framework for expanding the CRISPR toolbox, and repurposing the most abundant CRISPR-Cas systems for a wide range of applications.}, number={1}, journal={Biochemical Society Transactions}, publisher={Portland Press Ltd.}, author={Hidalgo-Cantabrana, Claudio and Barrangou, Rodolphe}, year={2020}, month={Feb}, pages={15–23} }
 @misc{pan_barrangou_2020, title={Combining omics technologies with CRISPR-based genome editing to study food microbes}, volume={61}, ISSN={["1879-0429"]}, DOI={10.1016/j.copbio.2019.12.027}, abstractNote={The implementation of omics technologies such as genomics, proteomics and transcriptomics has revolutionized our understanding of microbiomes, and shed light on the functional attributes and mechanisms of action underlying the ability of probiotics to impact host health and starter cultures to drive food fermentation. Recently, molecular machines from CRISPR-Cas systems have redefined the gene editing toolbox and democritized our ability to alter the genome of food microorganisms. An integrated approach in which CRISPR-based genome editing is informed by omics studies is poised to enable the engineering of microorganisms and the formulation of microbiomes impacting the food supply chain. Here, we highlight the current applications of omics technologies in food microorganisms and CRISPR-based genome editing technologies in bacteria, and discuss how this integrated approach enables effective engineering of food microbes to generate enhanced probiotic strains, develop novel biotherapeutics and alter microbial communities in food matrices.}, journal={CURRENT OPINION IN BIOTECHNOLOGY}, author={Pan, Meichen and Barrangou, Rodolphe}, year={2020}, month={Feb}, pages={198–208} }
 @article{pan_hidalgo-cantabrana_goh_sanozky-dawes_barrangou_2020, title={Comparative Analysis of Lactobacillus gasseri and Lactobacillus crispatus Isolated From Human Urogenital and Gastrointestinal Tracts}, volume={10}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2019.03146}, abstractNote={Lactobacillus crispatus and Lactobacillus gasseri are two of the main Lactobacillus species found in the healthy vaginal microbiome and have also previously been identified and isolated from the human gastrointestinal (GI) tract. These two ecological niches are fundamentally different, notably with regards to the epithelial cell type, nutrient availability, environmental conditions, pH, and microbiome composition. Given the dramatic differences between these two environments, we characterized strains within the same Lactobacillus species isolated from either the vaginal or intestinal tract to assess whether they are phenotypically and genetically different. We compared the genomes of the Lactobacillus strains selected in this study for genetic features of interest, and performed a series of comparative phenotypic assays including small intestinal juice and acid resistance, carbohydrate fermentation profiles, lactic acid production, and host interaction with intestinal Caco-2 and vaginal VK2 cell lines. We also developed a simulated vaginal fluid (SVF) to study bacterial growth in a proxy vaginal environment and conducted differential transcriptomic analysis between SVF and standard laboratory MRS medium. Overall, our results show that although strain-specific variation is observed, some phenotypic differences seem associated with the isolation source. We encourage future probiotic formulation to include isolation source and take into consideration genetic and phenotypic features for use at various body sites.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Pan, Meichen and Hidalgo-Cantabrana, Claudio and Goh, Yong Jun and Sanozky-Dawes, Rosemary and Barrangou, Rodolphe}, year={2020}, month={Jan} }
 @article{o'flaherty_foley_rivera_theriot_barrangou_2020, title={Complete Genome Sequence of Lactobacillus johnsonii NCK2677, Isolated from Mice}, volume={9}, url={https://doi.org/10.1128/MRA.00918-20}, DOI={10.1128/MRA.00918-20}, abstractNote={
            We report the closed genome sequence of a
            Lactobacillus johnsonii
            strain (NCK2677) that was isolated from a cefoperazone-treated mouse model designed for the study of
            Clostridioides difficile
            infection. Illumina and Nanopore sequencing reads were assembled into a circular 1,951,416-bp chromosome with a G+C content of 34.7%, containing 1,865 genes.
          }, number={43}, journal={Microbiology Resource Announcements}, publisher={American Society for Microbiology}, author={O'Flaherty, Sarah and Foley, Matthew H. and Rivera, Alissa J. and Theriot, Casey M. and Barrangou, Rodolphe}, editor={Rasko, DavidEditor}, year={2020}, month={Oct} }
 @article{pan_nethery_hidalgo-cantabrana_barrangou_2020, title={Comprehensive Mining and Characterization of CRISPR-Cas Systems in Bifidobacterium}, volume={8}, url={https://doi.org/10.3390/microorganisms8050720}, DOI={10.3390/microorganisms8050720}, abstractNote={The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated cas) systems constitute the adaptive immune system in prokaryotes, which provides resistance against bacteriophages and invasive genetic elements. The landscape of applications in bacteria and eukaryotes relies on a few Cas effector proteins that have been characterized in detail. However, there is a lack of comprehensive studies on naturally occurring CRISPR-Cas systems in beneficial bacteria, such as human gut commensal Bifidobacterium species. In this study, we mined 954 publicly available Bifidobacterium genomes and identified CRIPSR-Cas systems in 57% of these strains. A total of five CRISPR-Cas subtypes were identified as follows: Type I-E, I-C, I-G, II-A, and II-C. Among the subtypes, Type I-C was the most abundant (23%). We further characterized the CRISPR RNA (crRNA), tracrRNA, and PAM sequences to provide a molecular basis for the development of new genome editing tools for a variety of applications. Moreover, we investigated the evolutionary history of certain Bifidobacterium strains through visualization of acquired spacer sequences and demonstrated how these hypervariable CRISPR regions can be used as genotyping markers. This extensive characterization will enable the repurposing of endogenous CRISPR-Cas systems in Bifidobacteria for genome engineering, transcriptional regulation, genotyping, and screening of rare variants.}, number={5}, journal={Microorganisms}, publisher={MDPI AG}, author={Pan, Meichen and Nethery, Matthew A. and Hidalgo-Cantabrana, Claudio and Barrangou, Rodolphe}, year={2020}, month={May}, pages={720} }
 @article{klotz_goh_o'flaherty_johnson_barrangou_2020, title={Deletion of S-Layer Associated Ig-Like Domain Protein Disrupts the Lactobacillus acidophilus Cell Surface}, volume={11}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2020.00345}, abstractNote={Bacterial surface-layers (S-layers) are crystalline arrays of repeating proteinaceous subunits that coat the exterior of many cell envelopes. S-layers have demonstrated diverse functions in growth and survival, maintenance of cell integrity, and mediation of host interactions. Additionally, S-layers can act as scaffolds for the outward display of auxiliary proteins and glycoproteins. These non-covalently bound S-layer associated proteins (SLAPs) have characterized roles in cell division, adherence to intestinal cells, and modulation of the host immune response. Recently, IgdA (LBA0695), a Lactobacillus acidophilus SLAP that possesses a Group 3 immunoglobulin (Ig)-like domain and GW (Gly-Tryp) dipeptide surface anchor, was recognized for its high conservation among S-layer-forming lactobacilli, constitutive expression, and surface localization. These findings prompted its selection for examination within the present study. Although IgdA and corresponding orthologs were shown to be unique to host-adapted lactobacilli, the Ig domain itself was specific to vertebrate-adapted species suggesting a role in vertebrate adaptation. Using a counterselective gene replacement system, igdA was deleted from the L. acidophilus NCFM chromosome. The resultant mutant, NCK2532, exhibited a visibly disrupted cell surface which likely contributed to its higher salt sensitivity, severely reduced adhesive capacity, and altered immunogenicity profile. Transcriptomic analyses revealed the induction of several stress response genes and secondary surface proteins. Due to the broad impact of IgdA on the cellular physiology and probiotic attributes of L. acidophilus, identification of similar proteins in alternative bacterial species may help pinpoint next-generation host-adapted probiotic candidates.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Klotz, Courtney and Goh, Yong Jun and O'Flaherty, Sarah and Johnson, Brant and Barrangou, Rodolphe}, year={2020}, month={Mar} }
 @misc{makarova_wolf_iranzo_shmakov_alkhnbashi_brouns_charpentier_cheng_haft_horvath_et al._2020, title={Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants}, volume={18}, ISSN={["1740-1534"]}, DOI={10.1038/s41579-019-0299-x}, abstractNote={The number and diversity of known CRISPR-Cas systems have substantially increased in recent years. Here, we provide an updated evolutionary classification of CRISPR-Cas systems and cas genes, with an emphasis on the major developments that have occurred since the publication of the latest classification, in 2015. The new classification includes 2 classes, 6 types and 33 subtypes, compared with 5 types and 16 subtypes in 2015. A key development is the ongoing discovery of multiple, novel class 2 CRISPR-Cas systems, which now include 3 types and 17 subtypes. A second major novelty is the discovery of numerous derived CRISPR-Cas variants, often associated with mobile genetic elements that lack the nucleases required for interference. Some of these variants are involved in RNA-guided transposition, whereas others are predicted to perform functions distinct from adaptive immunity that remain to be characterized experimentally. The third highlight is the discovery of numerous families of ancillary CRISPR-linked genes, often implicated in signal transduction. Together, these findings substantially clarify the functional diversity and evolutionary history of CRISPR-Cas.}, number={2}, journal={NATURE REVIEWS MICROBIOLOGY}, author={Makarova, Kira S. and Wolf, Yuri I and Iranzo, Jaime and Shmakov, Sergey A. and Alkhnbashi, Omer S. and Brouns, Stan J. J. and Charpentier, Emmanuelle and Cheng, David and Haft, Daniel H. and Horvath, Philippe and et al.}, year={2020}, month={Feb}, pages={67–83} }
 @article{brandt_nethery_sarah_barrangou_2020, title={Genomic characterization of Lactobacillus fermentum DSM 20052}, volume={21}, url={https://doi.org/10.1186/s12864-020-6740-8}, DOI={10.1186/s12864-020-6740-8}, abstractNote={Abstract}, number={1}, journal={BMC Genomics}, publisher={Springer Science and Business Media LLC}, author={Brandt, Katelyn and Nethery, Matthew A. and Sarah, O’Flaherty and Barrangou, Rodolphe}, year={2020}, month={Dec} }
 @article{pan_hidalgo-cantabrana_barrangou_2020, title={Host and body site-specific adaptation of Lactobacillus crispatus genomes}, volume={2}, url={https://doi.org/10.1093/nargab/lqaa001}, DOI={10.1093/nargab/lqaa001}, abstractNote={Abstract}, number={1}, journal={NAR Genomics and Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Pan, Meichen and Hidalgo-Cantabrana, Claudio and Barrangou, Rodolphe}, year={2020}, month={Mar} }
 @article{selle_fletcher_tuson_schmitt_mcmillan_vridhambal_rivera_montgomery_fortier_barrangou_et al._2020, title={In Vivo Targeting of Clostridioides difficile Using Phage-Delivered CRISPR-Cas3 Antimicrobials}, volume={11}, url={https://doi.org/10.1128/mBio.00019-20}, DOI={10.1128/mBio.00019-20}, abstractNote={
            Clostridioides difficile
            is a bacterial pathogen responsible for significant morbidity and mortality across the globe. Current therapies based on broad-spectrum antibiotics have some clinical success, but approximately 30% of patients have relapses, presumably due to the continued perturbation to the gut microbiota. Here, we show that phages can be engineered with type I CRISPR-Cas systems and modified to reduce lysogeny and to enable the specific and efficient targeting and killing of
            C. difficile
            in vitro
            and
            in vivo.
            Additional genetic engineering to disrupt phage modulation of toxin expression by lysogeny or other mechanisms would be required to advance a CRISPR-enhanced phage antimicrobial for
            C. difficile
            toward clinical application. These findings provide evidence into how phage can be combined with CRISPR-based targeting to develop novel therapies and modulate microbiomes associated with health and disease.
          }, number={2}, journal={mBio}, publisher={American Society for Microbiology}, author={Selle, Kurt and Fletcher, Joshua R. and Tuson, Hannah and Schmitt, Daniel S. and McMillan, Lana and Vridhambal, Gowrinarayani S. and Rivera, Alissa J. and Montgomery, Stephanie A. and Fortier, Louis-Charles and Barrangou, Rodolphe and et al.}, editor={Ballard, Jimmy D.Editor}, year={2020}, month={Apr} }
 @article{angrist_barrangou_baylis_brokowski_burgio_caplan_chapman_church_cook-deegan_cwik_et al._2020, title={Reactions to the National Academies/Royal Society Report on Heritable Human Genome Editing}, volume={3}, ISSN={["2573-1602"]}, DOI={10.1089/crispr.2020.29106.man}, abstractNote={In September 2020, a detailed report on Heritable Human Genome Editing was published. The report offers a translational pathway for the limited approval of germline editing under limited circumstances and assuming various criteria have been met. In this perspective, some three dozen experts from the fields of genome editing, medicine, bioethics, law, and related fields offer their candid reactions to the National Academies/Royal Society report, highlighting areas of support, omissions, disagreements, and priorities moving forward.}, number={5}, journal={CRISPR JOURNAL}, author={Angrist, Misha and Barrangou, Rodolphe and Baylis, Francoise and Brokowski, Carolyn and Burgio, Gaetan and Caplan, Arthur and Chapman, Carolyn Riley and Church, George M. and Cook-Deegan, Robert and Cwik, Bryan and et al.}, year={2020}, month={Oct}, pages={332–349} }
 @article{klotz_goh_sarah_barrangou_2020, title={S-layer associated proteins contribute to the adhesive and immunomodulatory properties of Lactobacillus acidophilus NCFM}, volume={20}, url={https://doi.org/10.1186/s12866-020-01908-2}, DOI={10.1186/s12866-020-01908-2}, abstractNote={Abstract}, number={1}, journal={BMC Microbiology}, publisher={Springer Science and Business Media LLC}, author={Klotz, Courtney and Goh, Yong Jun and Sarah, O’Flaherty and Barrangou, Rodolphe}, year={2020}, month={Dec} }
 @article{lamanna_pyhtila_barrangou_2020, title={Sharing the CRISPR Toolbox with an Expanding Community}, volume={3}, ISSN={["2573-1602"]}, DOI={10.1089/crispr.2020.0075}, abstractNote={Over the past 8 years, the widespread adoption of CRISPR-based technologies has fueled the global genome editing revolution. This platform is based on Cas molecular machines such as Cas9, Cas12, Cas13, as well as other CRISPR effector proteins that are able to alter the genome, transcriptome, and epigenome of virtually any species. Technological improvements have rendered these tools more efficient and precise, and enabled functional diversification and specialization, as recently illustrated by the rise of base editing and the quickly growing demand for prime editing constructs. Here, we discuss the continued adoption of CRISPR tools and constructs distributed by the nonprofit organization Addgene, highlight the trends in the global demand for the CRISPR toolbox, and consider the widespread attitude changes around open sharing that are having a transformative effect on speeding up science.}, number={4}, journal={CRISPR JOURNAL}, author={LaManna, Caroline M. and Pyhtila, Brook and Barrangou, Rodolphe}, year={2020}, month={Aug}, pages={248–252} }
 @article{barrangou_sontheimer_2020, title={Shutting down RNA-targeting CRISPR}, volume={369}, ISSN={["1095-9203"]}, DOI={10.1126/science.abc8243}, abstractNote={The discovery of an anti-CRISPR reveals viral escape from CRISPR immunity}, number={6499}, journal={SCIENCE}, author={Barrangou, Rodolphe and Sontheimer, Erik J.}, year={2020}, month={Jul}, pages={31–32} }
 @article{reed_nethery_stewart_barrangou_theriot_2020, title={Strain-Dependent Inhibition of Clostridioides difficile by Commensal Clostridia Carrying the Bile Acid-Inducible ( bai ) Operon}, volume={202}, url={https://doi.org/10.1128/JB.00039-20}, DOI={10.1128/JB.00039-20}, abstractNote={ABSTRACT}, number={11}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Reed, A. D. and Nethery, M. A. and Stewart, A. and Barrangou, R. and Theriot, C. M.}, editor={Comstock, Laurie E.Editor}, year={2020}, month={May} }
 @article{reed_nethery_stewart_barrangou_theriot_2020, title={Strain-dependent inhibition of Clostridioides difficile by commensal Clostridia encoding the bile acid inducible (bai) operon}, volume={1}, url={https://doi.org/10.1101/2020.01.22.916304}, DOI={10.1101/2020.01.22.916304}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Reed, A.D. and Nethery, M.A. and Stewart, A. and Barrangou, R. and Theriot, C.M.}, year={2020}, month={Jan} }
 @article{brandt_barrangou_2019, title={Applications of CRISPR Technologies Across the Food Supply Chain}, volume={10}, ISSN={["1941-1413"]}, DOI={10.1146/annurev-food-032818-121204}, abstractNote={The food industry faces a 2050 deadline for the advancement and expansion of the food supply chain to support the world's growing population. Improvements are needed across crops, livestock, and microbes to achieve this goal. Since 2005, researchers have been attempting to make the necessary strides to reach this milestone, but attempts have fallen short. With the introduction of clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins, the food production field is now able to achieve some of its most exciting advancements since the Green Revolution. This review introduces the concept of applying CRISPR-Cas technology as a genome-editing tool for use in the food supply chain, focusing on its implementation to date in crop, livestock, and microbe production, advancement of products to market, and regulatory and societal hurdles that need to be overcome.}, number={1}, journal={ANNUAL REVIEW OF FOOD SCIENCE AND TECHNOLOGY, VOL 10}, publisher={Annual Reviews}, author={Brandt, Katelyn and Barrangou, Rodolphe}, year={2019}, pages={133–150} }
 @article{foley_o'flaherty_barrangou_theriot_2019, title={Bile salt hydrolases: Gatekeepers of bile acid metabolism and host-microbiome crosstalk in the gastrointestinal tract}, volume={15}, ISSN={["1553-7374"]}, url={https://doi.org/10.1371/journal.ppat.1007581}, DOI={10.1371/journal.ppat.1007581}, abstractNote={Research on bile acids has increased dramatically due to recent studies demonstrating their ability to significantly impact the host, microbiome, and various disease states [1–3]. Although these liver-synthesized molecules assist in the absorption and digestion of dietary fat in the intestine, their reabsorption and recirculation also gives them access to peripheral organs [4] (Fig 1A). Bile acids serve as substrates for bile acid receptors (BARs) found throughout the body that control critical regulatory and metabolic processes and therefore represent an important class of bioactive molecules [5]. Despite the importance of bile acids to host health, there remain gaps in our knowledge about the bacterial enzymes driving their composition and modification. 
 
 
 
 
 
 
Open in a separate window 
 
 
Fig 1 
 
Bile salt hydrolases act on circulating conjugated bile acids in the gut-liver axis. 
(A) Bile acids synthesized in the liver and stored in the gall bladder enter the small intestine through the duodenum where they reach millimolar concentrations. The majority of bile acids (95%) are reabsorbed in the ileum and recirculate to the liver through the portal vein. The remaining population transit to the colon as they continue to be reabsorbed, and a small (<5%) amount exit through the feces. Recirculating bile acids access host tissues outside the intestines to impart systemic effects on host physiology. (B) BSHs cleave the amide bond in conjugated bile acids to open up the bile acid pool to increased complexity. The gut microbiota performs additional chemistry on deconjugated bile acids to generate the secondary bile acid pool, which can undergo enterohepatic circulation and be reconjugated in the liver. These transformations are illustrated to the right as conjugated CA is deconjugated, subjected to 7 α-dehydroxylation to become DCA, and subsequently reconjugated. (C) Monomeric BSH overlay from Bifidobacterium longum (PDB ID 2HEZ), Enteroccocus faecalis (PDB ID 4WL3), Lactobacillus salivarius (PDB ID 5HKE), and Clostridium perfringens (PDB ID 2BJF). Hydrolyzed TDCA in the CpBSH active site is coordinated by several loops that contain the most variation in the peptide backbone compared to the other structures. BSH, bile salt hydrolase; CA, cholic acid; CpBSH, C. perfringens BSH; DCA,; TDCA, taurodeoxycholic acid; PDB ID, Protein Data Bank ID.}, number={3}, journal={PLOS PATHOGENS}, author={Foley, Matthew H. and O'Flaherty, Sarah and Barrangou, Rodolphe and Theriot, Casey M.}, editor={Knoll, Laura J.Editor}, year={2019}, month={Mar} }
 @article{barrangou_2019, title={Bringing CRISPR to the Cinema}, volume={2}, DOI={10.1089/crispr.2019.29070.rba}, abstractNote={The CRISPR JournalVol. 2, No. 4 EditorialBringing CRISPR to the CinemaRodolphe BarrangouRodolphe BarrangouEditor in Chief, The CRISPR Journal.Search for more papers by this authorPublished Online:16 Aug 2019https://doi.org/10.1089/crispr.2019.29070.rbaAboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"Bringing CRISPR to the Cinema." The CRISPR Journal, 2(4), p. 187FiguresReferencesRelatedDetails Volume 2Issue 4Aug 2019 InformationCopyright 2019, Mary Ann Liebert, Inc., publishersTo cite this article:Rodolphe Barrangou.Bringing CRISPR to the Cinema.The CRISPR Journal.Aug 2019.187-187.http://doi.org/10.1089/crispr.2019.29070.rbaPublished in Volume: 2 Issue 4: August 16, 2019PDF download}, number={4}, journal={The CRISPR Journal}, publisher={Mary Ann Liebert Inc}, author={Barrangou, Rodolphe}, year={2019}, month={Aug}, pages={187–187} }
 @article{nethery_barrangou_2019, title={CRISPR Visualizer: rapid identification and visualization of CRISPR loci via an automated high-throughput processing pipeline}, volume={16}, ISSN={["1555-8584"]}, url={https://doi.org/10.1080/15476286.2018.1493332}, DOI={10.1080/15476286.2018.1493332}, abstractNote={ABSTRACT A CRISPR locus, defined by an array of repeat and spacer elements, constitutes a genetic record of the ceaseless battle between bacteria and viruses, showcasing the genomic integration of spacers acquired from invasive DNA. In particular, iterative spacer acquisitions represent unique evolutionary histories and are often useful for high-resolution bacterial genotyping, including comparative analysis of closely related organisms, clonal lineages, and clinical isolates. Current spacer visualization methods are typically tedious and can require manual data manipulation and curation, including spacer extraction at each CRISPR locus from genomes of interest. Here, we constructed a high-throughput extraction pipeline coupled with a local web-based visualization tool which enables CRISPR spacer and repeat extraction, rapid visualization, graphical comparison, and progressive multiple sequence alignment. We present the bioinformatic pipeline and investigate the loci of reference CRISPR-Cas systems and model organisms in 4 well-characterized subtypes. We illustrate how this analysis uncovers the evolutionary tracks and homology shared between various organisms through visual comparison of CRISPR spacers and repeats, driven through progressive alignments. Due to the ability to process unannotated genome files with minimal preparation and curation, this pipeline can be implemented promptly. Overall, this efficient high-throughput solution supports accelerated analysis of genomic data sets and enables and expedites genotyping efforts based on CRISPR loci.}, number={4}, journal={RNA BIOLOGY}, publisher={Informa UK Limited}, author={Nethery, Matthew A. and Barrangou, Rodolphe}, year={2019}, month={Apr}, pages={577–584} }
 @article{barrangou_2019, title={CRISPR on the Move in 2019}, volume={2}, DOI={10.1089/crispr.2019.29043.rba}, abstractNote={The CRISPR JournalVol. 2, No. 1 EditorialCRISPR on the Move in 2019Rodolphe BarrangouRodolphe BarrangouDr. Barrangou is a co-founder of Intellia Therapeutics and Locus Biosciences.Editor-in-Chief, The CRISPR JournalSearch for more papers by this authorPublished Online:21 Feb 2019https://doi.org/10.1089/crispr.2019.29043.rbaAboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"CRISPR on the Move in 2019." The CRISPR Journal, 2(1), pp. 1–2FiguresReferencesRelatedDetails Volume 2Issue 1Feb 2019 InformationCopyright 2019, Mary Ann Liebert, Inc., publishersTo cite this article:Rodolphe Barrangou.CRISPR on the Move in 2019.The CRISPR Journal.Feb 2019.1-2.http://doi.org/10.1089/crispr.2019.29043.rbaPublished in Volume: 2 Issue 1: February 21, 2019PDF download}, number={1}, journal={The CRISPR Journal}, publisher={Mary Ann Liebert Inc}, author={Barrangou, Rodolphe}, year={2019}, month={Feb}, pages={1–2} }
 @misc{barrangou_notebaart_2019, title={CRISPR-Directed Microbiome Manipulation across the Food Supply Chain}, volume={27}, ISSN={["1878-4380"]}, url={https://doi.org/10.1016/j.tim.2019.03.006}, DOI={10.1016/j.tim.2019.03.006}, abstractNote={The advent of CRISPR-based technologies has revolutionized genetics over the past decade, and genome editing is now widely implemented for diverse medical and agricultural applications, such as correcting genetic disorders and improving crop and livestock breeding. CRISPR-based technologies are also of great potential to alter the genetic content of food bacteria in order to control the composition and activity of microbial populations across the food supply chain, from the farm to consumer products. Advancing the food supply chain is of great societal importance as it involves optimizing fermentation processes to enhance taste and sensory properties of food products, as well as improving food quality and safety by controlling spoilage bacteria and pathogens. Here, we discuss the various CRISPR technologies that can alter bacterial functionalities and modulate the composition of microbial communities in foods. We illustrate how these applications can be harnessed along the food supply chain to manipulate microbiomes that encompass spoilage and pathogenic bacteria as well as desirable starter cultures and health-promoting probiotics.}, number={6}, journal={TRENDS IN MICROBIOLOGY}, publisher={Elsevier BV}, author={Barrangou, Rodolphe and Notebaart, Richard A.}, year={2019}, month={Jun}, pages={489–496} }
 @misc{hidalgo-cantabrana_goh_barrangou_2019, title={Characterization and Repurposing of Type I and Type II CRISPR-Cas Systems in Bacteria}, volume={431}, ISSN={["1089-8638"]}, DOI={10.1016/j.jmb.2018.09.013}, abstractNote={CRISPR–Cas systems constitute the adaptive immune system of bacteria and archaea, as a sequence-specific nucleic acid targeting defense mechanism. The sequence-specific recognition and cleavage of Cas effector complexes has been harnessed to developed CRISPR-based technologies and drive the genome editing revolution underway, due to their efficacy, efficiency, and ease of implementation in a broad range of organisms. CRISPR-based technologies offer a wide variety of opportunities in genome remodeling and transcriptional regulation, opening new avenues for therapeutic and biotechnological applications. To repurpose CRISPR–Cas systems for these applications, the various elements of the system need to be first identified and functionally characterized in their native host. Bioinformatic tools are first used to identify putative CRISPR arrays and their associated genes, followed by a comprehensive characterization of the CRISPR–Cas system, encompassing predictions for guide and target sequences. Subsequently, interference assays and transcriptomic analyses should be performed to probe the functionality of the CRISPR–Cas system. Once an endogenous CRISPR–Cas system is characterized as functional, they can be readily repurposed by delivering an engineered synthetic CRISPR array or a small RNA guide for targeted gene manipulation. Alternatively, developing a plasmid-based system for heterologous expression of the necessary CRISPR components can enable exploitation in other organisms. Altogether, there is a wide diversity of native CRISPR–Cas systems in many bacteria and most archaea that await functional characterization and repurposing for genome editing applications in prokaryotes.}, number={1}, journal={JOURNAL OF MOLECULAR BIOLOGY}, publisher={Elsevier BV}, author={Hidalgo-Cantabrana, Claudio and Goh, Yong Jun and Barrangou, Rodolphe}, year={2019}, month={Jan}, pages={21–33} }
 @article{huang_porter_zhang_barrangou_2019, title={Collaborative networks in gene editing}, volume={37}, ISSN={["1546-1696"]}, DOI={10.1038/s41587-019-0275-z}, number={10}, journal={NATURE BIOTECHNOLOGY}, publisher={Springer Science and Business Media LLC}, author={Huang, Ying and Porter, Alan and Zhang, Yi and Barrangou, Rodolphe}, year={2019}, month={Oct}, pages={1107–1109} }
 @article{faure_shmakov_makarova_wolf_crawley_barrangou_koonin_2019, title={Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems}, volume={16}, ISSN={["1555-8584"]}, url={https://doi.org/10.1080/15476286.2018.1493331}, DOI={10.1080/15476286.2018.1493331}, abstractNote={ABSTRACT Trans-activating CRISPR (tracr) RNA is a distinct RNA species that interacts with the CRISPR (cr) RNA to form the dual guide (g) RNA in type II and subtype V-B CRISPR-Cas systems. The tracrRNA-crRNA interaction is essential for pre-crRNA processing as well as target recognition and cleavage. The tracrRNA consists of an antirepeat, which forms an imperfect hybrid with the repeat in the crRNA, and a distal region containing a Rho-independent terminator. Exhaustive comparative analysis of the sequences and predicted structures of the Class 2 CRISPR guide RNAs shows that all these guide RNAs share distinct structural features, in particular, the nexus stem-loop that separates the repeat-antirepeat hybrid from the distal portion of the tracrRNA and the conserved GU pair at that end of the hybrid. These structural constraints might ensure full exposure of the spacer for target recognition. Reconstruction of tracrRNA evolution for 4 tight bacterial groups demonstrates random drift of repeat-antirepeat complementarity within a window of hybrid stability that is, apparently, maintained by selection. An evolutionary scenario is proposed whereby tracrRNAs evolved on multiple occasions, via rearrangement of a CRISPR array to form the antirepeat in different locations with respect to the array. A functional tracrRNA would form if, in the new location, the antirepeat is flanked by sequences that meet the minimal requirements for a promoter and a Rho-independent terminator. Alternatively, or additionally, the antirepeat sequence could be occasionally ‘reset’ by recombination with a repeat, restoring the functionality of tracrRNAs that drift beyond the required minimal hybrid stability.}, number={4}, journal={RNA BIOLOGY}, publisher={Informa UK Limited}, author={Faure, Guilhem and Shmakov, Sergey A. and Makarova, Kira S. and Wolf, Yuri I. and Crawley, Alexandra B. and Barrangou, Rodolphe and Koonin, Eugene V.}, year={2019}, month={Apr}, pages={435–448} }
 @article{nethery_henriksen_daughtry_johanningsmeier_barrangou_2019, title={Comparative genomics of eight Lactobacillus buchneri strains isolated from food spoilage}, volume={20}, ISSN={["1471-2164"]}, url={https://doi.org/10.1186/s12864-019-6274-0}, DOI={10.1186/s12864-019-6274-0}, abstractNote={
                Abstract
              }, number={1}, journal={BMC GENOMICS}, publisher={Springer Science and Business Media LLC}, author={Nethery, Matthew A. and Henriksen, Emily DeCrescenzo and Daughtry, Katheryne V and Johanningsmeier, Suzanne D. and Barrangou, Rodolphe}, year={2019}, month={Nov} }
 @article{barrangou_2019, title={Foresight is 2020: Ten Bold Predictions for the New CRISPR Year}, volume={2}, DOI={10.1089/crispr.2019.29075.rba}, abstractNote={The CRISPR JournalVol. 2, No. 6 EditorialsFree AccessForesight is 2020: Ten Bold Predictions for the New CRISPR YearRodolphe BarrangouRodolphe BarrangouEditor-in-Chief, The CRISPR JournalSearch for more papers by this authorPublished Online:16 Dec 2019https://doi.org/10.1089/crispr.2019.29075.rbaAboutSectionsPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail Whereas most people use the last few days of the year to reflect on the events that shaped the previous 12 months, I have decided to embrace the disruptiveness of CRISPR and pre-emptively offer 10 bold predictions to set the stage for what promises to be yet another eventful, perhaps pivotal, year for genome editing.Rather than offer a linear progression of incremental insights into what is likely to come, I will channel the ability of our field to leap ahead and offer colorful, perhaps contrarian, predictions of what may (hopefully will) happen for CRISPR in the next 12 months.1.Notwithstanding lingering technical issues (e.g., off-target effects and immunogenicity concerns) and public apprehension, there will be several genome editing clinical successes. This year closes with promising early clinical news from Victoria Gray, the first U.S.–based sickle-cell patient treated with a CRISPR therapy. In 2020, investigational new drug filings will trend up and U.S. FDA regulators will support active recruiting for several clinical trials. I hope they will quickly generate positive results for several indications by various groups of investigators and clinicians. Both safety and efficacy for multiple indications may well be in the cards for 2020.2.In an era of scientific skepticism, the public will embrace CRISPR and increasingly appreciate the real-world benefits of genome editing. Despite widespread misinformation, distrust in the scientific enterprise, and low confidence in scientists dedicating their lives to solving real challenges, team science will step up and share more wonderful stories. In place of sensational media headlines and overdramatized fearmongering, I am looking for the real stories of the scientists leading the revolution and of the people benefiting from it.3.Europe catches up with the world. The good thing about science is that (sometimes) it is immune to politics—just sound thinking, creative minds, and the scientific method. European pundits and regulators will eventually open their eyes to see the light and objectively assess the upside of CRISPR for diverse applications for their health, food, environmental, and commercial benefits. #crispEUr4.Rather than continue with toolbox expansion, current CRISPR tools will be put to good use. After years of next-generation Cas mining and optimization of the Cas, dCas, nCas and fused-effector domains, we will appreciate that the current tools are polished enough for most users and uses. With a useful Cas (Cas-9, 12, 13, et al.) toolbox, diverse applications (editing the genome, transcriptome, and epigenome) and optimized technologies (such as prime editing), currently available tools will be harnessed and implemented with greater urgency and less concerns about technology enhancement.5.Beyond therapeutics. With increasingly promising signs of clinical success, the potential of genome editing will be unleashed for livestock, crops, and even trees for a more sustainable agriculture and healthier planet. Organisms spanning most branches of the tree of life will be enhanced for broad societal benefits.6.Cooler heads prevail. Despite the continuation of intellectual property disputes and interference proceedings, progress toward commercialization of actual products and the need to split large pies that cannot be eaten whole will compel dominant parties to partner and split the proceeds. After all, science is a team sport hinging on scientific collaborations, and the community spirit will behoove key players and leaders to play nice.7.Business dealmakers join the fray. Investors and strategists will be intrigued by deflated stock prices given the extraordinary potential. Underperforming CRISPR stocks and underwhelming financial performance—symptoms that have affected the biotech sector as a whole—have not dampened the upside of CRISPR. The recent report of sickle-cell clinical data pushed valuations significantly higher. It would not be a surprise to see pharma competitively bid for early-stage CRISPR companies and undervalued tickers. Will we see our first CRISPR start-up acquisition in 2020? #CRISPRM&A8.CRISPR responsibility. Two major reports on germline editing, from the National Academies/Royal Society and the World Health Organization, will be released in 2020. We hope the reports will coordinate, with all the voices of CRISPR being heard, so we can build consensual and broadly acceptable frameworks to ensure we use CRISPR responsibly, especially regarding usage in human embryos for germline editing. The public has asked for it, and the community has been working on it. The science versus society gap will be bridged.9.CRISPR fatigue. Despite all the fanfare, I suspect there will be some CRISPR fatigue in 2020: after years of Addgene-fueled democratization, Odin-fed biohacking, and inexorable publication and citation growth, the rate at which CRISPR is expanding will start to slow down and plateau. This is not necessarily a bad thing, as most users in need have already adopted this technology.10.CRISPR goes global. Beyond academic scientists blazing new trails and investors hunting for new technologies, nations will define visions and strategies to expand and build national CRISPR portfolios to harness the bio-economy and keep up with the competition. Leading nations have claimed a stake in the scientific literature and intellectual property arenas, but as business appetite broadens and commercialization success advances, it will be perilous not to seize editing opportunities.So get some rest to prepare for an exciting and eventful year ahead!FiguresReferencesRelatedDetails Volume 2Issue 6Dec 2019 InformationCopyright 2019, Mary Ann Liebert, Inc., publishersTo cite this article:Rodolphe Barrangou.Foresight is 2020: Ten Bold Predictions for the New CRISPR Year.The CRISPR Journal.Dec 2019.341-342.http://doi.org/10.1089/crispr.2019.29075.rbaPublished in Volume: 2 Issue 6: December 16, 2019PDF download}, number={6}, journal={The CRISPR Journal}, publisher={Mary Ann Liebert Inc}, author={Barrangou, Rodolphe}, year={2019}, pages={341–342} }
 @article{hidalgo-cantabrana_goh_pan_sanozky-dawes_barrangou_2019, title={Genome editing using the endogenous type I CRISPR-Cas system in Lactobacillus crispatus}, url={https://doi.org/10.1073/pnas.1905421116}, DOI={10.1073/pnas.1905421116}, abstractNote={
            CRISPR-Cas systems are now widely used for genome editing and transcriptional regulation in diverse organisms. The compact and portable nature of class 2 single effector nucleases, such as Cas9 or Cas12, has facilitated directed genome modifications in plants, animals, and microbes. However, most CRISPR-Cas systems belong to the more prevalent class 1 category, which hinges on multiprotein effector complexes. In the present study, we detail how the native type I-E CRISPR-Cas system, with a 5′-AAA-3′ protospacer adjacent motif (PAM) and a 61-nucleotide guide CRISPR RNA (crRNA) can be repurposed for efficient chromosomal targeting and genome editing in
            Lactobacillus crispatus
            , an important commensal and beneficial microbe in the vaginal and intestinal tracts. Specifically, we generated diverse mutations encompassing a 643-base pair (bp) deletion (100% efficiency), a stop codon insertion (36%), and a single nucleotide substitution (19%) in the exopolysaccharide priming-glycosyl transferase (
            p-gtf
            ). Additional genetic targets included a 308-bp deletion (20%) in the prophage DNA packaging
            Nu1
            and a 730-bp insertion of the green fluorescent protein gene downstream of enolase (23%). This approach enables flexible alteration of the formerly genetically recalcitrant species
            L. crispatus
            , with potential for probiotic enhancement, biotherapeutic engineering, and mucosal vaccine delivery. These results also provide a framework for repurposing endogenous CRISPR-Cas systems for flexible genome targeting and editing, while expanding the toolbox to include one of the most abundant and diverse systems found in nature.
          }, journal={Proceedings of the National Academy of Sciences}, author={Hidalgo-Cantabrana, Claudio and Goh, Yong Jun and Pan, Meichen and Sanozky-Dawes, Rosemary and Barrangou, Rodolphe}, year={2019}, month={Aug} }
 @misc{goh_barrangou_2019, title={Harnessing CRISPR-Cas systems for precision engineering of designer probiotic lactobacilli}, volume={56}, ISSN={["1879-0429"]}, url={https://doi.org/10.1016/j.copbio.2018.11.009}, DOI={10.1016/j.copbio.2018.11.009}, abstractNote={Our evolving understanding on the mechanisms underlying the health-promoting attributes of probiotic lactobacilli, together with an expanding genome editing toolbox have made this genus an ideal chassis for the development of living therapeutics. The rising adoption of CRISPR-based technologies for prokaryotic engineering has demonstrated precise, efficient and scalable genome editing and tunable transcriptional regulation that can be translated into next-generation development of probiotic lactobacilli with enhanced robustness and designer functionalities. Here, we discuss how these tools in conjunction with the naturally abundant and diverse native CRISPR-Cas systems can be harnessed for Lactobacillus cell surface engineering and the delivery of biotherapeutics.}, journal={CURRENT OPINION IN BIOTECHNOLOGY}, publisher={Elsevier BV}, author={Goh, Yong Jun and Barrangou, Rodolphe}, year={2019}, month={Apr}, pages={163–171} }
 @article{canez_selle_goh_barrangou_2019, title={Outcomes and characterization of chromosomal self-targeting by native CRISPR-Cas systems in Streptococcus thermophilus}, volume={366}, ISSN={["1574-6968"]}, url={https://doi.org/10.1093/femsle/fnz105}, DOI={10.1093/femsle/fnz105}, abstractNote={ABSTRACT}, number={9}, journal={FEMS MICROBIOLOGY LETTERS}, publisher={Oxford University Press (OUP)}, author={Canez, Cassandra and Selle, Kurt and Goh, Yong Jun and Barrangou, Rodolphe}, year={2019}, month={May} }
 @article{barrangou_2019, title={Partnering with bioRxiv}, volume={2}, DOI={10.1089/crispr.2019.29076.rba}, abstractNote={The CRISPR JournalVol. 2, No. 6 EditorialsPartnering with bioRxivRodolphe BarrangouRodolphe BarrangouSearch for more papers by this authorPublished Online:16 Dec 2019https://doi.org/10.1089/crispr.2019.29076.rbaAboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"Partnering with bioRxiv." The CRISPR Journal, 2(6), p. 342FiguresReferencesRelatedDetails Volume 2Issue 6Dec 2019 InformationCopyright 2019, Mary Ann Liebert, Inc., publishersTo cite this article:Rodolphe Barrangou.Partnering with bioRxiv.The CRISPR Journal.Dec 2019.342-342.http://doi.org/10.1089/crispr.2019.29076.rbaPublished in Volume: 2 Issue 6: December 16, 2019PDF download}, number={6}, journal={The CRISPR Journal}, publisher={Mary Ann Liebert Inc}, author={Barrangou, Rodolphe}, year={2019}, pages={342–342} }
 @article{nethery_barrangou_2019, title={Predicting and visualizing features of CRISPR-Cas systems}, volume={616}, ISSN={["0076-6879"]}, DOI={10.1016/bs.mie.2018.10.016}, abstractNote={Pervasive application of CRISPR-Cas systems in genome editing has prompted an increase in both interest and necessity to further elucidate existing systems as well as discover putative novel systems. The ubiquity and power of current computational platforms have made in silico approaches to CRISPR-Cas identification and characterization accessible to a wider audience and increasingly amenable for processing extensive data sets. Here, we describe in silico methods for predicting and visualizing notable features of CRISPR-Cas systems, including Cas domain determination, CRISPR array visualization, and inference of the protospacer-adjacent motif. The efficiency of these tools enables rapid exploration of CRISPR-Cas diversity across prokaryotic genomes and supports scalable analysis of large genomic data sets.}, journal={CRISPR-CAS ENZYMES}, author={Nethery, Matthew A. and Barrangou, Rodolphe}, year={2019}, pages={1–25} }
 @article{davis_2019, title={Profile of Rodolphe Barrangou}, volume={116}, DOI={10.1073/pnas.1911079116}, abstractNote={CRISPR, the Instapot of genome editing tools, has its origins in a bacterial immune system that recognizes and slices the genetic material of invading phages. Rodolphe Barrangou, a professor of food science at North Carolina State University, demonstrated the original function of the characteristic repeating genetic sequences long before it became a household word. Barrangou is now turning CRISPR inward, using bacterial cells’ own machinery to edit bacteria. “Unfortunately, bacteria do not typically have good DNA repair mechanisms, so self-targeting usually turns out to be lethal,” explains Barrangou, who was elected to the National Academy of Sciences in 2018. In his Inaugural Article, Barrangou outlines how repurposing the existing type I-E CRISPR-Cas3 system of Lactobacillus crispatus and inserting repair templates can enable targeted editing of this common member of the human microbiome (1).



Photograph of Rodolphe Barrangou. Image courtesy of North Carolina State University/Marc Hall.





Probiotic bacterium L. acidophilus NCFM. Image courtesy of North Carolina State University/Courtney Klotz, Valerie Lapham, and Charles Mooney.



Born in France in 1975, Barrangou found his appetite for science relatively late, when he decided to major in chemistry at the Universite Rene Descartes in Paris. After earning a bachelor’s degree in 1996, he pursued a master’s degree in biological engineering at the Universite de Technologie Compiegne. Barrangou could not envision spending “10 to 20 years working on 1 molecule, 1 project,” as an organic chemist, and engineering was not quite the right fit either. A microbiology class on fermentation propelled him toward a second master’s degree in food science and the field he has helped shape for the past 2 decades. “The living part of microbes was a whole different dimensionality.”}, number={32}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Davis, Tinsley H.}, year={2019}, month={Jul}, pages={15754–15756} }
 @article{varble_meaden_barrangou_westra_marraffini_2019, title={Recombination between phages and CRISPR-cas loci facilitates horizontal gene transfer in staphylococci}, volume={4}, ISSN={["2058-5276"]}, url={https://doi.org/10.1038/s41564-019-0400-2}, DOI={10.1038/s41564-019-0400-2}, abstractNote={CRISPR (clustered regularly interspaced short palindromic repeats) loci and their associated (cas) genes encode an adaptive immune system that protects prokaryotes from viral1 and plasmid2 invaders. Following viral (phage) infection, a small fraction of the prokaryotic cells are able to integrate a small sequence of the invader’s genome into the CRISPR array1. These sequences, known as spacers, are transcribed and processed into small CRISPR RNA guides3–5 that associate with Cas nucleases to specify a viral target for destruction6–9. Although CRISPR−cas loci are widely distributed throughout microbial genomes and often display hallmarks of horizontal gene transfer10–12, the drivers of CRISPR dissemination remain unclear. Here, we show that spacers can recombine with phage target sequences to mediate a form of specialized transduction of CRISPR elements. Phage targets in phage 85, ΦNM1, ΦNM4 and Φ12 can recombine with spacers in either chromosomal or plasmid-borne CRISPR loci in Staphylococcus, leading to either the transfer of CRISPR-adjacent genes or the propagation of acquired immunity to other bacteria in the population, respectively. Our data demonstrate that spacer sequences not only specify the targets of Cas nucleases but also can promote horizontal gene transfer. CRISPR spacers can recombine with phage target sequences to mediate a form of specialized transduction that can promote transfer of CRISPR elements to other bacteria in the population.}, number={6}, journal={NATURE MICROBIOLOGY}, publisher={Springer Nature}, author={Varble, Andrew and Meaden, Sean and Barrangou, Rodolphe and Westra, Edze R. and Marraffini, Luciano A.}, year={2019}, month={Jun}, pages={956–963} }
 @article{selle_andersen_barrangou_2019, title={Short communication: Transcriptional response to a large genomic island deletion in the dairy starter culture Streptococcus thermophilus}, volume={102}, ISSN={["1525-3198"]}, DOI={10.3168/jds.2019-16397}, abstractNote={Streptococcus thermophilus is a lactic acid bacterium widely used in the syntrophic fermentation of milk into yogurt and cheese. Streptococcus thermophilus has adapted to ferment milk primarily through reductive genome evolution but also through acquisition of genes conferring proto-cooperation with Lactobacillus bulgaricus and efficient metabolism of milk macronutrients. Genomic analysis of Strep. thermophilus strains suggests that mobile genetic elements have contributed to genomic evolution through horizontal gene transfer and genomic plasticity. We previously used the endogenous type II CRISPR-Cas [clustered regularly interspaced short palindromic repeats (CRISPR) with CRISPR-associated sequences (Cas)] system in Strep. thermophilus to isolate derivatives lacking the chromosomal mobile genetic element and expandable island that display decreased fitness under routine culturing conditions. Of note, the Lac operon and Leloir pathway genes were deleted in the largest expendable genomic island (102 kbp), rendering the strain incapable of acidifying milk. However, the removal of other open reading frames in the same island had unclear effects on the fitness and regulatory networks of Strep. thermophilus. To uncover the physiological basis for the observed phenotypic changes and underlying regulatory networks affected by deletion of the 102-kbp genomic island in Strep. thermophilus, we analyzed the transcriptome of the mutant that lacked ~5% of its genome. In addition to the loss of transcripts encoded by the deleted material, we detected a total of 56 genes that were differentially expressed, primarily encompassing 10 select operons. Several predicted metabolic pathways were affected, including amino acid and purine metabolism, oligopeptide transport, and iron transport. Collectively, these results suggest that deletion of a 102-kb genomic island in Strep. thermophilus influences compensatory transcription of starvation stress response genes and metabolic pathways involved in important niche-related adaptation.}, number={9}, journal={JOURNAL OF DAIRY SCIENCE}, publisher={American Dairy Science Association}, author={Selle, Kurt and Andersen, Joakim M. and Barrangou, Rodolphe}, year={2019}, month={Sep}, pages={7800–7806} }
 @article{barrangou_2019, title={Taking CRISPR to New Heights}, volume={2}, DOI={10.1089/crispr.2019.29064.rba}, abstractNote={The CRISPR JournalVol. 2, No. 3 EditorialTaking CRISPR to New HeightsRodolphe BarrangouRodolphe BarrangouEditor-in-Chief, The CRISPR Journal.Search for more papers by this authorPublished Online:21 Jun 2019https://doi.org/10.1089/crispr.2019.29064.rbaAboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"Taking CRISPR to New Heights." The CRISPR Journal, 2(3), p. 133FiguresReferencesRelatedDetails Volume 2Issue 3Jun 2019 InformationCopyright 2019, Mary Ann Liebert, Inc., publishersTo cite this article:Rodolphe Barrangou.Taking CRISPR to New Heights.The CRISPR Journal.Jun 2019.133-133.http://doi.org/10.1089/crispr.2019.29064.rbaPublished in Volume: 2 Issue 3: June 21, 2019PDF download}, number={3}, journal={The CRISPR Journal}, publisher={Mary Ann Liebert Inc}, author={Barrangou, Rodolphe}, year={2019}, month={Jun}, pages={133–133} }
 @article{pickar-oliver_black_lewis_mutchnick_klann_gilcrest_sitton_nelson_barrera_bartelt_et al._2019, title={Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells}, volume={37}, ISSN={["1546-1696"]}, DOI={10.1038/s41587-019-0235-7}, abstractNote={Class 2 CRISPR–Cas systems, such as Cas9 and Cas12, have been widely used to target DNA sequences in eukaryotic genomes. However, class 1 CRISPR–Cas systems, which represent about 90% of all CRISPR systems in nature, remain largely unexplored for genome engineering applications. Here, we show that class 1 CRISPR–Cas systems can be expressed in mammalian cells and used for DNA targeting and transcriptional control. We repurpose type I variants of class 1 CRISPR–Cas systems from Escherichia coli and Listeria monocytogenes, which target DNA via a multi-component RNA-guided complex termed Cascade. We validate Cascade expression, complex formation and nuclear localization in human cells, and demonstrate programmable CRISPR RNA (crRNA)-mediated targeting of specific loci in the human genome. By tethering activation and repression domains to Cascade, we modulate the expression of targeted endogenous genes in human cells. This study demonstrates the use of Cascade as a CRISPR-based technology for targeted eukaryotic gene regulation, highlighting class 1 CRISPR–Cas systems for further exploration. Type I CRISPR–Cas systems, the largest group of CRISPR systems in nature, can be repurposed for DNA targeting and gene regulation in human cells}, number={12}, journal={NATURE BIOTECHNOLOGY}, publisher={Springer Science and Business Media LLC}, author={Pickar-Oliver, Adrian and Black, Joshua B. and Lewis, Mae M. and Mutchnick, Kevin J. and Klann, Tyler S. and Gilcrest, Kylie A. and Sitton, Madeleine J. and Nelson, Christopher E. and Barrera, Alejandro and Bartelt, Luke C. and et al.}, year={2019}, month={Dec}, pages={1493-+} }
 @article{young_gasior_jones_wang_navarro_vickroy_barrangou_2019, title={The repurposing of type I-E CRISPR-Cascade for gene activation in plants}, url={https://doi.org/10.1038/s42003-019-0637-6}, DOI={10.1038/s42003-019-0637-6}, abstractNote={Abstract}, journal={Communications Biology}, author={Young, Joshua K. and Gasior, Stephen L. and Jones, Spencer and Wang, Lijuan and Navarro, Pedro and Vickroy, Becca and Barrangou, Rodolphe}, year={2019}, month={Oct} }
 @article{barrangou_2019, title={Thinking About CRISPR: The Ethics of Human Genome Editing}, volume={2}, DOI={10.1089/crispr.2019.29072.rba}, abstractNote={The CRISPR JournalVol. 2, No. 5 EditorialThinking About CRISPR: The Ethics of Human Genome EditingRodolphe BarrangouRodolphe BarrangouEditor-in-Chief, The CRISPR Journal.Search for more papers by this authorPublished Online:9 Oct 2019https://doi.org/10.1089/crispr.2019.29072.rbaAboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"Thinking About CRISPR: The Ethics of Human Genome Editing." The CRISPR Journal, 2(5), pp. 247–248FiguresReferencesRelatedDetailsCited byDemocratizing CRISPR? Stories, practices, and politics of science and governance on the agricultural gene editing frontier25 February 2020 | Elementa: Science of the Anthropocene, Vol. 8 Volume 2Issue 5Oct 2019 InformationCopyright 2019, Mary Ann Liebert, Inc., publishersTo cite this article:Rodolphe Barrangou.Thinking About CRISPR: The Ethics of Human Genome Editing.The CRISPR Journal.Oct 2019.247-248.http://doi.org/10.1089/crispr.2019.29072.rbaPublished in Volume: 2 Issue 5: October 9, 2019PDF download}, number={5}, journal={The CRISPR Journal}, publisher={Mary Ann Liebert Inc}, author={Barrangou, Rodolphe}, year={2019}, month={Oct}, pages={247–248} }
 @article{barrangou_2019, title={Time To Let CRISPR B.E.?}, volume={2}, DOI={10.1089/crispr.2019.29055.rdb}, abstractNote={The CRISPR JournalVol. 2, No. 2 EditorialTime To Let CRISPR B.E.?Rodolphe BarrangouRodolphe BarrangouEditor-in-Chief, The CRISPR JournalSearch for more papers by this authorPublished Online:18 Apr 2019https://doi.org/10.1089/crispr.2019.29055.rdbAboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"Time To Let CRISPR B.E.?." The CRISPR Journal, 2(2), p. 67FiguresReferencesRelatedDetails Volume 2Issue 2Apr 2019 InformationCopyright 2019, Mary Ann Liebert, Inc., publishersTo cite this article:Rodolphe Barrangou.Time To Let CRISPR B.E.?.The CRISPR Journal.Apr 2019.67-67.http://doi.org/10.1089/crispr.2019.29055.rdbPublished in Volume: 2 Issue 2: April 18, 2019PDF download}, number={2}, journal={The CRISPR Journal}, publisher={Mary Ann Liebert Inc}, author={Barrangou, Rodolphe}, year={2019}, month={Apr}, pages={67–67} }
 @misc{donohoue_barrangou_may_2018, title={Advances in Industrial Biotechnology Using CRISPR-Cas Systems}, volume={36}, ISSN={["1879-3096"]}, DOI={10.1016/j.tibtech.2017.07.007}, abstractNote={The term 'clustered regularly interspaced short palindromic repeats' (CRISPR) has recently become synonymous with the genome-editing revolution. The RNA-guided endonuclease CRISPR-associated protein 9 (Cas9), in particular, has attracted attention for its promise in basic research and gene editing-based therapeutics. CRISPR-Cas systems are efficient and easily programmable nucleic acid-targeting tools, with uses reaching beyond research and therapeutic development into the precision breeding of plants and animals and the engineering of industrial microbes. CRISPR-Cas systems have potential for many microbial engineering applications, including bacterial strain typing, immunization of cultures, autoimmunity or self-targeted cell killing, and the engineering or control of metabolic pathways for improved biochemical synthesis. In this review, we explore the fundamental characteristics of CRISPR-Cas systems and highlight how these features can be used in industrial settings.}, number={2}, journal={TRENDS IN BIOTECHNOLOGY}, publisher={Elsevier BV}, author={Donohoue, Paul D. and Barrangou, Rodolphe and May, Andrew P.}, year={2018}, month={Feb}, pages={134–146} }
 @article{barrangou_2018, title={CRISPR Craziness: A Response to the EU Court Ruling}, volume={1}, DOI={10.1089/crispr.2018.29025.edi}, abstractNote={The CRISPR JournalVol. 1, No. 4 EditorialsCRISPR Craziness: A Response to the EU Court RulingRodolphe BarrangouRodolphe BarrangouEditor-in-Chief, The CRISPR Journal.Search for more papers by this authorPublished Online:1 Aug 2018https://doi.org/10.1089/crispr.2018.29025.ediAboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"CRISPR Craziness: A Response to the EU Court Ruling." The CRISPR Journal, 1(4), pp. 251–252FiguresReferencesRelatedDetailsCited byCRISPR-Cas Genome Editing for Horticultural Crops Improvement: Advantages and Prospects30 December 2022 | Horticulturae, Vol. 9, No. 1Consumer Evaluation of Novel Plant-Breeding Technologies: A Decision-Focused Research Agenda4 January 2023CRISPR and Chromothripsis: Proceed with Caution Stephanie Mack and I. Alasdair Russell16 June 2021 | The CRISPR Journal, Vol. 4, No. 3A Field Day for Gene-Edited Brassicas and Crop Improvement Johnathan A. Napier16 June 2021 | The CRISPR Journal, Vol. 4, No. 3How should we regulate products of new breeding techniques? Opinion of surveyed experts in plant biotechnologyBiotechnology Reports, Vol. 26European Court of Justice ruling regarding new genetic engineering methods scientifically justified: a commentary on the biased reporting about the recent ruling20 December 2018 | Environmental Sciences Europe, Vol. 30, No. 1 Volume 1Issue 4Aug 2018 InformationCopyright 2018, Mary Ann Liebert, Inc.To cite this article:Rodolphe Barrangou.CRISPR Craziness: A Response to the EU Court Ruling.The CRISPR Journal.Aug 2018.251-252.http://doi.org/10.1089/crispr.2018.29025.ediPublished in Volume: 1 Issue 4: August 1, 2018PDF download}, number={4}, journal={The CRISPR Journal}, publisher={Mary Ann Liebert Inc}, author={Barrangou, Rodolphe}, year={2018}, month={Aug}, pages={251–252} }
 @article{barrangou_2018, title={CRISPR Crossroads for Genome Editing}, volume={1}, DOI={10.1089/crispr.2018.29040.rba}, abstractNote={The CRISPR JournalVol. 1, No. 6 EditorialCRISPR Crossroads for Genome EditingRodolphe BarrangouRodolphe BarrangouEditor-in-Chief, The CRISPR JournalSearch for more papers by this authorPublished Online:20 Dec 2018https://doi.org/10.1089/crispr.2018.29040.rbaAboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"CRISPR Crossroads for Genome Editing." The CRISPR Journal, 1(6), pp. 349–350FiguresReferencesRelatedDetailsCited byRealigning gene editing with clinical research ethics: What the “CRISPR Twins” debacle means for Chinese and international research ethics governance17 May 2019 | Accountability in Research, Vol. 26, No. 4 Volume 1Issue 6Dec 2018 InformationCopyright 2018, Mary Ann Liebert, Inc., publishersTo cite this article:Rodolphe Barrangou.CRISPR Crossroads for Genome Editing.The CRISPR Journal.Dec 2018.349-350.http://doi.org/10.1089/crispr.2018.29040.rbaPublished in Volume: 1 Issue 6: December 20, 2018PDF download}, number={6}, journal={The CRISPR Journal}, publisher={Mary Ann Liebert Inc}, author={Barrangou, Rodolphe}, year={2018}, pages={349–350} }
 @article{crawley_henriksan_barranaou_2018, title={CRISPRdisco: An Automated Pipeline for the Discovery and Analysis of CRISPR-Cas Systems}, volume={1}, ISSN={["2573-1602"]}, DOI={10.1089/crispr.2017.0022}, abstractNote={Abstract CRISPR-Cas adaptive immune systems of bacteria and archaea have catapulted into the scientific spotlight as genome editing tools. To aid researchers in the field, we have developed an automated pipeline, named CRISPRdisco (CRISPR discovery), to identify CRISPR repeats and cas genes in genome assemblies, determine type and subtype, and describe system completeness. All six major types and 23 currently recognized subtypes and novel putative V-U types are detected. Here, we use the pipeline to identify and classify putative CRISPR-Cas systems in 2,777 complete genomes from the NCBI RefSeq database. This allows comparison to previous publications and investigation of the occurrence and size of CRISPR-Cas systems. Software available at http://github.com/crisprlab/CRISPRdisco provides reproducible, standardized, accessible, transparent, and high-throughput analysis methods available to all researchers in and beyond the CRISPR-Cas research community. This tool opens new avenues to enable classification within a complex nomenclature and provides analytical methods in a field that has evolved rapidly.}, number={2}, journal={CRISPR JOURNAL}, publisher={Mary Ann Liebert Inc}, author={Crawley, Alexandra R. and Henriksan, Jams R. and Barranaou, Rodolphe}, year={2018}, month={Apr}, pages={171–181} }
 @article{crawley_henriksen_stout_brandt_barrangou_2018, title={Characterizing the activity of abundant, diverse and active CRISPR-Cas systems in lactobacilli}, volume={8}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/S41598-018-29746-3}, DOI={10.1038/s41598-018-29746-3}, abstractNote={Abstract}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Crawley, Alexandra B. and Henriksen, Emily D. and Stout, Emily and Brandt, Katelyn and Barrangou, Rodolphe}, year={2018}, month={Aug} }
 @article{crawley_barrangou_2018, title={Conserved Genome Organization and Core Transcriptome of the Lactobacillus acidophilus Complex}, volume={9}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2018.01834}, abstractNote={The Lactobacillus genus encompasses a genetically and functionally diverse group of species, and contains many strains widely formulated in the human food supply chain as probiotics and starter cultures. Within this genetically expansive group, there are several distinct clades that have high levels of homology, one of which is the Lactobacillus acidophilus group. Of the uniting features, small genomes, low GC content, adaptation to dairy environments, and fastidious growth requirements, are some of the most defining characteristics of this group. To better understand what truly links and defines this clade, we sought to characterize the genomic organization and content of the genomes of several members of this group. Through core genome analysis we explored the synteny and intrinsic genetic underpinnings of the L. acidophilus clade, and observed key features related to the evolution and adaptation of these organisms. While genetic content is able to provide a large map of the potential of each organism, it does not always reflect their functionality. Through transcriptomic data we inferred the core transcriptome of the L. acidophilus complex to better define the true metabolic capabilities that unite this clade. Using this approach we have identified seven small ORFs that are both highly conserved and transcribed in diverse members of this clade and could be potential novel small peptide or untranslated RNA regulators. Overall, our results reveal the core features of the L. acidophilus complex and open new avenues for the enhancement and formulation and of next generation probiotics and starter cultures.}, journal={FRONTIERS IN MICROBIOLOGY}, publisher={Frontiers Media SA}, author={Crawley, Alexandra B. and Barrangou, Rodolphe}, year={2018}, month={Aug} }
 @article{barrangou_2018, title={Cultivating CRISPR}, volume={1}, DOI={10.1089/crispr.2018.29011.rba}, abstractNote={The CRISPR JournalVol. 1, No. 2 EditorialCultivating CRISPRRodolphe BarrangouRodolphe BarrangouSearch for more papers by this authorPublished Online:1 Apr 2018https://doi.org/10.1089/crispr.2018.29011.rbaAboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"Cultivating CRISPR." The CRISPR Journal, 1(2), pp. 99–100FiguresReferencesRelatedDetails Volume 1Issue 2Apr 2018 InformationCopyright 2018, Mary Ann Liebert, Inc.To cite this article:Rodolphe Barrangou.Cultivating CRISPR.The CRISPR Journal.Apr 2018.99-100.http://doi.org/10.1089/crispr.2018.29011.rbaPublished in Volume: 1 Issue 2: April 1, 2018PDF download}, number={2}, journal={The CRISPR Journal}, publisher={Mary Ann Liebert Inc}, author={Barrangou, Rodolphe}, year={2018}, month={Apr}, pages={99–100} }
 @article{stout_sanozky-dawes_goh_crawley_klaenhammer_barrangou_2018, title={Deletion-based escape of CRISPR-Cas9 targeting in Lactobacillus gasseri}, volume={164}, ISSN={["1465-2080"]}, DOI={10.1099/mic.0.000689}, abstractNote={Lactobacillus gasseri is a human commensal which carries CRISPR-Cas, an adaptive immune system that protects the cell from invasive mobile genetic elements (MGEs). However, MGEs occasionally escape CRISPR targeting due to DNA mutations that occur in sequences involved in CRISPR interference. To better understand CRISPR escape processes, a plasmid interference assay was used to screen for mutants that escape CRISPR-Cas targeting. Plasmids containing a target sequence and a protospacer adjacent motif (PAM) were transformed for targeting by the native CRISPR-Cas system. Although the primary outcome of the assay was efficient interference, a small proportion of the transformed population overcame targeting. Mutants containing plasmids that had escaped were recovered to investigate the genetic routes of escape and their relative frequencies. Deletion of the targeting spacer in the native CRISPR array was the dominant pattern of escape, accounting for 52-70 % of the mutants from two L. gasseri strains. We repeatedly observed internal deletions in the chromosomal CRISPR array, characterized by polarized excisions from the leader end that spanned 1-15 spacers, and systematically included the leader-proximal targeting spacer. This study shows that deletions of spacers within CRISPR arrays constitute a key escape mechanism to evade CRISPR targeting, while preserving the functionality of the CRISPR-Cas system. This mechanism enables cells to maintain an active immune system, but allows the uptake of potentially beneficial plasmids. Our study revealed the co-occurrence of other genomic mutations associated with various phenotypes, showing how this selection process uncovers population diversification.}, number={9}, journal={MICROBIOLOGY-SGM}, publisher={Microbiology Society}, author={Stout, Emily A. and Sanozky-Dawes, Rosemary and Goh, Yong Jun and Crawley, Alexandra B. and Klaenhammer, Todd R. and Barrangou, Rodolphe}, year={2018}, month={Sep}, pages={1098–1111} }
 @article{lamanna_barrangou_2018, title={Enabling the Rise of a CRISPR World}, volume={1}, DOI={10.1089/crispr.2018.0022}, abstractNote={Abstract CRISPR technology has dramatically changed scientists' ability to conduct research in medicine, biotechnology, and agriculture through faster, more efficient genome editing. A key driver of the technology's adoption is the easy, fast, and inexpensive access to vectors and the resulting next-generation tools by the nonprofit plasmid repository Addgene. Since 2013, Addgene has shipped over 100,000 CRISPR plasmids to more than 75 countries worldwide. This pipeline of new technologies is enabling cutting-edge research to address the grand challenges of mankind.}, number={3}, journal={The CRISPR Journal}, publisher={Mary Ann Liebert Inc}, author={LaManna, Caroline M. and Barrangou, Rodolphe}, year={2018}, month={Jun}, pages={205–208} }
 @misc{klotz_barrangou_2018, title={Engineering Components of the Lactobacillus S-Layer for Biotherapeutic Applications}, volume={9}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2018.02264}, abstractNote={Lactic acid bacteria (LAB) are frequently harnessed for the delivery of biomolecules to mucosal tissues. Several species of Lactobacillus are commonly employed for this task, of which a subset are known to possess surface-layers (S-layers). S-layers are two-dimensional crystalline arrays of repeating proteinaceous subunits that form the outermost coating of many prokaryotic cell envelopes. Their periodicity and abundance have made them a target for numerous biotechnological applications. In the following review, we examine the multi-faceted S-layer protein (Slp), and its use in both heterologous protein expression systems and mucosal vaccine delivery frameworks, through its diverse genetic components: the strong native promoter, capable of synthesizing as many as 500 Slp subunits per second; the signal peptide that stimulates robust secretion of recombinant proteins; and the structural domains, which can be harnessed for both cell surface display of foreign peptides or adhesion enhancement of a host bacterium. Although numerous studies have established vaccine platforms based on one or more components of the Lactobacillus S-layer, this area of research still remains largely in its infancy, thus this review is meant to not only highlight past works, but also advocate for the future usage of Slps in biotherapeutic research.}, journal={FRONTIERS IN MICROBIOLOGY}, publisher={Frontiers Media SA}, author={Klotz, Courtney and Barrangou, Rodolphe}, year={2018}, month={Oct} }
 @article{barrangou_2018, title={Expanding the CRISPR Landscape on a cas by cas Basis}, volume={1}, DOI={10.1089/crispr.2018.29035.rba}, abstractNote={The CRISPR JournalVol. 1, No. 5 EditorialExpanding the CRISPR Landscape on a cas by cas BasisRodolphe BarrangouRodolphe BarrangouEditor-in-Chief, The CRISPR Journal.Search for more papers by this authorPublished Online:17 Oct 2018https://doi.org/10.1089/crispr.2018.29035.rbaAboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"Expanding the CRISPR Landscape on a cas by cas Basis." The CRISPR Journal, 1(5), p. 303FiguresReferencesRelatedDetails Volume 1Issue 5Oct 2018 InformationCopyright 2018, Mary Ann Liebert, Inc., publishersTo cite this article:Rodolphe Barrangou.Expanding the CRISPR Landscape on a cas by cas Basis.The CRISPR Journal.Oct 2018.303-303.http://doi.org/10.1089/crispr.2018.29035.rbaPublished in Volume: 1 Issue 5: October 17, 2018PDF download}, number={5}, journal={The CRISPR Journal}, publisher={Mary Ann Liebert Inc}, author={Barrangou, Rodolphe}, year={2018}, month={Oct}, pages={303–303} }
 @article{weissman_holmes_barrangou_moineau_fagan_levin_johnson_2018, title={Immune loss as a driver of coexistence during host-phage coevolution}, volume={12}, ISSN={["1751-7370"]}, DOI={10.1038/ismej.2017.194}, abstractNote={Abstract}, number={2}, journal={ISME JOURNAL}, publisher={Springer Science and Business Media LLC}, author={Weissman, Jake L. and Holmes, Rayshawn and Barrangou, Rodolphe and Moineau, Sylvain and Fagan, William F. and Levin, Bruce and Johnson, Philip L. F.}, year={2018}, month={Feb}, pages={585–597} }
 @misc{hidalgo-cantabrana_sanozky-dawes_barrangou_2018, title={Insights into the Human Virome Using CRISPR Spacers from Microbiomes}, volume={10}, ISSN={["1999-4915"]}, url={https://doi.org/10.3390/v10090479}, DOI={10.3390/v10090479}, abstractNote={Due to recent advances in next-generation sequencing over the past decade, our understanding of the human microbiome and its relationship to health and disease has increased dramatically. Yet, our insights into the human virome, and its interplay with important microbes that impact human health, is relatively limited. Prokaryotic and eukaryotic viruses are present throughout the human body, comprising a large and diverse population which influences several niches and impacts our health at various body sites. The presence of prokaryotic viruses like phages, has been documented at many different body sites, with the human gut being the richest ecological niche. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and associated proteins constitute the adaptive immune system of bacteria, which prevents attack by invasive nucleic acid. CRISPR-Cas systems function by uptake and integration of foreign genetic element sequences into the CRISPR array, which constitutes a genomic archive of iterative vaccination events. Consequently, CRISPR spacers can be investigated to reconstruct interplay between viruses and bacteria, and metagenomic sequencing data can be exploited to provide insights into host-phage interactions within a niche. Here, we show how the CRISPR spacer content of commensal and pathogenic bacteria can be used to determine the evidence of their phage exposure. This framework opens new opportunities for investigating host-virus dynamics in metagenomic data, and highlights the need to dedicate more efforts for virome sampling and sequencing.}, number={9}, journal={VIRUSES-BASEL}, author={Hidalgo-Cantabrana, Claudio and Sanozky-Dawes, Rosemary and Barrangou, Rodolphe}, year={2018}, month={Sep} }
 @article{barrangou_2018, title={Keep Calm and CRISPR On}, volume={1}, ISSN={["2573-1602"]}, DOI={10.1089/crispr.2017.29000.rba}, abstractNote={The CRISPR JournalVol. 1, No. 1 EditorialKeep Calm and CRISPR OnRodolphe BarrangouRodolphe BarrangouSearch for more papers by this authorPublished Online:1 Feb 2018https://doi.org/10.1089/crispr.2017.29000.rbaAboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View articleFiguresReferencesRelatedDetailsCited byDevelopment of CNN Model for Prediction of CRISPR/Cas12 Guide RNA Activity20 November 2019Breaking the germline barrier in a moral vacuum26 July 2019 | Accountability in Research, Vol. 26, No. 6Collateral damage and CRISPR genome editing14 March 2019 | PLOS Genetics, Vol. 15, No. 3How to talk about genome editing25 April 2018 | British Medical Bulletin, Vol. 126, No. 1 Volume 1Issue 1Feb 2018 InformationCopyright 2018, Mary Ann Liebert, Inc.To cite this article:Rodolphe Barrangou.Keep Calm and CRISPR On.The CRISPR Journal.Feb 2018.1-3.http://doi.org/10.1089/crispr.2017.29000.rbaPublished in Volume: 1 Issue 1: February 1, 2018Online Ahead of Print:January 8, 2018PDF download}, number={1}, journal={CRISPR JOURNAL}, publisher={Mary Ann Liebert Inc}, author={Barrangou, Rodolphe}, year={2018}, month={Feb}, pages={1–3} }
 @article{anderson_mcclelland_maksimova_strezoska_basila_briner_barrangou_smith_2018, title={Lactobacillus gasseri CRISPR-Cas9 characterization In Vitro reveals a flexible mode of protospacer-adjacent motif recognition}, volume={13}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0192181}, abstractNote={While the CRISPR-Cas9 system from S. pyogenes is a powerful genome engineering tool, additional programmed nucleases would enable added flexibility in targeting space and multiplexing. Here, we characterized a CRISPR-Cas9 system from L. gasseri and found that it has modest activity in a cell-free lysate assay but no activity in mammalian cells even when altering promoter, position of tag sequences and NLS, and length of crRNA:tracrRNA. In the lysate assay we tested over 400 sequential crRNA target sequences and found that the Lga Cas9 PAM is NNGA/NDRA, different than NTAA predicted from the native bacterial host. In addition, we found multiple instances of consecutive crRNA target sites, indicating flexibility in either PAM sequence or distance from the crRNA target site. This work highlights the need for characterization of new CRISPR systems and highlights the non-triviality of porting them into eukaryotes as gene editing tools.}, number={2}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Anderson, Emily M. and McClelland, Shawn and Maksimova, Elena and Strezoska, Zaklina and Basila, Megan and Briner, Alexandra E. and Barrangou, Rodolphe and Smith, Anja van Brabant}, editor={Xu, Shuang-yongEditor}, year={2018}, month={Feb} }
 @article{davies_barrangou_2018, title={MasterChef at Work: An Interview with Rodolphe Barrangou}, volume={1}, DOI={10.1089/crispr.2018.29015.int}, abstractNote={The CRISPR JournalVol. 1, No. 3 InterviewMasterChef at Work: An Interview with Rodolphe BarrangouKevin Davies and Rodolphe BarrangouKevin DaviesSearch for more papers by this author and Rodolphe BarrangouSearch for more papers by this authorPublished Online:1 Jun 2018https://doi.org/10.1089/crispr.2018.29015.intAboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View articleFiguresReferencesRelatedDetails Volume 1Issue 3Jun 2018 InformationCopyright 2018, Mary Ann Liebert, Inc.To cite this article:Kevin Davies and Rodolphe Barrangou.MasterChef at Work: An Interview with Rodolphe Barrangou.The CRISPR Journal.Jun 2018.219-222.http://doi.org/10.1089/crispr.2018.29015.intPublished in Volume: 1 Issue 3: June 1, 2018PDF download}, number={3}, journal={The CRISPR Journal}, publisher={Mary Ann Liebert Inc}, author={Davies, Kevin and Barrangou, Rodolphe}, year={2018}, month={Jun}, pages={219–222} }
 @article{barrangou_oost_2018, title={Mining for novel bacterial defence systems}, volume={3}, ISSN={["2058-5276"]}, DOI={10.1038/s41564-018-0149-z}, abstractNote={Bacteria encode many strategies to prevent or escape infection. Through the analysis of metagenomic dark matter, several novel defence systems were identified, some of which were engineered and characterized in vivo, showing that they provide resistance against viruses and plasmids.}, number={5}, journal={NATURE MICROBIOLOGY}, publisher={Springer Science and Business Media LLC}, author={Barrangou, Rodolphe and Oost, John}, year={2018}, month={May}, pages={535–536} }
 @article{daughtry_johanningsmeier_sanozky-dawes_klaenhammer_barrangou_2018, title={Phenotypic and genotypic diversity of Lactobacillus buchneri strains isolated from spoiled, fermented cucumber}, volume={280}, ISSN={["1879-3460"]}, DOI={10.1016/j.ijfoodmicro.2018.04.044}, abstractNote={Lactobacillus buchneri is a Gram-positive, obligate heterofermentative, facultative anaerobe commonly affiliated with spoilage of food products. Notably, L. buchneri is able to metabolize lactic acid into acetic acid and 1,2-propanediol. Although beneficial to the silage industry, this metabolic capability is detrimental to preservation of cucumbers by fermentation. The objective of this study was to characterize isolates of L. buchneri purified from both industrial and experimental fermented cucumber after the onset of secondary fermentation. Genotypic and phenotypic characterization included 16S rRNA sequencing, DiversiLab® rep-PCR, colony morphology, API 50 CH carbohydrate analysis, and ability to degrade lactic acid in modified MRS and fermented cucumber media. Distinct groups of isolates were identified with differing colony morphologies that varied in color (translucent white to opaque yellow), diameter (1 mm–11 mm), and shape (umbonate, flat, circular or irregular). Growth rates in MRS revealed strain differences, and a wide spectrum of carbon source utilization was observed. Some strains were able to ferment as many as 21 of 49 tested carbon sources, including inulin, fucose, gentiobiose, lactose, mannitol, potassium ketogluconate, saccharose, raffinose, galactose, and xylose, while others metabolized as few as eight carbohydrates as the sole source of carbon. All isolates degraded lactic acid in both fermented cucumber medium and modified MRS, but exhibited differences in the rate and extent of lactate degradation. Isolates clustered into eight distinct groups based on rep-PCR fingerprints with 20 of 36 of the isolates exhibiting >97% similarity. Although isolated from similar environmental niches, significant phenotypic and genotypic diversity was found among the L. buchneri cultures. A collection of unique L. buchneri strains was identified and characterized, providing the basis for further analysis of metabolic and genomic capabilities of this species to enable control of lactic acid degradation in fermented plant materials.}, journal={INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY}, publisher={Elsevier BV}, author={Daughtry, Katheryne V and Johanningsmeier, Suzanne D. and Sanozky-Dawes, Rosemary and Klaenhammer, Todd R. and Barrangou, Rodolphe}, year={2018}, month={Sep}, pages={46–56} }
 @article{curchoe_barrangou_2018, title={Pomp and Circumstance: Making the Case for CRISPR}, volume={1}, DOI={10.1089/crispr.2018.29030.oxf}, abstractNote={The CRISPR JournalVol. 1, No. 4 EditorialsPomp and Circumstance: Making the Case for CRISPRCarol Lynn Curchoe and Rodolphe BarrangouCarol Lynn CurchoeSan Diego Fertility Center and 32ATPs, San Diego, CaliforniaSearch for more papers by this author and Rodolphe BarrangouEditor-in-Chief, The CRISPR Journal.Search for more papers by this authorPublished Online:1 Aug 2018https://doi.org/10.1089/crispr.2018.29030.oxfAboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"Pomp and Circumstance: Making the Case for CRISPR." The CRISPR Journal, 1(4), pp. 253–254FiguresReferencesRelatedDetails Volume 1Issue 4Aug 2018 InformationCopyright 2018, Mary Ann Liebert, Inc.To cite this article:Carol Lynn Curchoe and Rodolphe Barrangou.Pomp and Circumstance: Making the Case for CRISPR.The CRISPR Journal.Aug 2018.253-254.http://doi.org/10.1089/crispr.2018.29030.oxfPublished in Volume: 1 Issue 4: August 1, 2018PDF download}, number={4}, journal={The CRISPR Journal}, publisher={Mary Ann Liebert Inc}, author={Curchoe, Carol Lynn and Barrangou, Rodolphe}, year={2018}, month={Aug}, pages={253–254} }
 @article{gersbach_barrangou_2018, title={Pulling the genome in opposite directions to dissect gene networks}, volume={19}, DOI={10.1186/s13059-018-1425-1}, abstractNote={Orthogonal CRISPR-Cas systems have been integrated into combinatorial screens to decipher complex genetic relationships in two recent studies.}, number={1}, journal={Genome Biology}, publisher={Springer Science and Business Media LLC}, author={Gersbach, Charles A. and Barrangou, Rodolphe}, year={2018}, month={Mar} }
 @article{gersbach_barrangou_2018, title={Pulling the genome in opposite directions to dissect gene networks}, volume={19}, journal={Genome Biology}, author={Gersbach, C. A. and Barrangou, R.}, year={2018} }
 @article{barrangou_2018, title={The Democratization of CRISPR}, volume={1}, DOI={10.1089/crispr.2018.29019.rba}, abstractNote={The CRISPR JournalVol. 1, No. 3 EditorialFree AccessThe Democratization of CRISPRRodolphe BarrangouRodolphe BarrangouSearch for more papers by this authorPublished Online:1 Jun 2018https://doi.org/10.1089/crispr.2018.29019.rbaAboutSectionsPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail By many measures, CRISPR*-based technologies and their applications have taken over the world in the past few years, and the CRISPR era is upon us. Much like cloning and PCR in prior decades, CRISPR stands to become a generation-defining technology. Indeed, as illustrated on the cover of this issue and discussed in the Perspective by LaManna and Barrangou on page 205, researchers continue to advance, develop, and implement a wide array of CRISPR tools, which are now being circulated globally in real time by Addgene. Embraced by commercial entities and fueled by motivated investors, the commercialization of CRISPR is next.The goal of making CRISPR openly available, regardless of location, political, or regulatory consideration, epitomizes the mission of Addgene, a nonprofit organization aimed at empowering academic laboratories by granting access to cutting-edge technologies and advance science. This is a noteworthy departure from ongoing intellectual-property disputes—and a refreshing digression from some perplexing steep licensing fees charged by not-for-profit academic institutions that hold rights to CRISPR tools.The numbers alone reflect the Addgene-enabled pervasiveness of CRISPR, not just in North America, Europe, and Asia, but also in many third world countries. CRISPR is no longer an exclusive technology but rather universal—internationally, culturally, and socially. For example, new applications of CRISPR in a diagnostic context offer great potential in territories at risk of disease outbreaks with limited resources (see the First Cut article by Karl Petri and Vikram Pattanayak, page 209). Naturally, governments and the public are actively evaluating how this technology should be managed; their opinions and actions will have widespread impact on both science and society.Public opinion has proven to be a powerful modulator of scientific progress, leading to long-lasting repercussions for many countries. As always, one hopes that scientifically informed decisions will be made, but history and recent events remind us that this is not always the case, given the public perception about science, use of misguided terms such as “frankenfood” and “designer babies” by the media, and historical shortcomings displayed by the agriculture (Ag) industry with regard to public relations, communications, and stewardship. Yet, there is hope. While much focus has been on the science, we should be mindful of the people driving these efforts. Indeed, scientists spend decades training and preparing for such opportunities and dedicate most of their lives to solving problems and creating solutions. The recent “Unite to Cure” conference at the Vatican signaled a new chapter for CRISPR acceptance and stewardship (see the First Cut by Davies on page 213) and extends a crucial dialogue about ethical implications and societal engagement.Already, CRISPR is transcending not just scientific and economic boundaries for medicine and agriculture, but also religious, ethical, and societal frontiers. Besides the well-documented therapeutic implications, notwithstanding recent Food and Drug Administration clarification requests, many signs already point to tremendous benefits pending in agriculture (see the First Cut by Willmann on page 211). Arguably, agriculture is poised to win the CRISPR race: teams of scientists in academia and industry, including “big Ag” and several new start-up companies, are harnessing next-generation breeding of crops and livestock to help feed the world. The benefits comprise classical targets such as increased yield, pest management, and drought resistance to address the food gap for our rapidly expanding population. Efforts increasingly encompass sustainability, with improved water usage and efficient land management receiving critical attention. We need more food, but also a safer and healthier supply chain, globally.Our ability to bring CRISPR to the people hinges on both supportive adjudication by regulatory agencies and legislators as well as public acceptance of science and technology. The challenges are formidable given skepticism of “big Ag” along with confusion and uncertainty over what CRISPR actually entails. Actually, there is an opportunity for both sides to discuss how to best regulate genome editing to encourage support rather than constrain the advancement and exploitation of these beneficial technologies.A major milestone was the March 2018 announcement by the U.S. Department of Agriculture stating that it will not regulate genetically edited plants that recapitulate traditional breeding results is encouraging, but this is only the beginning. Concerted efforts by multiple communities and stakeholders are underway to formalize the regulatory landscape with input from academics and PR experts. Those addressing the food gap and harnessing CRISPR-based technologies to ensure a healthier and more sustainable food supply must better convey how critical, impactful, and noble their efforts are. Unity, caution, transparency, and engagement constitute the path forward. A series of recent and forthcoming meetings will define the ability of CRISPR to make progress in the short term.For CRISPR to realize its obvious potential, the scientific community must strive to share its progress with all stakeholders: we all need to do a better job at communicating about science in general and telling and spreading the CRISPR story in particular. It is unclear if and how quickly we will get there.* Clustered Regularly Interspaced Short Palindromic Repeats.FiguresReferencesRelatedDetails Volume 1Issue 3Jun 2018 InformationCopyright 2018, Mary Ann Liebert, Inc.To cite this article:Rodolphe Barrangou.The Democratization of CRISPR.The CRISPR Journal.Jun 2018.203-204.http://doi.org/10.1089/crispr.2018.29019.rbaPublished in Volume: 1 Issue 3: June 1, 2018PDF download}, number={3}, journal={The CRISPR Journal}, publisher={Mary Ann Liebert Inc}, author={Barrangou, Rodolphe}, year={2018}, month={Jun}, pages={203–204} }
 @article{o'flaherty_crawley_theriot_barrangou_2018, title={The Lactobacillus Bile Salt Hydrolase Repertoire Reveals Niche-Specific Adaptation}, volume={3}, ISSN={["2379-5042"]}, url={https://doi.org/10.1128/mSphere.00140-18}, DOI={10.1128/msphere.00140-18}, abstractNote={
            Bile acids play an integral role in shaping the gut microbiota and host physiology by regulating metabolic signaling, weight gain, and serum cholesterol and liver triglyceride levels. Given these important roles of bile acids, we investigated the presence of bile salt hydrolase (BSH) in
            Lactobacillus
            genomes representing 170 different species, determined strain- and species-specific patterns of occurrences, and expanded on the diversity of the BSH repertoire in this genus. While our data showed that 28% of
            Lactobacillus
            species encode BSH proteins, these species are associated mainly with vertebrate-adapted niches, demonstrating selective pressure on lactobacilli to evolve to adapt to specific environments. These new data will allow targeted selection of specific strains of lactobacilli and BSH proteins for future mechanistic studies to explore their therapeutic potential for treating metabolic disorders.
          }, number={3}, journal={MSPHERE}, publisher={American Society for Microbiology}, author={O'Flaherty, Sarah and Crawley, Alexandra Briner and Theriot, Casey M. and Barrangou, Rodolphe}, editor={Ellermeier, Craig D.Editor}, year={2018} }
 @article{morovic_roos_zabel_hidalgo-cantabrana_kiefer_barrangou_2018, title={Transcriptional and Functional Analysis of Bifidobacterium animalis subsp. lactis Exposure to Tetracycline}, volume={84}, ISSN={["1098-5336"]}, url={https://doi.org/10.1128/AEM.01999-18}, DOI={10.1128/AEM.01999-18}, abstractNote={
            Bifidobacterium animalis
            subsp.
            lactis
            is widely used in human food and dietary supplements. Although well documented to be safe,
            B. animalis
            subsp.
            lactis
            strains must not contain transferable antibiotic resistance elements. Many
            B. animalis
            subsp.
            lactis
            strains have different resistance measurements despite being genetically similar, and the reasons for this are not well understood. In the current study, we sought to examine how genomic differences between two closely related industrial
            B. animalis
            subsp.
            lactis
            strains contribute to different resistance levels. This will lead to a better understanding of resistance, identify future targets for analysis of transferability, and expand our understanding of tetracycline resistance in bacteria.
          }, number={23}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, publisher={American Society for Microbiology}, author={Morovic, Wesley and Roos, Paige and Zabel, Bryan and Hidalgo-Cantabrana, Claudio and Kiefer, Anthony and Barrangou, Rodolphe}, editor={Müller, VolkerEditor}, year={2018}, month={Dec} }
 @article{brandt_barrangou_2018, title={Using glycolysis enzyme sequences to inform Lactobacillus phylogeny}, volume={4}, DOI={10.1099/mgen.0.000187}, abstractNote={The genus Lactobacillus encompasses a diversity of species that occur widely in nature and encode a plethora of metabolic pathways reflecting their adaptation to various ecological niches, including humans, animals, plants and food products. Accordingly, their functional attributes have been exploited industrially and several strains are commonly formulated as probiotics or starter cultures in the food industry. Although divergent evolutionary processes have yielded the acquisition and evolution of specialized functionalities, all Lactobacillus species share a small set of core metabolic properties, including the glycolysis pathway. Thus, the sequences of glycolytic enzymes afford a means to establish phylogenetic groups with the potential to discern species that are too closely related from a 16S rRNA standpoint. Here, we identified and extracted glycolysis enzyme sequences from 52 species, and carried out individual and concatenated phylogenetic analyses. We show that a glycolysis-based phylogenetic tree can robustly segregate lactobacilli into distinct clusters and discern very closely related species. We also compare and contrast evolutionary patterns with genome-wide features and transcriptomic patterns, reflecting genomic drift trends. Overall, results suggest that glycolytic enzymes provide valuable phylogenetic insights and may constitute practical targets for evolutionary studies.}, number={6}, journal={Microbial Genomics}, publisher={Microbiology Society}, author={Brandt, Katelyn and Barrangou, Rodolphe}, year={2018}, month={Jun} }
 @article{barrangou_horvath_2017, title={A decade of discovery: CRISPR functions and applications}, volume={2}, ISSN={["2058-5276"]}, DOI={10.1038/nmicrobiol.2017.92}, abstractNote={This year marks the tenth anniversary of the identification of the biological function of CRISPR–Cas as adaptive immune systems in bacteria. In just a decade, the characterization of CRISPR–Cas systems has established a novel means of adaptive immunity in bacteria and archaea and deepened our understanding of the interplay between prokaryotes and their environment, and CRISPR-based molecular machines have been repurposed to enable a genome editing revolution. Here, we look back on the historical milestones that have paved the way for the discovery of CRISPR and its function, and discuss the related technological applications that have emerged, with a focus on microbiology. Lastly, we provide a perspective on the impacts the field has had on science and beyond. In this Review Article, Horvath and Barrangou describe the discovery of CRISPR–Cas systems as mechanisms of adaptive immunity in prokaryotes and explore the technological applications that have emerged from studying these molecular machines.}, number={7}, journal={NATURE MICROBIOLOGY}, publisher={Springer Nature}, author={Barrangou, Rodolphe and Horvath, Philippe}, year={2017}, month={Jul} }
 @article{stout_klaenhammer_barrangou_2017, title={CRISPR-Cas Technologies and Applications in Food Bacteria}, volume={8}, ISSN={["1941-1421"]}, DOI={10.1146/annurev-food-072816-024723}, abstractNote={ Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins form adaptive immune systems that occur in many bacteria and most archaea. In addition to protecting bacteria from phages and other invasive mobile genetic elements, CRISPR-Cas molecular machines can be repurposed as tool kits for applications relevant to the food industry. A primary concern of the food industry has long been the proper management of food-related bacteria, with a focus on both enhancing the outcomes of beneficial microorganisms such as starter cultures and probiotics and limiting the presence of detrimental organisms such as pathogens and spoilage microorganisms. This review introduces CRISPR-Cas as a novel set of technologies to manage food bacteria and offers insights into CRISPR-Cas biology. It primarily focuses on the applications of CRISPR-Cas systems and tools in starter cultures and probiotics, encompassing strain-typing, phage resistance, plasmid vaccination, genome editing, and antimicrobial activity. }, number={1}, journal={ANNUAL REVIEW OF FOOD SCIENCE AND TECHNOLOGY, VOL 8}, publisher={Annual Reviews}, author={Stout, Emily and Klaenhammer, Todd and Barrangou, Rodolphe}, year={2017}, pages={413–437} }
 @misc{hidalgo-cantabrana_o'flaherty_barrangou_2017, title={CRISPR-based engineering of next-generation lactic acid bacteria}, volume={37}, ISSN={["1879-0364"]}, DOI={10.1016/j.mib.2017.05.015}, abstractNote={The advent of CRISPR-based technologies has opened new avenues for the development of next-generation food microorganisms and probiotics with enhanced functionalities. Building off two decades of functional genomics studies unraveling the genetic basis for food fermentations and host–probiotic interactions, CRISPR technologies offer a wide range of opportunities to engineer commercially-relevant Lactobacillus and Bifidobacteria. Endogenous CRISPR–Cas systems can be repurposed to enhance gene expression or provide new features to improve host colonization and promote human health. Alternatively, engineered CRISPR–Cas systems can be harnessed to genetically modify probiotics and enhance their therapeutic potential to deliver vaccines or modulate the host immune response.}, journal={CURRENT OPINION IN MICROBIOLOGY}, publisher={Elsevier BV}, author={Hidalgo-Cantabrana, Claudio and O'Flaherty, Sarah and Barrangou, Rodolphe}, year={2017}, month={Jun}, pages={79–87} }
 @article{hidalgo-cantabrana_crawley_sanchez_barrangou_2017, title={Characterization and Exploitation of CRISPR Loci in Bifidobacterium longum}, volume={8}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2017.01851}, abstractNote={Diverse CRISPR-Cas systems provide adaptive immunity in many bacteria and most archaea, via a DNA-encoded, RNA-mediated, nucleic-acid targeting mechanism. Over time, CRISPR loci expand via iterative uptake of invasive DNA sequences into the CRISPR array during the adaptation process. These genetic vaccination cards thus provide insights into the exposure of strains to phages and plasmids in space and time, revealing the historical predatory exposure of a strain. These genetic loci thus constitute a unique basis for genotyping of strains, with potential of resolution at the strain-level. Here, we investigate the occurrence and diversity of CRISPR-Cas systems in the genomes of various Bifidobacterium longum strains across three sub-species. Specifically, we analyzed the genomic content of 66 genomes belonging to B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis, and identified 25 strains that carry 29 total CRISPR-Cas systems. We identify various Type I and Type II CRISPR-Cas systems that are widespread in this species, notably I-C, I-E, and II-C. Noteworthy, Type I-C systems showed extended CRISPR arrays, with extensive spacer diversity. We show how these hypervariable loci can be used to gain insights into strain origin, evolution and phylogeny, and can provide discriminatory sequences to distinguish even clonal isolates. By investigating CRISPR spacer sequences, we reveal their origin and implicate phages and prophages as drivers of CRISPR immunity expansion in this species, with redundant targeting of select prophages. Analysis of CRISPR spacer origin also revealed novel PAM sequences. Our results suggest that CRISPR-Cas immune systems are instrumental in mounting diversified viral resistance in B. longum, and show that these sequences are useful for typing across three subspecies.}, journal={FRONTIERS IN MICROBIOLOGY}, publisher={Frontiers Media SA}, author={Hidalgo-Cantabrana, Claudio and Crawley, Alexandra B. and Sanchez, Borja and Barrangou, Rodolphe}, year={2017}, month={Sep} }
 @article{selle_goh_johnson_sarah_andersen_barrangou_klaenhammer_2017, title={Deletion of Lipoteichoic Acid Synthase Impacts Expression of Genes Encoding Cell Surface Proteins in Lactobacillus acidophilus}, volume={8}, DOI={10.3389/fmicb.2017.00553}, abstractNote={Lactobacillus acidophilus NCFM is a well-characterized probiotic microorganism, supported by a decade of genomic and functional phenotypic investigations. L. acidophilus deficient in lipoteichoic acid (LTA), a major immunostimulant in Gram-positive bacteria, has been shown to shift immune system responses in animal disease models. However, the pleiotropic effects of removing LTA from the cell surface in lactobacilli are unknown. In this study, we surveyed the global transcriptional and extracellular protein profiles of two strains of L. acidophilus deficient in LTA. Twenty-four differentially expressed genes specific to the LTA-deficient strains were identified, including a predicted heavy metal resistance operon and several putative peptidoglycan hydrolases. Cell morphology and manganese sensitivity phenotypes were assessed in relation to the putative functions of differentially expressed genes. LTA-deficient L. acidophilus exhibited elongated cellular morphology and their growth was severely inhibited by elevated manganese concentrations. Exoproteomic surveys revealed distinct changes in the composition and relative abundances of several extracellular proteins and showed a bias of intracellular proteins in LTA-deficient strains of L. acidophilus. Taken together, these results elucidate the impact of ltaS deletion on the transcriptome and extracellular proteins of L. acidophilus, suggesting roles of LTA in cell morphology and ion homeostasis as a structural component of the Gram positive cell wall.}, journal={Frontiers in Microbiology}, publisher={Frontiers Media SA}, author={Selle, Kurt and Goh, Yong J. and Johnson, Brant R. and Sarah, O’Flaherty and Andersen, Joakim M. and Barrangou, Rodolphe and Klaenhammer, Todd R.}, year={2017}, month={Apr} }
 @article{barrangou_gersbach_2017, title={Expanding the CRISPR Toolbox: Targeting RNA with Cas13b}, volume={65}, ISSN={["1097-4164"]}, DOI={10.1016/j.molcel.2017.02.002}, abstractNote={In this issue of <i>Molecular Cell</i>, Smargon et al. (2017) unearth Cas13b from type VI-B CRISPR-Cas immune systems and characterize its RNA-guided, RNA-targeting activity, including regulation by the novel co-factors Csx27 and Csx28, as well as non-specific collateral RNA damage.}, number={4}, journal={MOLECULAR CELL}, publisher={Elsevier BV}, author={Barrangou, Rodolphe and Gersbach, Charles A.}, year={2017}, month={Feb}, pages={582–584} }
 @article{pijkeren_barrangou_2017, title={Genome Editing of Food-Grade Lactobacilli To Develop Therapeutic Probiotics}, volume={5}, DOI={10.1128/microbiolspec.bad-0013-2016}, abstractNote={ABSTRACT}, number={5}, journal={Microbiology Spectrum}, publisher={American Society for Microbiology}, author={Pijkeren, Jan-Peter and Barrangou, Rodolphe}, year={2017}, month={Oct} }
 @article{barrangou_bikard_2017, title={Guest editorial: CRISPRcas9: CRISPR-Cas systems: at the cutting edge of microbiology}, volume={37}, DOI={10.1016/j.mib.2017.09.015}, journal={Current Opinion in Microbiology}, publisher={Elsevier BV}, author={Barrangou, Rodolphe and Bikard, David}, year={2017}, month={Jun}, pages={vii-viii} }
 @article{weissman_holmes_barrangou_moineau_fagan_levin_johnson_2017, title={Immune Loss as a Driver of Coexistence During Host-Phage Coevolution}, volume={2}, url={https://doi.org/10.1101/105908}, DOI={10.1101/105908}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Weissman, Jake L and Holmes, Rayshawn and Barrangou, Rodolphe and Moineau, Sylvain and Fagan, William F and Levin, Bruce and Johnson, Philip L F}, year={2017}, month={Feb} }
 @article{klotz_o'flaherty_goh_barrangou_2017, title={Investigating the Effect of Growth Phase on the Surface-Layer Associated Proteome of Lactobacillus acidophilus Using Quantitative Proteomics}, volume={8}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2017.02174}, abstractNote={Bacterial surface-layers (S-layers) are semi-porous crystalline arrays that self-assemble to form the outermost layer of some cell envelopes. S-layers have been shown to act as scaffolding structures for the display of auxiliary proteins externally. These S-layer associated proteins have recently gained attention in probiotics due to their direct physical contact with the intestinal mucosa and potential role in cell proliferation, adhesion, and immunomodulation. A number of studies have attempted to catalog the S-layer associated proteome of Lactobacillus acidophilus NCFM under a single condition. However, due to the versatility of the cell surface, we chose to employ a multiplexing-based approach with the intention of accurately contrasting multiple conditions. In this study, a previously described lithium chloride isolation protocol was used to release proteins bound to the L. acidophilus S-layer during logarithmic and early stationary growth phases. Protein quantification values were obtained via TMT (tandem mass tag) labeling combined with a triple-stage mass spectrometry (MS3) method. Results showed significant growth stage-dependent alterations to the surface-associated proteome while simultaneously highlighting the sensitivity and reproducibility of the technology. Thus, this study establishes a framework for quantifying condition-dependent changes to cell surface proteins that can easily be applied to other S-layer forming bacteria.}, journal={FRONTIERS IN MICROBIOLOGY}, publisher={Frontiers Media SA}, author={Klotz, Courtney and O'Flaherty, Sarah and Goh, Yong Jun and Barrangou, Rodolphe}, year={2017}, month={Nov} }
 @article{theilmann_goh_nielsen_klaenhammer_barrangou_abou hachem_2017, title={Lactobacillus acidophilus Metabolizes Dietary Plant Glucosides and Externalizes Their Bioactive Phytochemicals}, volume={8}, ISSN={["2150-7511"]}, url={https://doi.org/10.1128/mBio.01421-17}, DOI={10.1128/mbio.01421-17}, abstractNote={ABSTRACT}, number={6}, journal={MBIO}, publisher={American Society for Microbiology}, author={Theilmann, Mia C. and Goh, Yong Jun and Nielsen, Kristian Fog and Klaenhammer, Todd R. and Barrangou, Rodolphe and Abou Hachem, Maher}, editor={Martens, Eric and McFall-Ngai, Margaret J.Editors}, year={2017} }
 @article{bikard_barrangou_2017, title={Les systèmes CRISPR-Cas comme arme contre les bactéries pathogènes}, volume={211}, ISSN={2105-0678 2105-0686}, url={http://dx.doi.org/10.1051/JBIO/2018004}, DOI={10.1051/jbio/2018004}, abstractNote={CRISPR-Cas systems (Clustered Regularly Interspaced Short Palindromic Repeats) are the adaptive immune system of bacteria and archaea. They target foreign genetic elements thanks to small RNAs able to guide Cas nucleases to destroy them. These nucleases can be reprogrammed to target chromosomal sequences rather than invasive genetic elements. Whereas targeting the genome of eukaryotic cells enables the efficient genesis of mutations, DNA breaks induced by Cas nucleases are lethal in bacteria. This property can be used in the development of novel antimicrobial strategies. CRISPR-Cas systems can be delivered to target bacteria using bacteriophage capsids in order to specifically eliminate bacteria carrying antibiotic resistance genes or virulence factors. These technologies enable the development of novel tools based on CRISPR-Cas systems to specifically eliminate pathogenic bacteria and precisely modify the composition of various microbiomes.}, number={4}, journal={Biologie Aujourd'hui}, publisher={EDP Sciences}, author={Bikard, David and Barrangou, Rodolphe}, year={2017}, pages={265–270} }
 @article{toms_barrangou_2017, title={On the global CRISPR array behavior in class I systems}, volume={12}, ISSN={["1745-6150"]}, DOI={10.1186/s13062-017-0193-2}, abstractNote={Much effort is underway to build and upgrade databases and tools related to occurrence, diversity, and characterization of CRISPR-Cas systems. As microbial communities and their genome complements are unearthed, much emphasis has been placed on details of individual strains and model systems within the CRISPR-Cas classification, and that collection of information as a whole affords the opportunity to analyze CRISPR-Cas systems from a quantitative perspective to gain insight into distribution of CRISPR array sizes across the different classes, types and subtypes. CRISPR diversity, nomenclature, occurrence, and biological functions have generated a plethora of data that created a need to understand the size and distribution of these various systems to appreciate their features and complexity.By utilizing a statistical framework and visual analytic techniques, we have been able to test several hypotheses about CRISPR loci in bacterial class I systems. Quantitatively, though CRISPR loci can expand to hundreds of spacers, the mean and median sizes are 40 and 25, respectively, reflecting rather modest acquisition and/or retention overall. Histograms uncovered that CRISPR array size displayed a parametric distribution, which was confirmed by a goodness-of fit test. Mapping the frequency of CRISPR loci on a standardized chromosome plot revealed that CRISPRs have a higher probability of occurring at clustered locations along the positive or negative strand. Lastly, when multiple arrays occur in a particular system, the size of a particular CRISPR array varies with its distance from the cas operon, reflecting acquisition and expansion biases.This study establishes that bacterial Class I CRISPR array size tends to follow a geometric distribution; these CRISPRs are not randomly distributed along the chromosome; and the CRISPR array closest to the cas genes is typically larger than loci in trans. Overall, we provide an analytical framework to understand the features and behavior of CRISPR-Cas systems through a quantitative lens.This article was reviewed by Eugene Koonin (NIH-NCBI) and Uri Gophna (Tel Aviv University).}, journal={BIOLOGY DIRECT}, author={Toms, Alice and Barrangou, Rodolphe}, year={2017}, month={Aug} }
 @article{nair_2017, title={QnAs with Rodolphe Barrangou}, volume={114}, DOI={10.1073/pnas.1710348114}, abstractNote={The past decade in biological research might well be christened the age of CRISPR, a once-curious feature of bacterial genomes that spawned a handy tool for editing genes. Using CRISPR-based tools, researchers are making leaps in basic clinical research, and biotechnology companies are racing to launch trials of gene therapies for an array of diseases. Yet the immediate gains from this game-changing technique might spring from its application to agriculture. Hornless dairy cattle, drought-resistant wheat, and nonbrowning mushrooms are merely the harbingers of an approaching agricultural revolution, says Rodolphe Barrangou, a molecular biologist and food scientist at North Carolina State University. Barrangou’s foresight stems from his long familiarity with CRISPR. More than a decade ago, while working at the Danish food ingredient manufacturer Danisco (now DuPont), Barrangou furnished experimental proof for the notion that CRISPR confers a form of adaptive immunity that helps bacteria fend off invading viruses. For this crucial insight into the fundamental biology of CRISPR, Barrangou was honored with 2017 National Academy of Sciences Award in molecular biology. PNAS spoke to Barrangou about his wide-ranging work on CRISPR.



Rodolphe Barrangou. Image courtesy of North Carolina State University (Raleigh, NC).



> PNAS:CRISPR entered the spotlight when its potential as a genome editor became apparent, but your tryst with it began more than a decade ago while working with Philippe Horvath in the food industry. Those efforts led to a milestone 2007 article in Science , in which you demonstrated that bacteria use CRISPR-Cas systems as a form of adaptive immunity against viruses (1). Could you take our readers down memory lane?

> Barrangou:For a long time, people didn’t really have a clue what these repeated DNA sequences—the CRISPR arrays—in …}, number={28}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Nair, Prashant}, year={2017}, month={Jul}, pages={7183–7184} }
 @article{barrangou_ousterout_2017, title={Repurposing CRISPR-Cas systems as DNA-based smart antimicrobials}, volume={3}, DOI={10.18609/cgti.2017.008}, number={1}, journal={Cell and Gene Therapy Insights}, publisher={BioInsights Publishing, Ltd.}, author={Barrangou, Rodolphe and Ousterout, David G}, year={2017}, month={Feb}, pages={63–72} }
 @article{johnson_o'flaherty_goh_carroll_barrangou_klaenhammer_2017, title={The S-layer Associated Serine Protease Homolog PrtX Impacts Cell Surface-Mediated Microbe-Host Interactions of Lactobacillus acidophilus NCFM}, volume={8}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2017.01185}, abstractNote={Health-promoting aspects attributed to probiotic microorganisms, including adhesion to intestinal epithelia and modulation of the host mucosal immune system, are mediated by proteins found on the bacterial cell surface. Notably, certain probiotic and commensal bacteria contain a surface (S-) layer as the outermost stratum of the cell wall. S-layers are non-covalently bound semi-porous, crystalline arrays of self-assembling, proteinaceous subunits called S-layer proteins (SLPs). Recent evidence has shown that multiple proteins are non-covalently co-localized within the S-layer, designated S-layer associated proteins (SLAPs). In Lactobacillus acidophilus NCFM, SLP and SLAPs have been implicated in both mucosal immunomodulation and adhesion to the host intestinal epithelium. In this study, a S-layer associated serine protease homolog, PrtX (prtX, lba1578), was deleted from the chromosome of L. acidophilus NCFM. Compared to the parent strain, the PrtX-deficient strain (ΔprtX) demonstrated increased autoaggregation, an altered cellular morphology, and pleiotropic increases in adhesion to mucin and fibronectin, in vitro. Furthermore, ΔprtX demonstrated increased in vitro immune stimulation of IL-6, IL-12, and IL-10 compared to wild-type, when exposed to mouse dendritic cells. Finally, in vivo colonization of germ-free mice with ΔprtX led to an increase in epithelial barrier integrity. The absence of PrtX within the exoproteome of a ΔprtX strain caused morphological changes, resulting in a pleiotropic increase of the organisms’ immunomodulatory properties and interactions with some intestinal epithelial cell components.}, journal={FRONTIERS IN MICROBIOLOGY}, publisher={Frontiers Media SA}, author={Johnson, Brant R. and O'Flaherty, Sarah and Goh, Yong Jun and Carroll, Ian and Barrangou, Rodolphe and Klaenhammer, Todd R.}, year={2017}, month={Jun} }
 @misc{bikard_barrangou_2017, title={Using CRISPR-Cas systems as antimicrobials}, volume={37}, ISSN={["1879-0364"]}, DOI={10.1016/j.mib.2017.08.005}, abstractNote={Although CRISPR-Cas systems naturally evolved to provide adaptive immunity in bacteria and archaea, Cas nucleases can be co-opted to target chromosomal sequences rather than invasive genetic elements. Although genome editing is the primary outcome of self-targeting using CRISPR-based technologies in eukaryotes, self-targeting by CRISPR is typically lethal in bacteria. Here, we discuss how DNA damage introduced by Cas nucleases in bacteria can efficiently and specifically lead to plasmid curing or drive cell death. Specifically, we discuss how various CRISPR-Cas systems can be engineered and delivered using phages or phagemids as vectors. These principles establish CRISPR-Cas systems as potent and programmable antimicrobials, and open new avenues for the development of CRISPR-based tools for selective removal of bacterial pathogens and precise microbiome composition alteration.}, journal={CURRENT OPINION IN MICROBIOLOGY}, publisher={Elsevier BV}, author={Bikard, David and Barrangou, Rodolphe}, year={2017}, month={Jun}, pages={155–160} }
 @misc{barrangou_doudna_2016, title={Applications of CRISPR technologies in research and beyond}, volume={34}, ISSN={["1546-1696"]}, url={https://doi.org/10.1038/nbt.3659}, DOI={10.1038/nbt.3659}, abstractNote={Programmable DNA cleavage using CRISPR-Cas9 enables efficient, site-specific genome engineering in single cells and whole organisms. In the research arena, versatile CRISPR-enabled genome editing has been used in various ways, such as controlling transcription, modifying epigenomes, conducting genome-wide screens and imaging chromosomes. CRISPR systems are already being used to alleviate genetic disorders in animals and are likely to be employed soon in the clinic to treat human diseases of the eye and blood. Two clinical trials using CRISPR-Cas9 for targeted cancer therapies have been approved in China and the United States. Beyond biomedical applications, these tools are now being used to expedite crop and livestock breeding, engineer new antimicrobials and control disease-carrying insects with gene drives.}, number={9}, journal={NATURE BIOTECHNOLOGY}, publisher={Springer Nature}, author={Barrangou, Rodolphe and Doudna, Jennifer A.}, year={2016}, month={Sep}, pages={933–941} }
 @article{andersen_shoup_robinson_bitton_olsen_barrangou_2016, title={CRISPR Diversity and Microevolution in Clostridium difficile}, volume={8}, ISSN={["1759-6653"]}, DOI={10.1093/gbe/evw203}, abstractNote={Abstract Virulent strains of Clostridium difficile have become a global health problem associated with morbidity and mortality. Traditional typing methods do not provide ideal resolution to track outbreak strains, ascertain genetic diversity between isolates, or monitor the phylogeny of this species on a global basis. Here, we investigate the occurrence and diversity of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (cas) in C. difficile to assess the potential of CRISPR-based phylogeny and high-resolution genotyping. A single Type-IB CRISPR-Cas system was identified in 217 analyzed genomes with cas gene clusters present at conserved chromosomal locations, suggesting vertical evolution of the system, assessing a total of 1,865 CRISPR arrays. The CRISPR arrays, markedly enriched (8.5 arrays/genome) compared with other species, occur both at conserved and variable locations across strains, and thus provide a basis for typing based on locus occurrence and spacer polymorphism. Clustering of strains by array composition correlated with sequence type (ST) analysis. Spacer content and polymorphism within conserved CRISPR arrays revealed phylogenetic relationship across clades and within ST. Spacer polymorphisms of conserved arrays were instrumental for differentiating closely related strains, e.g., ST1/RT027/B1 strains and pathogenicity locus encoding ST3/RT001 strains. CRISPR spacers showed sequence similarity to phage sequences, which is consistent with the native role of CRISPR-Cas as adaptive immune systems in bacteria. Overall, CRISPR-Cas sequences constitute a valuable basis for genotyping of C. difficile isolates, provide insights into the micro-evolutionary events that occur between closely related strains, and reflect the evolutionary trajectory of these genomes.}, number={9}, journal={GENOME BIOLOGY AND EVOLUTION}, publisher={Oxford University Press (OUP)}, author={Andersen, Joakim M. and Shoup, Madelyn and Robinson, Cathy and Bitton, Robert and Olsen, Katharina E. P. and Barrangou, Rodolphe}, year={2016}, month={Sep}, pages={2841–2855} }
 @article{barrangou_dudley_2016, title={CRISPR-Based Typing and Next-Generation Tracking Technologies}, volume={7}, DOI={10.1146/annurev-food-022814-015729}, abstractNote={ Bacteria occur ubiquitously in nature and are broadly relevant throughout the food supply chain, with diverse and variable tolerance levels depending on their origin, biological role, and impact on the quality and safety of the product as well as on the health of the consumer. With increasing knowledge of and accessibility to the microbial composition of our environments, food supply, and host-associated microbiota, our understanding of and appreciation for the ratio of beneficial to undesirable bacteria are rapidly evolving. Therefore, there is a need for tools and technologies that allow definite, accurate, and high-resolution identification and typing of various groups of bacteria that include beneficial microbes such as starter cultures and probiotics, innocuous commensals, and undesirable pathogens and spoilage organisms. During the transition from the current molecular biology–based PFGE (pulsed-field gel electrophoresis) gold standard to the increasingly accessible omics-level whole-genome sequencing (WGS) N-gen standard, high-resolution technologies such as CRISPR-based genotyping constitute practical and powerful alternatives that provide valuable insights into genome microevolution and evolutionary trajectories. Indeed, several studies have shown potential for CRISPR-based typing of industrial starter cultures, health-promoting probiotic strains, animal commensal species, and problematic pathogens. Emerging CRISPR-based typing methods open new avenues for high-resolution typing of a broad range of bacteria and constitute a practical means for rapid tracking of a diversity of food-associated microbes. }, number={1}, journal={Annual Review of Food Science and Technology}, publisher={Annual Reviews}, author={Barrangou, Rodolphe and Dudley, Edward G.}, year={2016}, month={Feb}, pages={395–411} }
 @misc{barrangou_dudley_2016, title={CRISPR-based typing and next-generation tracking technologies}, volume={7}, journal={Annual review of food science and technology, vol 7}, author={Barrangou, R. and Dudley, E. G.}, year={2016}, pages={395–411} }
 @article{johnson_hymes_sanozky-dawes_henriksen_barrangou_klaenhammer_2016, title={Conserved S-Layer-Associated Proteins Revealed by Exoproteomic Survey of S-Layer-Forming Lactobacilli}, volume={82}, ISSN={["1098-5336"]}, url={https://doi.org/10.1128/AEM.01968-15}, DOI={10.1128/aem.01968-15}, abstractNote={ABSTRACT}, number={1}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, publisher={American Society for Microbiology}, author={Johnson, Brant R. and Hymes, Jeffrey and Sanozky-Dawes, Rosemary and Henriksen, Emily DeCrescenzo and Barrangou, Rodolphe and Klaenhammer, Todd R.}, editor={Nojiri, H.Editor}, year={2016}, month={Jan}, pages={134–145} }
 @misc{briner_barrangou_2016, title={Deciphering and shaping bacterial diversity through CRISPR}, volume={31}, ISSN={["1879-0364"]}, url={https://doi.org/10.1016/j.mib.2016.03.006}, DOI={10.1016/j.mib.2016.03.006}, abstractNote={Phage and bacteria have engaged in a sustainable arms race, a seemingly endless conflict, since the beginning of time. CRISPR-Cas systems shape and generate environmental diversity through evolution of both predator and prey genomes. Indeed, the gain or loss of CRISPR-mediated immunity and genome maintenance can spark speciation in bacteria. Alternatively, turning CRISPR-Cas on the host by targeting chromosomal DNA has led to the development of next-generation smart antimicrobials and genetic screening and engineering technologies. Although the ability to target and cleave DNA in a sequence-specific manner is a powerful mechanism utilized by bacteria to fend off phage, plasmids, and potentially harmful nucleic acids, it is also a promising technology for programmable targeting of undesirable bacteria in microbiome consortia.}, journal={CURRENT OPINION IN MICROBIOLOGY}, publisher={Elsevier BV}, author={Briner, Alexandra E. and Barrangou, Rodolphe}, year={2016}, month={Jun}, pages={101–108} }
 @misc{barrangou_pijkeren_2016, title={Exploiting CRISPR-Cas immune systems for genome editing in bacteria}, volume={37}, ISSN={["1879-0429"]}, DOI={10.1016/j.copbio.2015.10.003}, abstractNote={The CRISPR-Cas immune system is a DNA-encoded, RNA-mediated, DNA-targeting defense mechanism, which provides sequence-specific targeting of DNA. This molecular machinery can be engineered into the sgRNA:Cas9 technology, for programmable cleavage of DNA. Following the genesis of double-stranded DNA breaks, the DNA repair machinery generates mutations at the cleavage site using various pathways. This technology has revolutionized eukaryotic genome editing, and we are at the cusp of full exploitation in bacteria. Here, we discuss the potential of CRISPR-based technologies for use in bacteria, and highlight the application of single stranded DNA recombineering combined with CRISPR-Cas selection to edit the genome of a probiotic organism. We envision that CRISPR-Cas technologies will play a key role in the development of next-generation industrial bacteria.}, journal={CURRENT OPINION IN BIOTECHNOLOGY}, publisher={Elsevier BV}, author={Barrangou, Rodolphe and Pijkeren, Jan-Peter}, year={2016}, month={Feb}, pages={61–68} }
 @article{hymes_johnson_barrangou_klaenhammer_2016, title={Functional Analysis of an S-Layer-Associated Fibronectin-Binding Protein in Lactobacillus acidophilus NCFM}, volume={82}, ISSN={["1098-5336"]}, DOI={10.1128/aem.00024-16}, abstractNote={ABSTRACT}, number={9}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, publisher={American Society for Microbiology}, author={Hymes, Jeffrey P. and Johnson, Brant R. and Barrangou, Rodolphe and Klaenhammer, Todd R.}, editor={Dudley, E. G.Editor}, year={2016}, month={May}, pages={2676–2685} }
 @article{morovic_hibberd_zabel_barrangou_stahl_2016, title={Genotyping by PCR and High-Throughput Sequencing of Commercial Probiotic Products Reveals Composition Biases}, volume={7}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2016.01747}, abstractNote={Recent advances in microbiome research have brought renewed focus on beneficial bacteria, many of which are available in food and dietary supplements. Although probiotics have historically been defined as microorganisms that convey health benefits when ingested in sufficient viable amounts, this description now includes the stipulation “well defined strains,” encompassing definitive taxonomy for consumer consideration and regulatory oversight. Here, we evaluated 52 commercial dietary supplements covering a range of labeled species using plate counting and targeted genotyping. Strain identities were assessed using methods recently published by the United States Pharmacopeial Convention. We also determined the relative abundance of individual bacteria by high-throughput sequencing (HTS) of the 16S rRNA sequence using paired-end 2 × 250 bp Illumina MiSeq technology. Using these methods, we tested the hypothesis that products do contain the quantitative and qualitative list of labeled microbial species. We found that 17 samples (33%) were below label claim for CFU prior to their expiration dates. A multiplexed-PCR scheme showed that only 30/52 (58%) of the products contained a correctly labeled classification, with issues encompassing incorrect taxonomy, missing species, and un-labeled species. The HTS revealed that many blended products consisted predominantly of Lactobacillus acidophilus and Bifidobacterium animalis subsp. lactis. These results highlight the need for reliable methods to determine the correct taxonomy and quantify the relative amounts of mixed microbial populations in commercial probiotic products.}, journal={FRONTIERS IN MICROBIOLOGY}, publisher={Frontiers Media SA}, author={Morovic, Wesley and Hibberd, Ashley A. and Zabel, Bryan and Barrangou, Rodolphe and Stahl, Buffy}, year={2016}, month={Nov} }
 @article{briner_barrangou_2016, title={Guide RNAs: A Glimpse at the Sequences that Drive CRISPR–Cas Systems}, volume={2016}, DOI={10.1101/pdb.top090902}, abstractNote={CRISPR–Cas systems provide adaptive immunity in bacteria and archaea. Although there are two main classes of CRISPR–Cas systems defined by gene content, interfering RNA biogenesis, and effector proteins, Type II systems have recently been exploited on a broad scale to develop next-generation genetic engineering and genome-editing tools. Conveniently, Type II systems are streamlined and rely on a single protein, Cas9, and a guide RNA molecule, comprised of a CRISPR RNA (crRNA) and trans-acting CRISPR RNA (tracrRNA), to achieve effective and programmable nucleic acid targeting and cleavage. Currently, most commercially available Cas9-based genome-editing tools use the CRISPR–Cas system from Streptococcus pyogenes (SpyCas9), although many orthogonal Type II systems are available for diverse and multiplexable genome engineering applications. Here, we discuss the biological significance of Type II CRISPR–Cas elements, including the tracrRNA, crRNA, Cas9, and protospacer-adjacent motif (PAM), and look at the native function of these elements to understand how they can be engineered, enhanced, and optimized for genome editing applications. Additionally, we discuss the basis for orthogonal Cas9 and guide RNA systems that would allow researchers to concurrently use multiple Cas9-based systems for different purposes. Understanding the native function of endogenous Type II CRISPR–Cas systems can lead to new Cas9 tool development to expand the genetic manipulation toolbox.}, number={7}, journal={Cold Spring Harbor Protocols}, publisher={Cold Spring Harbor Laboratory}, author={Briner, Alexandra E. and Barrangou, Rodolphe}, year={2016}, month={Jul}, pages={pdb.top090902} }
 @article{leenay_maksimchuk_slotkowski_agrawal_gomaa_briner_barrangou_beisel_2016, title={Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems}, volume={62}, ISSN={["1097-4164"]}, DOI={10.1016/j.molcel.2016.02.031}, abstractNote={<h2>Summary</h2> CRISPR-Cas adaptive immune systems in prokaryotes boast a diversity of protein families and mechanisms of action, where most systems rely on protospacer-adjacent motifs (PAMs) for DNA target recognition. Here, we developed an in vivo, positive, and tunable screen termed PAM-SCANR (PAM screen achieved by NOT-gate repression) to elucidate functional PAMs as well as an interactive visualization scheme termed the PAM wheel to convey individual PAM sequences and their activities. PAM-SCANR and the PAM wheel identified known functional PAMs while revealing complex sequence-activity landscapes for the <i>Bacillus halodurans</i> I-C (Cascade), <i>Escherichia coli</i> I-E (Cascade), <i>Streptococcus thermophilus</i> II-A CRISPR1 (Cas9), and <i>Francisella novicida</i> V-A (Cpf1) systems. The PAM wheel was also readily applicable to existing high-throughput screens and garnered insights into SpyCas9 and SauCas9 PAM diversity. These tools offer powerful means of elucidating and visualizing functional PAMs toward accelerating our ability to understand and exploit the multitude of CRISPR-Cas systems in nature.}, number={1}, journal={MOLECULAR CELL}, publisher={Elsevier BV}, author={Leenay, Ryan T. and Maksimchuk, Kenneth R. and Slotkowski, Rebecca A. and Agrawal, Roma N. and Gomaa, Ahmed A. and Briner, Alexandra E. and Barrangou, Rodolphe and Beisel, Chase L.}, year={2016}, month={Apr}, pages={137–147} }
 @article{sun_thomas_barrangou_banfield_2016, title={Metagenomic reconstructions of bacterial CRISPR loci constrain population histories}, volume={10}, ISSN={["1751-7370"]}, DOI={10.1038/ismej.2015.162}, abstractNote={Abstract}, number={4}, journal={ISME JOURNAL}, publisher={Springer Nature}, author={Sun, Christine L. and Thomas, Brian C. and Barrangou, Rodolphe and Banfield, Jillian F.}, year={2016}, month={Apr}, pages={858–870} }
 @article{brandt_barrangou_2016, title={Phylogenetic Analysis of the Bifidobacterium Genus Using Glycolysis Enzyme Sequences}, volume={7}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2016.00657}, abstractNote={Bifidobacteria are important members of the human gastrointestinal tract that promote the establishment of a healthy microbial consortium in the gut of infants. Recent studies have established that the Bifidobacterium genus is a polymorphic phylogenetic clade, which encompasses a diversity of species and subspecies that encode a broad range of proteins implicated in complex and non-digestible carbohydrate uptake and catabolism, ranging from human breast milk oligosaccharides, to plant fibers. Recent genomic studies have created a need to properly place Bifidobacterium species in a phylogenetic tree. Current approaches, based on core-genome analyses come at the cost of intensive sequencing and demanding analytical processes. Here, we propose a typing method based on sequences of glycolysis genes and the proteins they encode, to provide insights into diversity, typing, and phylogeny in this complex and broad genus. We show that glycolysis genes occur broadly in these genomes, to encode the machinery necessary for the biochemical spine of the cell, and provide a robust phylogenetic marker. Furthermore, glycolytic sequences-based trees are congruent with both the classical 16S rRNA phylogeny, and core genome-based strain clustering. Furthermore, these glycolysis markers can also be used to provide insights into the adaptive evolution of this genus, especially with regards to trends toward a high GC content. This streamlined method may open new avenues for phylogenetic studies on a broad scale, given the widespread occurrence of the glycolysis pathway in bacteria, and the diversity of the sequences they encode.}, journal={FRONTIERS IN MICROBIOLOGY}, publisher={Frontiers Media SA}, author={Brandt, Katelyn and Barrangou, Rodolphe}, year={2016}, month={May} }
 @article{briner_henriksen_barrangou_2016, title={Prediction and Validation of Native and Engineered Cas9 Guide Sequences}, volume={2016}, DOI={10.1101/pdb.prot086785}, abstractNote={Cas9-based technologies rely on native elements of Type II CRISPR–Cas bacterial immune systems, including the trans-activating CRISPR RNA (tracrRNA), CRISPR RNA (crRNA), Cas9 protein, and protospacer-adjacent motif (PAM). The tracrRNA and crRNA form an RNA duplex that guides the Cas9 endonuclease to complementary nucleic acid sequences. Mechanistically, Cas9 initiates interactions by binding to the target PAM sequence and interrogating the target DNA in a 3′-to-5′ manner. Complementarity between the guide RNA and the target DNA is key. In natural systems, precise cleavage occurs when the target DNA sequence contains a PAM flanking a sequence homologous to the crRNA spacer sequence. Currently, the majority of commercial Cas9-based genome-editing tools are derived from the Type II CRISPR–Cas system of Streptococcus pyogenes. However, a diverse set of Type II CRISPR–Cas systems exist in nature that are potentially valuable for genome engineering applications. Exploitation of these systems requires prediction and validation of both native and engineered dual and single guide RNAs to drive Cas9 functionality. Here, we discuss how to identify the elements of these immune systems to develop next-generation Cas9-based genome-editing tools. We first discuss how to predict tracrRNA sequences and suggest a method for designing single guide RNAs containing only critical structural modules. We then outline how to predict the PAM sequence, which is crucial for determining potential targets for Cas9. Finally, validation of the system elements through transcriptome analysis and interference assays is essential for developing next-generation Cas9-based genome-editing tools.}, number={7}, journal={Cold Spring Harbor Protocols}, publisher={Cold Spring Harbor Laboratory}, author={Briner, Alexandra E. and Henriksen, Emily D. and Barrangou, Rodolphe}, year={2016}, month={Jul}, pages={pdb.prot086785} }
 @article{barrangou_birmingham_wiemann_beijersbergen_hornung_smith_2015, title={Advances in CRISPR-Cas9 genome engineering: lessons learned from RNA interference}, volume={43}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkv226}, abstractNote={The discovery that the machinery of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 bacterial immune system can be re-purposed to easily create deletions, insertions and replacements in the mammalian genome has revolutionized the field of genome engineering and re-invigorated the field of gene therapy. Many parallels have been drawn between the newly discovered CRISPR-Cas9 system and the RNA interference (RNAi) pathway in terms of their utility for understanding and interrogating gene function in mammalian cells. Given this similarity, the CRISPR-Cas9 field stands to benefit immensely from lessons learned during the development of RNAi technology. We examine how the history of RNAi can inform today's challenges in CRISPR-Cas9 genome engineering such as efficiency, specificity, high-throughput screening and delivery for in vivo and therapeutic applications.}, number={7}, journal={NUCLEIC ACIDS RESEARCH}, publisher={Oxford University Press (OUP)}, author={Barrangou, Rodolphe and Birmingham, Amanda and Wiemann, Stefan and Beijersbergen, Roderick L. and Hornung, Veit and Smith, Anja van Brabant}, year={2015}, month={Apr}, pages={3407–3419} }
 @misc{makarova_wolf_alkhnbashi_costa_shah_saunders_barrangou_brouns_charpentier_haft_et al._2015, title={An updated evolutionary classification of CRISPR-Cas systems}, volume={13}, number={11}, journal={Nature Reviews. Microbiology}, author={Makarova, K. S. and Wolf, Y. I. and Alkhnbashi, O. S. and Costa, F. and Shah, S. A. and Saunders, S. J. and Barrangou, R. and Brouns, S. J. J. and Charpentier, E. and Haft, D. H. and et al.}, year={2015}, pages={722–736} }
 @article{makarova_wolf_alkhnbashi_costa_shah_saunders_barrangou_brouns_charpentier_haft_et al._2015, title={An updated evolutionary classification of CRISPR–Cas systems}, volume={13}, ISSN={1740-1526 1740-1534}, url={http://dx.doi.org/10.1038/NRMICRO3569}, DOI={10.1038/nrmicro3569}, abstractNote={CRISPR–Cas systems provide bacteria and archaea with adaptive immunity to invading foreign DNA. In an Analysis article, Koonin and colleagues update a previous classification of these systems to incorporate the large volume of genomic data generated in recent years. The evolution of CRISPR–cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR–cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR–Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized.}, number={11}, journal={Nature Reviews Microbiology}, publisher={Springer Science and Business Media LLC}, author={Makarova, Kira S. and Wolf, Yuri I. and Alkhnbashi, Omer S. and Costa, Fabrizio and Shah, Shiraz A. and Saunders, Sita J. and Barrangou, Rodolphe and Brouns, Stan J. J. and Charpentier, Emmanuelle and Haft, Daniel H. and et al.}, year={2015}, month={Sep}, pages={722–736} }
 @article{barrangou_oost_2015, title={Bacteriophage exclusion, a new defense system}, volume={34}, ISSN={["1460-2075"]}, DOI={10.15252/embj.201490620}, abstractNote={The ability to withstand viral predation is critical for survival of most microbes. Accordingly, a plethora of phage resistance systems has been identified in bacterial genomes (Labrie et al, ), including restriction‐modification systems (R‐M) (Tock & Dryden, ), abortive infection (Abi) (Chopin et al, ), Argonaute‐based interference (Swarts et al, ), as well as clustered regularly interspaced short palindromic repeats (CRISPR) and associated protein (Cas) adaptive immune system (CRISPR‐Cas) (Barrangou & Marraffini, ; Van der Oost et al, ). Predictably, the dark matter of bacterial genomes contains a wealth of genetic gold. A study published in this issue of The EMBO Journal by Goldfarb et al ( ) unveils bacteriophage exclusion (BREX) as a novel, widespread bacteriophage resistance system that provides innate immunity against virulent and temperate phage in bacteria.}, number={2}, journal={EMBO JOURNAL}, publisher={EMBO}, author={Barrangou, Rodolphe and Oost, John}, year={2015}, month={Jan}, pages={134–135} }
 @article{paez-espino_sharon_morovic_stahl_thomas_barrangou_banfield_2015, title={CRISPR Immunity Drives Rapid Phage Genome Evolution in Streptococcus thermophilus}, volume={6}, ISSN={["2150-7511"]}, DOI={10.1128/mbio.00262-15}, abstractNote={ABSTRACT}, number={2}, journal={MBIO}, publisher={American Society for Microbiology}, author={Paez-Espino, David and Sharon, Itai and Morovic, Wesley and Stahl, Buffy and Thomas, Brian C. and Barrangou, Rodolphe and Banfield, Jillian F.}, year={2015} }
 @article{selle_barrangou_2015, title={CRISPR-Based Technologies and the Future of Food Science}, volume={80}, DOI={10.1111/1750-3841.13094}, abstractNote={Abstract}, number={11}, journal={Journal of Food Science}, publisher={Wiley-Blackwell}, author={Selle, Kurt and Barrangou, Rodolphe}, year={2015}, month={Oct}, pages={R2367–R2372} }
 @article{selle_klaenhammer_barrangou_2015, title={CRISPR-based screening of genomic island excision events in bacteria}, volume={112}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1508525112}, abstractNote={Significance}, number={26}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Selle, Kurt and Klaenhammer, Todd R. and Barrangou, Rodolphe}, year={2015}, month={Jun}, pages={8076–8081} }
 @article{shariat_timme_pettengill_barrangou_dudley_2015, title={Characterization and evolution of Salmonella CRISPR-Cas systems}, volume={161}, ISSN={["1465-2080"]}, DOI={10.1099/mic.0.000005}, abstractNote={Prokaryotic CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated genes) systems provide adaptive immunity from invasive genetic elements and encompass three essential features: (i) cas genes, (ii) a CRISPR array composed of spacers and direct repeats and (iii) an AT-rich leader sequence upstream of the array. We performed in-depth sequence analysis of the CRISPR-Cas systems in >600 Salmonella, representing four clinically prevalent serovars. Each CRISPR-Cas feature is extremely conserved in the Salmonella, and the CRISPR1 locus is more highly conserved than CRISPR2. Array composition is serovar-specific, although no convincing evidence of recent spacer acquisition against exogenous nucleic acids exists. Only 12 % of spacers match phage and plasmid sequences and self-targeting spacers are associated with direct repeat variants. High nucleotide identity (>99.9 %) exists across the cas operon among isolates of a single serovar and in some cases this conservation extends across divergent serovars. These observations reflect historical CRISPR-Cas immune activity, showing that this locus has ceased undergoing adaptive events. Intriguingly, the high level of conservation across divergent serovars shows that the genetic integrity of these inactive loci is maintained over time, contrasting with the canonical view that inactive CRISPR loci degenerate over time. This thorough characterization of Salmonella CRISPR-Cas systems presents new insights into Salmonella CRISPR evolution, particularly with respect to cas gene conservation, leader sequences, organization of direct repeats and protospacer matches. Collectively, our data suggest that Salmonella CRISPR-Cas systems are no longer immunogenic; rather, their impressive conservation indicates they may have an alternative function in Salmonella.}, journal={MICROBIOLOGY-SGM}, author={Shariat, Nikki and Timme, Ruth E. and Pettengill, James B. and Barrangou, Rodolphe and Dudley, Edward G.}, year={2015}, month={Feb}, pages={374–386} }
 @article{barrangou_2015, title={Diversity of CRISPR-Cas immune systems and molecular machines}, volume={16}, DOI={10.1186/s13059-015-0816-9}, abstractNote={Bacterial adaptive immunity hinges on CRISPR-Cas systems that provide DNA-encoded, RNA-mediated targeting of exogenous nucleic acids. A plethora of CRISPR molecular machines occur broadly in prokaryotic genomes, with a diversity of Cas nucleases that can be repurposed for various applications.}, number={1}, journal={Genome Biology}, publisher={Springer Nature}, author={Barrangou, Rodolphe}, year={2015}, month={Nov} }
 @misc{barrangou_2015, title={Diversity of CRISPR-Cas immune systems and molecular machines}, volume={16}, journal={Genome Biology}, author={Barrangou, R.}, year={2015} }
 @article{sun_harris_mccann_guo_argimon_zhang_yang_jeffery_cooney_kagawa_et al._2015, title={Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera}, volume={6}, ISSN={["2041-1723"]}, DOI={10.1038/ncomms9322}, abstractNote={Abstract}, journal={NATURE COMMUNICATIONS}, publisher={Springer Nature}, author={Sun, Zhihong and Harris, Hugh M. B. and McCann, Angela and Guo, Chenyi and Argimon, Silvia and Zhang, Wenyi and Yang, Xianwei and Jeffery, Ian B. and Cooney, Jakki C. and Kagawa, Todd F. and et al.}, year={2015}, month={Sep} }
 @misc{selle_barrangou_2015, title={Harnessing CRISPR-Cas systems for bacterial genome editing}, volume={23}, ISSN={["1878-4380"]}, DOI={10.1016/j.tim.2015.01.008}, abstractNote={Manipulation of genomic sequences facilitates the identification and characterization of key genetic determinants in the investigation of biological processes. Genome editing via clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) constitutes a next-generation method for programmable and high-throughput functional genomics. CRISPR-Cas systems are readily reprogrammed to induce sequence-specific DNA breaks at target loci, resulting in fixed mutations via host-dependent DNA repair mechanisms. Although bacterial genome editing is a relatively unexplored and underrepresented application of CRISPR-Cas systems, recent studies provide valuable insights for the widespread future implementation of this technology. This review summarizes recent progress in bacterial genome editing and identifies fundamental genetic and phenotypic outcomes of CRISPR targeting in bacteria, in the context of tool development, genome homeostasis, and DNA repair.}, number={4}, journal={TRENDS IN MICROBIOLOGY}, publisher={Elsevier BV}, author={Selle, Kurt and Barrangou, Rodolphe}, year={2015}, month={Apr}, pages={225–232} }
 @article{selle_barrangou_2015, title={JFS Special Issue: 75 years of advancing food science, and preparing for the next 75 CRISPR-based technologies and the future of food science}, volume={80}, number={11}, journal={Journal of Food Science}, author={Selle, K. and Barrangou, R.}, year={2015}, pages={R2367–2372} }
 @article{kyung_medina pradas_kim_lee_kim_choi_cho_chung_barrangou_breidt_2015, title={Microbial Ecology of Watery Kimchi}, volume={80}, ISSN={["1750-3841"]}, DOI={10.1111/1750-3841.12848}, abstractNote={Abstract}, number={5}, journal={JOURNAL OF FOOD SCIENCE}, publisher={Wiley-Blackwell}, author={Kyung, Kyu Hang and Medina Pradas, Eduardo and Kim, Song Gun and Lee, Yong Jae and Kim, Kyong Ho and Choi, Jin Joo and Cho, Joo Hyong and Chung, Chang Ho and Barrangou, Rodolphe and Breidt, Frederick}, year={2015}, month={May}, pages={M1031–M1038} }
 @article{briner_lugli_milani_duranti_turroni_gueimonde_margolles_sinderen_ventura_barrangou_2015, title={Occurrence and Diversity of CRISPR-Cas Systems in the Genus Bifidobacterium}, volume={10}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0133661}, abstractNote={CRISPR-Cas systems constitute adaptive immune systems for antiviral defense in bacteria. We investigated the occurrence and diversity of CRISPR-Cas systems in 48 Bifidobacterium genomes to gain insights into the diversity and co-evolution of CRISPR-Cas systems within the genus and investigate CRISPR spacer content. We identified the elements necessary for the successful targeting and inference of foreign DNA in select Type II CRISPR-Cas systems, including the tracrRNA and target PAM sequence. Bifidobacterium species have a very high frequency of CRISPR-Cas occurrence (77%, 37 of 48). We found that many Bifidobacterium species have unusually large and diverse CRISPR-Cas systems that contain spacer sequences showing homology to foreign genetic elements like prophages. A large number of CRISPR spacers in bifidobacteria show perfect homology to prophage sequences harbored in the chromosomes of other species of Bifidobacterium, including some spacers that self-target the chromosome. A correlation was observed between strains that lacked CRISPR-Cas systems and the number of times prophages in that chromosome were targeted by other CRISPR spacers. The presence of prophage-targeting CRISPR spacers and prophage content may shed light on evolutionary processes and strain divergence. Finally, elements of Type II CRISPR-Cas systems, including the tracrRNA and crRNAs, set the stage for the development of genome editing and genetic engineering tools.}, number={7}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Briner, Alexandra E. and Lugli, Gabriele Andrea and Milani, Christian and Duranti, Sabrina and Turroni, Francesca and Gueimonde, Miguel and Margolles, Abelardo and Sinderen, Douwe and Ventura, Marco and Barrangou, Rodolphe}, editor={Riedel, Christian U.Editor}, year={2015}, month={Jul} }
 @article{sanozky-dawes_selle_o'flaherty_klaenhammer_barrangou_2015, title={Occurrence and activity of a type II CRISPR-Cas system in Lactobacillus gasseri}, volume={161}, ISSN={["1350-0872"]}, DOI={10.1099/mic.0.000129}, abstractNote={Bacteria encode clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated genes (cas), which collectively form an RNA-guided adaptive immune system against invasive genetic elements. In silico surveys have revealed that lactic acid bacteria harbour a prolific and diverse set of CRISPR-Cas systems. Thus, the natural evolutionary role of CRISPR-Cas systems may be investigated in these ecologically, industrially, scientifically and medically important microbes. In this study, 17 Lactobacillus gasseri strains were investigated and 6 harboured a type II-A CRISPR-Cas system, with considerable diversity in array size and spacer content. Several of the spacers showed similarity to phage and plasmid sequences, which are typical targets of CRISPR-Cas immune systems. Aligning the protospacers facilitated inference of the protospacer adjacent motif sequence, determined to be 5'-NTAA-3' flanking the 3' end of the protospacer. The system in L. gasseri JV-V03 and NCK 1342 interfered with transforming plasmids containing sequences matching the most recently acquired CRISPR spacers in each strain. We report the distribution and function of a native type II-A CRISPR-Cas system in the commensal species L. gasseri. Collectively, these results open avenues for applications for bacteriophage protection and genome modification in L. gasseri, and contribute to the fundamental understanding of CRISPR-Cas systems in bacteria.}, journal={MICROBIOLOGY-SGM}, author={Sanozky-Dawes, Rosemary and Selle, Kurt and O'Flaherty, Sarah and Klaenhammer, Todd and Barrangou, Rodolphe}, year={2015}, month={Sep}, pages={1752–1761} }
 @misc{sontheimer_barrangou_2015, title={The Bacterial Origins of the CRISPR Genome-Editing Revolution}, volume={26}, ISSN={["1557-7422"]}, DOI={10.1089/hum.2015.091}, abstractNote={Like most of the tools that enable modern life science research, the recent genome-editing revolution has its biological roots in the world of bacteria and archaea. Clustered, regularly interspaced, short palindromic repeats (CRISPR) loci are found in the genomes of many bacteria and most archaea, and underlie an adaptive immune system that protects the host cell against invasive nucleic acids such as viral genomes. In recent years, engineered versions of these systems have enabled efficient DNA targeting in living cells from dozens of species (including humans and other eukaryotes), and the exploitation of the resulting endogenous DNA repair pathways has provided a route to fast, easy, and affordable genome editing. In only three years after RNA-guided DNA cleavage was first harnessed, the ability to edit genomes via simple, user-defined RNA sequences has already revolutionized nearly all areas of biological science. CRISPR-based technologies are now poised to similarly revolutionize many facets of clinical medicine, and even promise to advance the long-term goal of directly editing genomic sequences of patients with inherited disease. In this review, we describe the biological and mechanistic basis for these remarkable immune systems, and how their engineered derivatives are revolutionizing basic and clinical research.}, number={7}, journal={HUMAN GENE THERAPY}, publisher={Mary Ann Liebert Inc}, author={Sontheimer, Erik J. and Barrangou, Rodolphe}, year={2015}, month={Jul}, pages={413–424} }
 @misc{barrangou_2015, title={The roles of CRISPR-Cas systems in adaptive immunity and beyond}, volume={32}, ISSN={["1879-0372"]}, DOI={10.1016/j.coi.2014.12.008}, abstractNote={Clustered regularly interspaced short palindromic repeats (CRISPR) and accompanying Cas proteins constitute the adaptive CRISPR-Cas immune system in bacteria and archaea. This DNA-encoded, RNA-mediated defense system provides sequence-specific recognition, targeting and degradation of exogenous nucleic acid. Though the primary established role of CRISPR-Cas systems is in bona fide adaptive antiviral defense in bacteria, a growing body of evidence indicates that it also plays critical functional roles beyond immunity, such as endogenous transcriptional control. Furthermore, benefits inherent to maintaining genome homeostasis also come at the cost of reduced uptake of beneficial DNA, and preventing strategic adaptation to the environment. This opens new avenues for the investigation of CRISPR-Cas systems and their functional characterization beyond adaptive immunity.}, journal={CURRENT OPINION IN IMMUNOLOGY}, publisher={Elsevier BV}, author={Barrangou, Rodolphe}, year={2015}, month={Feb}, pages={36–41} }
 @article{barrangou_may_2015, title={Unraveling the potential of CRISPR-Cas9 for gene therapy}, volume={15}, ISSN={["1744-7682"]}, DOI={10.1517/14712598.2015.994501}, abstractNote={The molecular machinery from the prokaryotic clustered regularly interspaced short palindromic repeats (CRISPR)-Cas immune system has broadly been repurposed for genome editing in eukaryotes. In particular, the sequence-specific Cas9 endonuclease can be flexibly harnessed for the genesis of precise double-stranded DNA breaks, using single guide RNAs that are readily programmable. The endogenous DNA repair machinery subsequently generates genome modifications, either by random insertion or deletions using non-homologous end joining (NHEJ), or designed integration of mutations or genetic material using homology-directed repair (HDR) templates. This technology has opened new avenues for the investigation of genetic diseases in general, and for gene therapy applications in particular.}, number={3}, journal={EXPERT OPINION ON BIOLOGICAL THERAPY}, publisher={Informa Healthcare}, author={Barrangou, Rodolphe and May, Andrew P.}, year={2015}, month={Mar}, pages={311–314} }
 @article{beisel_gomaa_barrangou_2014, title={A CRISPR design for next-generation antimicrobials}, volume={15}, ISSN={["1474-760X"]}, DOI={10.1186/s13059-014-0516-x}, abstractNote={Two recent publications have demonstrated how delivering CRISPR nucleases provides a promising solution to the growing problem of bacterial antibiotic resistance.}, number={11}, journal={GENOME BIOLOGY}, publisher={Springer Nature}, author={Beisel, Chase L. and Gomaa, Ahmed A. and Barrangou, Rodolphe}, year={2014} }
 @article{toro_cao_ju_allard_barrangou_zhao_brown_meng_2014, title={Association of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Elements with Specific Serotypes and Virulence Potential of Shiga Toxin-Producing Escherichia coli}, volume={80}, ISSN={["1098-5336"]}, DOI={10.1128/aem.03018-13}, abstractNote={ABSTRACT}, number={4}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, publisher={American Society for Microbiology}, author={Toro, Magaly and Cao, Guojie and Ju, Wenting and Allard, Marc and Barrangou, Rodolphe and Zhao, Shaohua and Brown, Eric and Meng, Jianghong}, year={2014}, month={Feb}, pages={1411–1420} }
 @misc{barrangou_marraffini_2014, title={CRISPR-Cas Systems: Prokaryotes Upgrade to Adaptive Immunity}, volume={54}, ISSN={["1097-4164"]}, DOI={10.1016/j.molcel.2014.03.011}, abstractNote={Clustered regularly interspaced short palindromic repeats (CRISPR), and associated proteins (Cas) comprise the CRISPR-Cas system, which confers adaptive immunity against exogenic elements in many bacteria and most archaea. CRISPR-mediated immunization occurs through the uptake of DNA from invasive genetic elements such as plasmids and viruses, followed by its integration into CRISPR loci. These loci are subsequently transcribed and processed into small interfering RNAs that guide nucleases for specific cleavage of complementary sequences. Conceptually, CRISPR-Cas shares functional features with the mammalian adaptive immune system, while also exhibiting characteristics of Lamarckian evolution. Because immune markers spliced from exogenous agents are integrated iteratively in CRISPR loci, they constitute a genetic record of vaccination events and reflect environmental conditions and changes over time. Cas endonucleases, which can be reprogrammed by small guide RNAs have shown unprecedented potential and flexibility for genome editing and can be repurposed for numerous DNA targeting applications including transcriptional control.}, number={2}, journal={MOLECULAR CELL}, publisher={Elsevier BV}, author={Barrangou, Rodolphe and Marraffini, Luciano A.}, year={2014}, month={Apr}, pages={234–244} }
 @article{barrangou_2014, title={Cas9 Targeting and the CRISPR Revolution}, volume={344}, ISSN={["1095-9203"]}, DOI={10.1126/science.1252964}, abstractNote={Uncovering how an RNA-protein molecular scalpel targets DNA will advance our ability to engineer genomes.}, number={6185}, journal={SCIENCE}, publisher={American Association for the Advancement of Science (AAAS)}, author={Barrangou, Rodolphe}, year={2014}, month={May}, pages={707–708} }
 @article{barrangou_horvath_2014, title={Functions and Applications of RNA-Guided CRISPR-Cas Immune Systems}, DOI={10.1002/3527600906.mcb.20130001}, abstractNote={Clustered regularly interspaced short palindromic repeats (CRISPRs), together with CRISPR-associated sequences (cas) constitute the CRISPR-Cas adaptive immune system in bacteria and archaea. Adaptive immunity is built into CRISPR arrays through the uptake of small pieces of invasive nucleic acids, such as viruses and plasmids. Acquired immunity is subsequently mediated by small interfering RNAs transcribed from these loci, that guide specific cleavage of complementary sequences by nucleases. Studies have established that CRISPR loci and their RNA-guided interference machinery can be exploited for a broad array of applications. Adaptive immunity can be built against viruses, or to preclude the uptake of undesirable sequences. The inheritable and hypervariable nature of these loci can be used to track the phylogenetic path of an organism and reveal the evolutionary interplay between hosts and their viruses. Recently, a new customizable genome editing system was developed based on these versatile interfering RNAs to specifically guide nucleases for sequence cleavage. 
 
 
Keywords: 
 
Cas; 
Cas9; 
Cascade; 
CRISPR; 
crRNA; 
Interference}, journal={Encyclopedia of Molecular Cell Biology and Molecular Medicine}, author={Barrangou, Rodolphe and Horvath, Philippe}, year={2014}, month={Oct} }
 @article{milani_lugli_duranti_turroni_bottacini_mangifesta_sanchez_viappiani_mancabelli_taminiau_et al._2014, title={Genomic Encyclopedia of Type Strains of the Genus Bifidobacterium}, volume={80}, ISSN={["1098-5336"]}, DOI={10.1128/aem.02308-14}, abstractNote={ABSTRACT}, number={20}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, publisher={American Society for Microbiology}, author={Milani, Christian and Lugli, Gabriele Andrea and Duranti, Sabrina and Turroni, Francesca and Bottacini, Francesca and Mangifesta, Marta and Sanchez, Borja and Viappiani, Alice and Mancabelli, Leonardo and Taminiau, Bernard and et al.}, year={2014}, month={Oct}, pages={6290–6302} }
 @article{briner_donohoue_gomaa_selle_slorach_nye_haurwitz_beisel_may_barrangou_2014, title={Guide RNA Functional Modules Direct Cas9 Activity and Orthogonality}, volume={56}, ISSN={["1097-4164"]}, DOI={10.1016/j.molcel.2014.09.019}, abstractNote={The RNA-guided Cas9 endonuclease specifically targets and cleaves DNA in a sequence-dependent manner and has been widely used for programmable genome editing. Cas9 activity is dependent on interactions with guide RNAs, and evolutionarily divergent Cas9 nucleases have been shown to work orthogonally. However, the molecular basis of selective Cas9:guide-RNA interactions is poorly understood. Here, we identify and characterize six conserved modules within native crRNA:tracrRNA duplexes and single guide RNAs (sgRNAs) that direct Cas9 endonuclease activity. We show the bulge and nexus are necessary for DNA cleavage and demonstrate that the nexus and hairpins are instrumental in defining orthogonality between systems. In contrast, the crRNA:tracrRNA complementary region can be modified or partially removed. Collectively, our results establish guide RNA features that drive DNA targeting by Cas9 and open new design and engineering avenues for CRISPR technologies.}, number={2}, journal={MOLECULAR CELL}, publisher={Elsevier BV}, author={Briner, Alexandra E. and Donohoue, Paul D. and Gomaa, Ahmed A. and Selle, Kurt and Slorach, Euan M. and Nye, Christopher H. and Haurwitz, Rachel E. and Beisel, Chase L. and May, Andrew P. and Barrangou, Rodolphe}, year={2014}, month={Oct}, pages={333–339} }
 @article{briner_barrangou_2014, title={Lactobacillus buchneri Genotyping on the Basis of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Locus Diversity}, volume={80}, ISSN={["1098-5336"]}, DOI={10.1128/aem.03015-13}, abstractNote={ABSTRACT}, number={3}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, publisher={American Society for Microbiology}, author={Briner, Alexandra E. and Barrangou, Rodolphe}, year={2014}, month={Feb}, pages={994–1001} }
 @article{barrangou_klaenhammer_2014, title={Microbiology: Bacteria get vaccinated}, volume={513}, DOI={10.1038/513175a}, number={7517}, journal={Nature}, publisher={Springer Nature}, author={Barrangou, Rodolphe and Klaenhammer, Todd R.}, year={2014}, month={Sep}, pages={175–176} }
 @article{gomaa_klumpe_luo_selle_barrangou_beisel_2014, title={Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR-Cas Systems}, volume={5}, ISSN={["2150-7511"]}, DOI={10.1128/mbio.00928-13}, abstractNote={ABSTRACT}, number={1}, journal={MBIO}, publisher={American Society for Microbiology}, author={Gomaa, Ahmed A. and Klumpe, Heidi E. and Luo, Michelle L. and Selle, Kurt and Barrangou, Rodolphe and Beisel, Chase L.}, year={2014} }
 @article{wehnes_rehberger_barrangou_smith_2014, title={Short communication: Determination of Salmonella clustered regularly interspaced short palindromic repeats (CRISPR) diversity on dairy farms in Wisconsin and Minnesota}, volume={97}, DOI={10.3168/jds.2013-7595}, abstractNote={Salmonella enterica ssp. enterica is a foodborne pathogen able to cause disease in both humans and animals. Diverse serovars of this pathogen exist, some of which are host specific, causing a range of clinical symptoms from asymptomatic infection through morbidity and mortality. According to a 2007 survey by the USDA National Animal Health Monitoring System, fecal shedding of Salmonella from healthy cows occurs on 39.7% of dairy farms in the United States. Certain serovars are frequently isolated from dairy farms and the majority of isolates from the National Animal Health Monitoring System study were represented by 5 serovars; however, genotypic diversity was not examined. The objective of this study was to determine the diversity of clustered regularly interspaced short palindromic repeats (CRISPR) loci in Salmonella collected from 8 dairy farms with a previous history of salmonellosis. None of the cows or calves sampled on 2 of the 8 dairy farms were shedding Salmonella, although Salmonella was detected in a cow bedding sample on 1 of these farms. Salmonella populations were discrete on each farm, according to CRISPR typing, with the exception of an Anatum var. 15+ type on farms 5 and 6 and the Montevideo type on farms 1 and 2. One to 4 distinct CRISPR genotypes were identified per farm. The CRISPR typing differed within serovars, as Montevideo, Anatum var. 15+, and Muenster serovars had no overlap of spacer content, even on the same farm, reflecting between- and within-serovar genetic diversity. The dynamic nature of Salmonella populations was shown in a farm that was sampled longitudinally over 13.5 mo. Changes in serovar from 3,19:-:z27 to Montevideo was observed between the first sampling time and 8 mo later, with concomitant change in CRISPR alleles. The results indicate that Salmonella strains present in smaller dairy herds (<500 head) are specific to that farm and new Salmonella strains may emerge over time.}, number={10}, journal={Journal of Dairy Science}, publisher={American Dairy Science Association}, author={Wehnes, C.A. and Rehberger, T.G. and Barrangou, R. and Smith, A.H.}, year={2014}, month={Oct}, pages={6370–6377} }
 @article{pettengill_timme_barrangou_toro_allard_strain_musser_brown_2014, title={The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp enterica}, volume={2}, ISSN={["2167-8359"]}, DOI={10.7717/peerj.340}, abstractNote={Evolutionary studies of clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated (cas) genes can provide insights into host-pathogen co-evolutionary dynamics and the frequency at which different genomic events (e.g., horizontal vs. vertical transmission) occur. Within this study, we used whole genome sequence (WGS) data to determine the evolutionary history and genetic diversity of CRISPR loci and cas genes among a diverse set of 427 Salmonella enterica ssp. enterica isolates representing 64 different serovars. We also evaluated the performance of CRISPR loci for typing when compared to whole genome and multilocus sequence typing (MLST) approaches. We found that there was high diversity in array length within both CRISPR1 (median = 22; min = 3; max = 79) and CRISPR2 (median = 27; min = 2; max = 221). There was also much diversity within serovars (e.g., arrays differed by as many as 50 repeat-spacer units among Salmonella ser. Senftenberg isolates). Interestingly, we found that there are two general cas gene profiles that do not track phylogenetic relationships, which suggests that non-vertical transmission events have occurred frequently throughout the evolutionary history of the sampled isolates. There is also considerable variation among the ranges of pairwise distances estimated within each cas gene, which may be indicative of the strength of natural selection acting on those genes. We developed a novel clustering approach based on CRISPR spacer content, but found that typing based on CRISPRs was less accurate than the MLST-based alternative; typing based on WGS data was the most accurate. Notwithstanding cost and accessibility, we anticipate that draft genome sequencing, due to its greater discriminatory power, will eventually become routine for traceback investigations.}, journal={PEERJ}, publisher={PeerJ}, author={Pettengill, James B. and Timme, Ruth E. and Barrangou, Rodolphe and Toro, Magaly and Allard, Marc W. and Strain, Errol and Musser, Steven M. and Brown, Eric W.}, year={2014}, month={Apr} }
 @article{carte_christopher_smith_olson_barrangou_moineau_glover_graveley_terns_terns_2014, title={The three major types of CRISPR-Cas systems function independently in CRISPR RNA biogenesis in Streptococcus thermophilus}, volume={93}, ISSN={["1365-2958"]}, DOI={10.1111/mmi.12644}, abstractNote={Summary}, number={1}, journal={MOLECULAR MICROBIOLOGY}, publisher={Wiley-Blackwell}, author={Carte, Jason and Christopher, Ross T. and Smith, Justin T. and Olson, Sara and Barrangou, Rodolphe and Moineau, Sylvain and Glover, Claiborne V. C., III and Graveley, Brenton R. and Terns, Rebecca M. and Terns, Michael P.}, year={2014}, month={Jul}, pages={98–112} }
 @article{hachem_møller_andersen_fredslund_majumder_nakai_leggio_goh_barrangou_klaenhammer_et al._2013, title={A Snapshot into the Metabolism of Isomalto-oligosaccharides in Probiotic Bacteria}, volume={60}, DOI={10.5458/jag.jag.jag-2012_022}, abstractNote={In vitro and in vivo studies have demonstrated the prebiotic potential of isomalto-oligosaccharides (IMO), comprising α -(1,6)-gluco-oligosaccharides and panose, which selectively stimulate the growth of probiotic bifidobacteria and lactobacilli. The protein machinery conferring the utilization of IMO by probiotics, however, remains vaguely described. We have used genomic, transcriptomic, enzymatic, and biophysical analyses to explore IMO utilization routes in probiotic lactobacilli and bifidobacteria as represented by Lactobacillus acidophilus NCFM and Bifidobacterium animalis subsp. lactis Bl-04, respectively. Utilization of IMO and malto-oligosaccharide ( α -(1,4)-glucosides) appears to be linked both at the genetic and transcriptomic level in the acidophilus group lactobacilli as suggested by reverse transcriptase PCR (RT-PCR) and gene landscape analysis. Canonical intracellular GH13_31 glucan 1,6- α -glucosidases active on IMO longer than isomaltose occur widely in acidophilus group lactobacilli. Interestingly, however, isomaltose, isomaltulose and panose seem to be internalized through a phosphoenoyl pyruvate transferase system (PTS) and subsequently hydrolyzed by a GH4 6-phosphate- α -glucosidases based on whole genome microarray analysis. This sub-specificity within GH4 seems to be unique for lactobacilli mainly from the gut niche, as the sequences from this group segregate from characterized GH4 maltose-6-phosphate- α -glucosidases in other organisms. By comparison, IMO is linked α -galactosidases, GH13_31 oligo 1,6- α -glucosidases and a dual specificity ATP-binding cassette (ABC) transport system active in the uptake of both classes of α -(1,6) glycosides. These data bring novel insight to advance our understanding of the basis of selectivity of IMO metabolism by important gut microbiome members.}, number={2}, journal={Journal of Applied Glycoscience}, publisher={The Japanese Society of Applied Glycoscience}, author={Hachem, Maher Abou and Møller, Marie S. and Andersen, Joakim M. and Fredslund, Folmer and Majumder, Avishek and Nakai, Hiroyuki and Leggio, Leila Lo and Goh, Yong-Jun and Barrangou, Rodolphe and Klaenhammer, Todd R. and et al.}, year={2013}, pages={95–100} }
 @article{dimarzio_shariat_kariyawasam_barrangou_dudley_2013, title={Antibiotic Resistance in Salmonella enterica Serovar Typhimurium Associates with CRISPR Sequence Type}, volume={57}, ISSN={["1098-6596"]}, DOI={10.1128/aac.00913-13}, abstractNote={ABSTRACT}, number={9}, journal={ANTIMICROBIAL AGENTS AND CHEMOTHERAPY}, publisher={American Society for Microbiology}, author={DiMarzio, Michael and Shariat, Nikki and Kariyawasam, Subhashinie and Barrangou, Rodolphe and Dudley, Edward G.}, year={2013}, month={Sep}, pages={4282–4289} }
 @article{loquasto_barrangou_dudley_stahl_chen_roberts_2013, title={Bifidobacterium animalis subsp lactis ATCC 27673 Is a Genomically Unique Strain within Its Conserved Subspecies}, volume={79}, ISSN={["1098-5336"]}, DOI={10.1128/aem.01777-13}, abstractNote={ABSTRACT}, number={22}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, publisher={American Society for Microbiology}, author={Loquasto, Joseph R. and Barrangou, Rodolphe and Dudley, Edward G. and Stahl, Buffy and Chen, Chun and Roberts, Robert F.}, year={2013}, month={Nov}, pages={6903–6910} }
 @book{barrangou_oost_2013, title={CRISPR-Cas Systems}, DOI={10.1007/978-3-642-34657-6}, publisher={Springer Berlin Heidelberg}, year={2013} }
 @book{barrangou_oost_2013, title={CRISPR-Cas Systems}, DOI={10.1007/978-3-662-45794-8}, publisher={Springer Berlin Heidelberg}, year={2013} }
 @misc{barrangou_2013, title={CRISPR-Cas systems and RNA-guided interference}, volume={4}, ISSN={["1757-7012"]}, DOI={10.1002/wrna.1159}, abstractNote={Abstract}, number={3}, journal={WILEY INTERDISCIPLINARY REVIEWS-RNA}, publisher={Wiley-Blackwell}, author={Barrangou, Rodolphe}, year={2013}, pages={267–278} }
 @article{shariat_sandt_dimarzio_barrangou_dudley_2013, title={CRISPR-MVLST subtyping of Salmonella enterica subsp. enterica serovars Typhimurium and Heidelberg and application in identifying outbreak isolates}, volume={13}, DOI={10.1186/1471-2180-13-254}, abstractNote={Abstract}, number={1}, journal={BMC Microbiology}, publisher={Springer Nature}, author={Shariat, Nikki and Sandt, Carol H and DiMarzio, Michael J and Barrangou, Rodolphe and Dudley, Edward G}, year={2013}, pages={254} }
 @article{stahl_barrangou_2013, title={Complete Genome Sequence of Probiotic Strain Lactobacillus acidophilus La-14}, volume={1}, DOI={10.1128/genomea.00376-13}, abstractNote={ABSTRACT}, number={3}, journal={Genome Announcements}, publisher={American Society for Microbiology}, author={Stahl, B. and Barrangou, R.}, year={2013}, month={Jun}, pages={e00376–13-e00376–13} }
 @article{barrangou_coute-monvoisin_stahl_chavichvily_damange_romero_boyaval_fremaux_horvath_2013, title={Genomic impact of CRISPR immunization against bacteriophages}, volume={41}, ISSN={["1470-8752"]}, DOI={10.1042/bst20130160}, abstractNote={CRISPR (clustered regularly interspaced short palindromic repeats) together with cas (CRISPR-associated) genes form the CRISPR–Cas immune system, which provides sequence-specific adaptive immunity against foreign genetic elements in bacteria and archaea. Immunity is acquired by the integration of short stretches of invasive DNA as novel ‘spacers’ into CRISPR loci. Subsequently, these immune markers are transcribed and generate small non-coding interfering RNAs that specifically guide nucleases for sequence-specific cleavage of complementary sequences. Among the four CRISPR–Cas systems present in Streptococcus thermophilus, CRISPR1 and CRISPR3 have the ability to readily acquire new spacers following bacteriophage or plasmid exposure. In order to investigate the impact of building CRISPR-encoded immunity on the host chromosome, we determined the genome sequence of a BIM (bacteriophage-insensitive mutant) derived from the DGCC7710 model organism, after four consecutive rounds of bacteriophage challenge. As expected, active CRISPR loci evolved via polarized addition of several novel spacers following exposure to bacteriophages. Although analysis of the draft genome sequence revealed a variety of SNPs (single nucleotide polymorphisms) and INDELs (insertions/deletions), most of the in silico differences were not validated by Sanger re-sequencing. In addition, two SNPs and two small INDELs were identified and tracked in the intermediate variants. Overall, building CRISPR-encoded immunity does not significantly affect the genome, which allows the maintenance of important functional properties in isogenic CRISPR mutants. This is critical for the development and formulation of sustainable and robust next-generation starter cultures with increased industrial lifespans.}, number={6}, journal={BIOCHEMICAL SOCIETY TRANSACTIONS}, publisher={Portland Press Ltd.}, author={Barrangou, Rodolphe and Coute-Monvoisin, Anne-Claire and Stahl, Buffy and Chavichvily, Isabelle and Damange, Florian and Romero, Dennis A. and Boyaval, Patrick and Fremaux, Christophe and Horvath, Philippe}, year={2013}, month={Dec}, pages={1383–1391} }
 @article{sinkunas_gasiunas_waghmare_dickman_barrangou_horvath_siksnys_2013, title={In vitro reconstitution of Cascade-mediated CRISPR immunity in Streptococcus thermophilus}, volume={32}, DOI={10.1038/emboj.2012.352}, abstractNote={Clustered regularly interspaced short palindromic repeats (CRISPR)-encoded immunity in Type I systems relies on the Cascade (CRISPR-associated complex for antiviral defence) ribonucleoprotein complex, which triggers foreign DNA degradation by an accessory Cas3 protein. To establish the mechanism for adaptive immunity provided by the Streptococcus thermophilus CRISPR4-Cas (CRISPR-associated) system (St-CRISPR4-Cas), we isolated an effector complex (St-Cascade) containing 61-nucleotide CRISPR RNA (crRNA). We show that St-Cascade, guided by crRNA, binds in vitro to a matching proto-spacer if a proto-spacer adjacent motif (PAM) is present. Surprisingly, the PAM sequence determined from binding analysis is promiscuous and limited to a single nucleotide (A or T) immediately upstream (-1 position) of the proto-spacer. In the presence of a correct PAM, St-Cascade binding to the target DNA generates an R-loop that serves as a landing site for the Cas3 ATPase/nuclease. We show that Cas3 binding to the displaced strand in the R-loop triggers DNA cleavage, and if ATP is present, Cas3 further degrades DNA in a unidirectional manner. These findings establish a molecular basis for CRISPR immunity in St-CRISPR4-Cas and other Type I systems.}, number={3}, journal={The EMBO Journal}, publisher={Wiley-Blackwell}, author={Sinkunas, Tomas and Gasiunas, Giedrius and Waghmare, Sakharam P and Dickman, Mark J and Barrangou, Rodolphe and Horvath, Philippe and Siksnys, Virginijus}, year={2013}, month={Jan}, pages={385–394} }
 @article{timme_pettengill_allard_strain_barrangou_wehnes_van kessel_karns_musser_brown_2013, title={Phylogenetic Diversity of the Enteric Pathogen Salmonella enterica subsp enterica Inferred from Genome-Wide Reference-Free SNP Characters}, volume={5}, ISSN={["1759-6653"]}, DOI={10.1093/gbe/evt159}, abstractNote={The enteric pathogen Salmonella enterica is one of the leading causes of foodborne illness in the world. The species is extremely diverse, containing more than 2,500 named serovars that are designated for their unique antigen characters and pathogenicity profiles—some are known to be virulent pathogens, while others are not. Questions regarding the evolution of pathogenicity, significance of antigen characters, diversity of clustered regularly interspaced short palindromic repeat (CRISPR) loci, among others, will remain elusive until a strong evolutionary framework is established. We present the first large-scale S. enterica subsp. enterica phylogeny inferred from a new reference-free k-mer approach of gathering single nucleotide polymorphisms (SNPs) from whole genomes. The phylogeny of 156 isolates representing 78 serovars (102 were newly sequenced) reveals two major lineages, each with many strongly supported sublineages. One of these lineages is the S. Typhi group; well nested within the phylogeny. Lineage-through-time analyses suggest there have been two instances of accelerated rates of diversification within the subspecies. We also found that antigen characters and CRISPR loci reveal different evolutionary patterns than that of the phylogeny, suggesting that a horizontal gene transfer or possibly a shared environmental acquisition might have influenced the present character distribution. Our study also shows the ability to extract reference-free SNPs from a large set of genomes and then to use these SNPs for phylogenetic reconstruction. This automated, annotation-free approach is an important step forward for bacterial disease tracking and in efficiently elucidating the evolutionary history of highly clonal organisms.}, number={11}, journal={GENOME BIOLOGY AND EVOLUTION}, publisher={Oxford University Press (OUP)}, author={Timme, Ruth E. and Pettengill, James B. and Allard, Marc W. and Strain, Errol and Barrangou, Rodolphe and Wehnes, Chris and Van Kessel, JoAnn S. and Karns, Jeffrey S. and Musser, Steven M. and Brown, Eric W.}, year={2013}, pages={2109–2123} }
 @article{horvath_barrangou_2013, title={RNA-guided genome editing à la carte}, volume={23}, DOI={10.1038/cr.2013.39}, abstractNote={Two recent papers in Science illustrate how the prokaryotic CRISPR-Cas immune system machinery, which typically targets invasive genetic elements such as viruses and plasmids, can be converted into a sophisticated molecular tool for next-generation human genome editing. The versatile Cas9 RNA-guided endonuclease can be readily reprogrammed using customizable small RNAs for sequence-specific single- or double-stranded DNA cleavage.}, number={6}, journal={Cell Research}, publisher={Springer Nature}, author={Horvath, Philippe and Barrangou, Rodolphe}, year={2013}, month={Mar}, pages={733–734} }
 @misc{abou hachem_andersen_barrangou_moller_fredslund_majumder_ejby_lahtinen_jacobsen_lo leggio_et al._2013, title={Recent insight into oligosaccharide uptake and metabolism in probiotic bacteria}, volume={31}, ISSN={["1029-2446"]}, DOI={10.3109/10242422.2013.828048}, abstractNote={Abstract In recent years, a plethora of studies have demonstrated the paramount physiological importance of the gut microbiota on various aspects of human health and development. Particular focus has been set on probiotic members of this community, the best studied of which are assigned into the Lactobacillus and Bifidobacterium genera. Effects such as pathogen exclusion, alleviation of inflammation and allergies, colon cancer, and other bowel disorders are attributed to the activity of probiotic bacteria, which selectively ferment prebiotics comprising mainly non-digestible oligosaccharides. Thus, glycan metabolism is an important attribute of probiotic action and a factor influencing the composition of the gut microbiota. In the quest to understand the molecular mechanism of this selectivity for certain glycans, we have explored the routes of uptake and utilization of a variety of oligosaccharides differing in size, composition, and glycosidic linkages. A combination of “omics” technologies bioinformatics, enzymology and protein characterization proved fruitful in elucidating the protein transport and catabolic machinery conferring the utilization of glucosides, galactosides, and xylosides in the two clinically validated probiotic strains Lactobacillus acidophilus NCFM and Bifidobacterium animalis subsp. lactis Bl-04. Importantly, we have been able to identify and in some cases validate the specificity of several transport systems, which are otherwise poorly annotated. Further, we have demonstrated for the first time that non-naturally occurring tri- and tetra-saccharides are internalized and efficiently utilized by probiotic bacteria in some cases better than well-established natural prebiotics. Selected highlights of these data are presented, emphasising the importance and the diversity of oligosaccharide transport in probiotic bacteria.}, number={4}, journal={BIOCATALYSIS AND BIOTRANSFORMATION}, publisher={Informa UK Limited}, author={Abou Hachem, Maher and Andersen, Joakim M. and Barrangou, Rodolphe and Moller, Marie S. and Fredslund, Folmer and Majumder, Avishek and Ejby, Morten and Lahtinen, Sampo J. and Jacobsen, Susanne and Lo Leggio, Leila and et al.}, year={2013}, month={Aug}, pages={226–235} }
 @article{paez-espino_morovic_sun_thomas_ueda_stahl_barrangou_banfield_2013, title={Strong bias in the bacterial CRISPR elements that confer immunity to phage}, volume={4}, DOI={10.1038/ncomms2440}, abstractNote={Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems provide adaptive immunity against phage via spacer-encoded CRISPR RNAs that are complementary to invasive nucleic acids. Here, we challenge Streptococcus thermophilus with a bacteriophage, and used PCR-based metagenomics to monitor phage-derived spacers daily for 15 days in two experiments. Spacers that target the host chromosome are infrequent and strongly selected against, suggesting autoimmunity is lethal. In experiments that recover over half a million spacers, we observe early dominance by a few spacer sub-populations and rapid oscillations in sub-population abundances. In two CRISPR systems and in replicate experiments, a few spacers account for the majority of spacer sequences. Nearly all phage locations targeted by the acquired spacers have a proto-spacer adjacent motif (PAM), indicating PAMs are involved in spacer acquisition. We detect a strong and reproducible bias in the phage genome locations from which spacers derive. This may reflect selection for specific spacers based on location and effectiveness.}, journal={Nature Communications}, publisher={Springer Nature}, author={Paez-Espino, David and Morovic, Wesley and Sun, Christine L. and Thomas, Brian C. and Ueda, Ken-ichi and Stahl, Buffy and Barrangou, Rodolphe and Banfield, Jillian F.}, year={2013}, month={Feb}, pages={1430} }
 @article{shariat_kirchner_sandt_trees_barrangou_dudley_2013, title={Subtyping of Salmonella enterica Serovar Newport Outbreak Isolates by CRISPR-MVLST and Determination of the Relationship between CRISPR-MVLST and PFGE Results}, volume={51}, ISSN={["0095-1137"]}, DOI={10.1128/jcm.00608-13}, abstractNote={ABSTRACT}, number={7}, journal={JOURNAL OF CLINICAL MICROBIOLOGY}, publisher={American Society for Microbiology}, author={Shariat, Nikki and Kirchner, Margaret K. and Sandt, Carol H. and Trees, Eija and Barrangou, Rodolphe and Dudley, Edward G.}, year={2013}, month={Jul}, pages={2328–2336} }
 @article{yin_jensen_bai_debroy_barrangou_dudley_2013, title={The Evolutionary Divergence of Shiga Toxin-Producing Escherichia coli Is Reflected in Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Spacer Composition}, volume={79}, DOI={10.1128/aem.00950-13}, abstractNote={ABSTRACT}, number={18}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Yin, S. and Jensen, M. A. and Bai, J. and DebRoy, C. and Barrangou, R. and Dudley, E. G.}, year={2013}, month={Jul}, pages={5710–5720} }
 @article{levin_moineau_bushman_barrangou_2013, title={The Population and Evolutionary Dynamics of Phage and Bacteria with CRISPR–Mediated Immunity}, volume={9}, DOI={10.1371/journal.pgen.1003312}, abstractNote={Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), together with associated genes (cas), form the CRISPR–cas adaptive immune system, which can provide resistance to viruses and plasmids in bacteria and archaea. Here, we use mathematical models, population dynamic experiments, and DNA sequence analyses to investigate the host–phage interactions in a model CRISPR–cas system, Streptococcus thermophilus DGCC7710 and its virulent phage 2972. At the molecular level, the bacteriophage-immune mutant bacteria (BIMs) and CRISPR–escape mutant phage (CEMs) obtained in this study are consistent with those anticipated from an iterative model of this adaptive immune system: resistance by the addition of novel spacers and phage evasion of resistance by mutation in matching sequences or flanking motifs. While CRISPR BIMs were readily isolated and CEMs generated at high rates (frequencies in excess of 10−6), our population studies indicate that there is more to the dynamics of phage–host interactions and the establishment of a BIM–CEM arms race than predicted from existing assumptions about phage infection and CRISPR–cas immunity. Among the unanticipated observations are: (i) the invasion of phage into populations of BIMs resistant by the acquisition of one (but not two) spacers, (ii) the survival of sensitive bacteria despite the presence of high densities of phage, and (iii) the maintenance of phage-limited communities due to the failure of even two-spacer BIMs to become established in populations with wild-type bacteria and phage. We attribute (i) to incomplete resistance of single-spacer BIMs. Based on the results of additional modeling and experiments, we postulate that (ii) and (iii) can be attributed to the phage infection-associated production of enzymes or other compounds that induce phenotypic phage resistance in sensitive bacteria and kill resistant BIMs. We present evidence in support of these hypotheses and discuss the implications of these results for the ecology and (co)evolution of bacteria and phage.}, number={3}, journal={PLoS Genetics}, publisher={Public Library of Science (PLoS)}, author={Levin, Bruce R. and Moineau, Sylvain and Bushman, Mary and Barrangou, Rodolphe}, editor={Hughes, DiarmaidEditor}, year={2013}, month={Mar}, pages={e1003312} }
 @article{shariat_dimarzio_yin_dettinger_sandt_lute_barrangou_dudley_2013, title={The combination of CRISPR-MVLST and PFGE provides increased discriminatory power for differentiating human clinical isolates of Salmonella enterica subsp. enterica serovar Enteritidis}, volume={34}, DOI={10.1016/j.fm.2012.11.012}, abstractNote={Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) is a major cause of foodborne salmonellosis. Rapid, efficient and accurate methods for identification are required to track specific strains of S. Enteritidis during outbreaks of human salmonellosis. By exploiting the hypervariable nature of virulence genes and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs), we previously developed a powerful sequence-based subtyping approach, designated CRISPR-MVLST. To substantiate the applicability of CRISPR-MVLST, we analyzed a broad set of S. Enteritidis isolates collected over a six-year period. Among 141 isolates we defined 22 Enteritidis Sequence Types (ESTs), the majority of which were novel. Notably, strains exhibiting the common PFGE pattern, JEGX01.0004 (characteristic of ∼40% of S. Enteritidis isolates in the United States), were separated into twelve distinct sequence types. Conversely, isolates of EST4, the most predominant EST we observed, comprised eight different PFGE patterns. Importantly, we showed that some genotypes that were previously associated with the food supply chain at the farm level have now been identified in clinical samples. CRISPR sequence data shows subtle but distinct differences among different alleles of S. Enteritidis, suggesting that evolution of these loci occurs vertically, as opposed to previously reported evolution by spacer acquisition in other bacteria.}, number={1}, journal={Food Microbiology}, publisher={Elsevier BV}, author={Shariat, Nikki and DiMarzio, Michael J. and Yin, Shuang and Dettinger, Lisa and Sandt, Carol H. and Lute, James R. and Barrangou, Rodolphe and Dudley, Edward G.}, year={2013}, month={May}, pages={164–173} }
 @article{andersen_barrangou_abou hachem_lahtinen_goh_svensson_klaenhammer_2013, title={Transcriptional analysis of oligosaccharide utilization by Bifidobacterium lactis Bl-04}, volume={14}, ISSN={["1471-2164"]}, DOI={10.1186/1471-2164-14-312}, abstractNote={Abstract}, number={1}, journal={BMC GENOMICS}, publisher={Springer Nature}, author={Andersen, Joakim M. and Barrangou, Rodolphe and Abou Hachem, Maher and Lahtinen, Sampo J. and Goh, Yong Jun and Svensson, Birte and Klaenhammer, Todd R.}, year={2013}, month={May} }
 @article{karvelis_gasiunas_miksys_barrangou_horvath_siksnys_2013, title={crRNA and tracrRNA guide Cas9-mediated DNA interference in Streptococcus thermophilus}, volume={10}, ISSN={["1555-8584"]}, DOI={10.4161/rna.24203}, abstractNote={The Cas9-crRNA complex of the Streptococcus thermophilus DGCC7710 CRISPR3-Cas system functions as an RNA-guided endonuclease with crRNA-directed target sequence recognition and protein-mediated DNA cleavage. We show here that an additional RNA molecule, tracrRNA (trans-activating CRISPR RNA), co-purifies with the Cas9 protein isolated from the heterologous E. coli strain carrying the S. thermophilus DGCC7710 CRISPR3-Cas system. We provide experimental evidence that tracrRNA is required for Cas9-mediated DNA interference both in vitro and in vivo. We show that Cas9 specifically promotes duplex formation between the precursor crRNA (pre-crRNA) transcript and tracrRNA, in vitro. Furthermore, the housekeeping RNase III contributes to primary pre-crRNA-tracrRNA duplex cleavage for mature crRNA biogenesis. RNase III, however, is not required in the processing of a short pre-crRNA transcribed from a minimal CRISPR array containing a single spacer. Finally, we show that an in vitro-assembled ternary Cas9-crRNA-tracrRNA complex cleaves DNA. This study further specifies the molecular basis for crRNA-based re-programming of Cas9 to specifically cleave any target DNA sequence for precise genome surgery. The processes for crRNA maturation and effector complex assembly established here will contribute to the further development of the Cas9 re-programmable system for genome editing applications.}, number={5}, journal={RNA BIOLOGY}, publisher={Informa UK Limited}, author={Karvelis, Tautvydas and Gasiunas, Giedrius and Miksys, Algirdas and Barrangou, Rodolphe and Horvath, Philippe and Siksnys, Virginijus}, year={2013}, month={May}, pages={841–851} }
 @article{broadbent_neeno-eckwall_stahl_tandee_cai_morovic_horvath_heidenreich_perna_barrangou_et al._2012, title={Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation}, volume={13}, DOI={10.1186/1471-2164-13-533}, abstractNote={The broad ecological distribution of L. casei makes it an insightful subject for research on genome evolution and lifestyle adaptation. To explore evolutionary mechanisms that determine genomic diversity of L. casei, we performed comparative analysis of 17 L. casei genomes representing strains collected from dairy, plant, and human sources.Differences in L. casei genome inventory revealed an open pan-genome comprised of 1,715 core and 4,220 accessory genes. Extrapolation of pan-genome data indicates L. casei has a supragenome approximately 3.2 times larger than the average genome of individual strains. Evidence suggests horizontal gene transfer from other bacterial species, particularly lactobacilli, has been important in adaptation of L. casei to new habitats and lifestyles, but evolution of dairy niche specialists also appears to involve gene decay.Genome diversity in L. casei has evolved through gene acquisition and decay. Acquisition of foreign genomic islands likely confers a fitness benefit in specific habitats, notably plant-associated niches. Loss of unnecessary ancestral traits in strains collected from bacterial-ripened cheeses supports the hypothesis that gene decay contributes to enhanced fitness in that niche. This study gives the first evidence for a L. casei supragenome and provides valuable insights into mechanisms for genome evolution and lifestyle adaptation of this ecologically flexible and industrially important lactic acid bacterium. Additionally, our data confirm the Distributed Genome Hypothesis extends to non-pathogenic, ecologically flexible species like L. casei.}, number={1}, journal={BMC Genomics}, publisher={Springer Nature}, author={Broadbent, Jeff R and Neeno-Eckwall, Eric C and Stahl, Buffy and Tandee, Kanokwan and Cai, Hui and Morovic, Wesley and Horvath, Philippe and Heidenreich, Jessie and Perna, Nicole T and Barrangou, Rodolphe and et al.}, year={2012}, pages={533} }
 @article{horvath_gasiunas_siksnys_barrangou_2012, title={Applications of the Versatile CRISPR-Cas Systems}, DOI={10.1007/978-3-662-45794-8_11}, journal={CRISPR-Cas Systems}, publisher={Springer Berlin Heidelberg}, author={Horvath, Philippe and Gasiunas, Giedrius and Siksnys, Virginijus and Barrangou, Rodolphe}, year={2012}, pages={267–286} }
 @article{horvath_gasiunas_siksnys_barrangou_2012, title={Applications of the Versatile CRISPR-Cas Systems}, DOI={10.1007/978-3-642-34657-6_11}, journal={CRISPR-Cas Systems}, publisher={Springer Berlin Heidelberg}, author={Horvath, Philippe and Gasiunas, Giedrius and Siksnys, Virginijus and Barrangou, Rodolphe}, year={2012}, pages={267–286} }
 @article{barrangou_horvath_2012, title={CRISPR: New Horizons in Phage Resistance and Strain Identification}, volume={3}, DOI={10.1146/annurev-food-022811-101134}, abstractNote={ Bacteria have been widely used as starter cultures in the food industry, notably for the fermentation of milk into dairy products such as cheese and yogurt. Lactic acid bacteria used in food manufacturing, such as lactobacilli, lactococci, streptococci, Leuconostoc, pediococci, and bifidobacteria, are selectively formulated based on functional characteristics that provide idiosyncratic flavor and texture attributes, as well as their ability to withstand processing and manufacturing conditions. Unfortunately, given frequent viral exposure in industrial environments, starter culture selection and development rely on defense systems that provide resistance against bacteriophage predation, including restriction-modification, abortive infection, and recently discovered CRISPRs (clustered regularly interspaced short palindromic repeats). CRISPRs, together with CRISPR-associated genes (cas), form the CRISPR/Cas immune system, which provides adaptive immunity against phages and invasive genetic elements. The immunization process is based on the incorporation of short DNA sequences from virulent phages into the CRISPR locus. Subsequently, CRISPR transcripts are processed into small interfering RNAs that guide a multifunctional protein complex to recognize and cleave matching foreign DNA. Hypervariable CRISPR loci provide insights into the phage and host population dynamics, and new avenues for enhanced phage resistance and genetic typing and tagging of industrial strains. }, number={1}, journal={Annual Review of Food Science and Technology}, publisher={Annual Reviews}, author={Barrangou, Rodolphe and Horvath, Philippe}, year={2012}, month={Apr}, pages={143–162} }
 @article{gasiunas_barrangou_horvath_siksnys_2012, title={Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria}, volume={109}, DOI={10.1073/pnas.1208507109}, abstractNote={
            Clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide adaptive immunity against viruses and plasmids in bacteria and archaea. The silencing of invading nucleic acids is executed by ribonucleoprotein complexes preloaded with small, interfering CRISPR RNAs (crRNAs) that act as guides for targeting and degradation of foreign nucleic acid. Here, we demonstrate that the Cas9–crRNA complex of the
            Streptococcus thermophilus
            CRISPR3/Cas system introduces in vitro a double-strand break at a specific site in DNA containing a sequence complementary to crRNA. DNA cleavage is executed by Cas9, which uses two distinct active sites, RuvC and HNH, to generate site-specific nicks on opposite DNA strands. Results demonstrate that the Cas9–crRNA complex functions as an RNA-guided endonuclease with RNA-directed target sequence recognition and protein-mediated DNA cleavage. These findings pave the way for engineering of universal programmable RNA-guided DNA endonucleases.
          }, number={39}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Gasiunas, G. and Barrangou, R. and Horvath, P. and Siksnys, V.}, year={2012}, month={Sep}, pages={E2579–E2586} }
 @article{stahl_barrangou_2012, title={Complete Genome Sequences of Probiotic Strains Bifidobacterium animalis subsp. lactis B420 and Bi-07}, volume={194}, DOI={10.1128/jb.00766-12}, abstractNote={ABSTRACT}, number={15}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Stahl, B. and Barrangou, R.}, year={2012}, month={Jul}, pages={4131–4132} }
 @article{weinberger_sun_pluciński_denef_thomas_horvath_barrangou_gilmore_getz_banfield_2012, title={Persisting Viral Sequences Shape Microbial CRISPR-based Immunity}, volume={8}, DOI={10.1371/journal.pcbi.1002475}, abstractNote={Well-studied innate immune systems exist throughout bacteria and archaea, but a more recently discovered genomic locus may offer prokaryotes surprising immunological adaptability. Mediated by a cassette-like genomic locus termed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), the microbial adaptive immune system differs from its eukaryotic immune analogues by incorporating new immunities unidirectionally. CRISPR thus stores genomically recoverable timelines of virus-host coevolution in natural organisms refractory to laboratory cultivation. Here we combined a population genetic mathematical model of CRISPR-virus coevolution with six years of metagenomic sequencing to link the recoverable genomic dynamics of CRISPR loci to the unknown population dynamics of virus and host in natural communities. Metagenomic reconstructions in an acid-mine drainage system document CRISPR loci conserving ancestral immune elements to the base-pair across thousands of microbial generations. This ‘trailer-end conservation’ occurs despite rapid viral mutation and despite rapid prokaryotic genomic deletion. The trailer-ends of many reconstructed CRISPR loci are also largely identical across a population. ‘Trailer-end clonality’ occurs despite predictions of host immunological diversity due to negative frequency dependent selection (kill the winner dynamics). Statistical clustering and model simulations explain this lack of diversity by capturing rapid selective sweeps by highly immune CRISPR lineages. Potentially explaining ‘trailer-end conservation,’ we record the first example of a viral bloom overwhelming a CRISPR system. The polyclonal viruses bloom even though they share sequences previously targeted by host CRISPR loci. Simulations show how increasing random genomic deletions in CRISPR loci purges immunological controls on long-lived viral sequences, allowing polyclonal viruses to bloom and depressing host fitness. Our results thus link documented patterns of genomic conservation in CRISPR loci to an evolutionary advantage against persistent viruses. By maintaining old immunities, selection may be tuning CRISPR-mediated immunity against viruses reemerging from lysogeny or migration.}, number={4}, journal={PLoS Computational Biology}, publisher={Public Library of Science (PLoS)}, author={Weinberger, Ariel D. and Sun, Christine L. and Pluciński, Mateusz M. and Denef, Vincent J. and Thomas, Brian C. and Horvath, Philippe and Barrangou, Rodolphe and Gilmore, Michael S. and Getz, Wayne M. and Banfield, Jillian F.}, editor={Mering, ChristianEditor}, year={2012}, month={Apr}, pages={e1002475} }
 @article{sun_barrangou_thomas_horvath_fremaux_banfield_2012, title={Phage mutations in response to CRISPR diversification in a bacterial population}, volume={15}, DOI={10.1111/j.1462-2920.2012.02879.x}, abstractNote={Summary}, number={2}, journal={Environmental Microbiology}, publisher={Wiley-Blackwell}, author={Sun, Christine L. and Barrangou, Rodolphe and Thomas, Brian C. and Horvath, Philippe and Fremaux, Christophe and Banfield, Jillian F.}, year={2012}, month={Oct}, pages={463–470} }
 @article{young_dill_pan_hettich_banfield_shah_fremaux_horvath_barrangou_verberkmoes_2012, title={Phage-Induced Expression of CRISPR-Associated Proteins Is Revealed by Shotgun Proteomics in Streptococcus thermophilus}, volume={7}, DOI={10.1371/journal.pone.0038077}, abstractNote={The CRISPR/Cas system, comprised of clustered regularly interspaced short palindromic repeats along with their associated (Cas) proteins, protects bacteria and archaea from viral predation and invading nucleic acids. While the mechanism of action for this acquired immunity is currently under investigation, the response of Cas protein expression to phage infection has yet to be elucidated. In this study, we employed shotgun proteomics to measure the global proteome expression in a model system for studying the CRISPR/Cas response in S. thermophilus DGCC7710 infected with phage 2972. Host and viral proteins were simultaneously measured following inoculation at two different multiplicities of infection and across various time points using two-dimensional liquid chromatography tandem mass spectrometry. Thirty-seven out of forty predicted viral proteins were detected, including all proteins of the structural virome and viral effector proteins. In total, 1,013 of 2,079 predicted S. thermophilus proteins were detected, facilitating the monitoring of host protein synthesis changes in response to virus infection. Importantly, Cas proteins from all four CRISPR loci in the S. thermophilus DGCC7710 genome were detected, including loci previously thought to be inactive. Many Cas proteins were found to be constitutively expressed, but several demonstrated increased abundance following infection, including the signature Cas9 proteins from the CRISPR1 and CRISPR3 loci, which are key players in the interference phase of the CRISPR/Cas response. Altogether, these results provide novel insights into the proteomic response of S. thermophilus, specifically CRISPR-associated proteins, upon phage 2972 infection.}, number={5}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Young, Jacque C. and Dill, Brian D. and Pan, Chongle and Hettich, Robert L. and Banfield, Jillian F. and Shah, Manesh and Fremaux, Christophe and Horvath, Philippe and Barrangou, Rodolphe and VerBerkmoes, Nathan C.}, editor={Bruggemann, HolgerEditor}, year={2012}, month={May}, pages={e38077} }
 @article{barrangou_2012, title={RNA-mediated programmable DNA cleavage}, volume={30}, DOI={10.1038/nbt.2357}, number={9}, journal={Nature Biotechnology}, publisher={Springer Nature}, author={Barrangou, Rodolphe}, year={2012}, month={Sep}, pages={836–838} }
 @article{andersen_barrangou_abou hachem_lahtinen_goh_svensson_klaenhammer_2012, title={Transcriptional Analysis of Prebiotic Uptake and Catabolism by Lactobacillus acidophilus NCFM}, volume={7}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0044409}, abstractNote={The human gastrointestinal tract can be positively modulated by dietary supplementation of probiotic bacteria in combination with prebiotic carbohydrates. Here differential transcriptomics and functional genomics were used to identify genes in Lactobacillus acidophilus NCFM involved in the uptake and catabolism of 11 potential prebiotic compounds consisting of α- and β- linked galactosides and glucosides. These oligosaccharides induced genes encoding phosphoenolpyruvate-dependent sugar phosphotransferase systems (PTS), galactoside pentose hexuronide (GPH) permease, and ATP-binding cassette (ABC) transporters. PTS systems were upregulated primarily by di- and tri-saccharides such as cellobiose, isomaltose, isomaltulose, panose and gentiobiose, while ABC transporters were upregulated by raffinose, Polydextrose, and stachyose. A single GPH transporter was induced by lactitol and galactooligosaccharides (GOS). The various transporters were associated with a number of glycoside hydrolases from families 1, 2, 4, 13, 32, 36, 42, and 65, involved in the catabolism of various α- and β-linked glucosides and galactosides. Further subfamily specialization was also observed for different PTS-associated GH1 6-phospho-β-glucosidases implicated in the catabolism of gentiobiose and cellobiose. These findings highlight the broad oligosaccharide metabolic repertoire of L. acidophilus NCFM and establish a platform for selection and screening of both probiotic bacteria and prebiotic compounds that may positively influence the gastrointestinal microbiota.}, number={9}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Andersen, Joakim Mark and Barrangou, Rodolphe and Abou Hachem, Maher and Lahtinen, Sampo J. and Goh, Yong-Jun and Svensson, Birte and Klaenhammer, Todd R.}, editor={Gibas, CynthiaEditor}, year={2012}, month={Sep} }
 @article{bhaya_davison_barrangou_2011, title={CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation}, volume={45}, DOI={10.1146/annurev-genet-110410-132430}, abstractNote={Bacteria and archaea have evolved defense and regulatory mechanisms to cope with various environmental stressors, including virus attack. This arsenal has been expanded by the recent discovery of the versatile CRISPR-Cas system, which has two novel features. First, the host can specifically incorporate short sequences from invading genetic elements (virus or plasmid) into a region of its genome that is distinguished by clustered regularly interspaced short palindromic repeats (CRISPRs). Second, when these sequences are transcribed and precisely processed into small RNAs, they guide a multifunctional protein complex (Cas proteins) to recognize and cleave incoming foreign genetic material. This adaptive immunity system, which uses a library of small noncoding RNAs as a potent weapon against fast-evolving viruses, is also used as a regulatory system by the host. Exciting breakthroughs in understanding the mechanisms of the CRISPR-Cas system and its potential for biotechnological applications and understanding evolutionary dynamics are discussed.}, number={1}, journal={Annual Review of Genetics}, publisher={Annual Reviews}, author={Bhaya, Devaki and Davison, Michelle and Barrangou, Rodolphe}, year={2011}, pages={273–297} }
 @article{sinkunas_gasiunas_fremaux_barrangou_horvath_siksnys_2011, title={Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system}, volume={30}, DOI={10.1038/emboj.2011.41}, abstractNote={Clustered regularly interspaced short palindromic repeat (CRISPR) is a recently discovered adaptive prokaryotic immune system that provides acquired immunity against foreign nucleic acids by utilizing small guide crRNAs (CRISPR RNAs) to interfere with invading viruses and plasmids. In Escherichia coli, Cas3 is essential for crRNA-guided interference with virus proliferation. Cas3 contains N-terminal HD phosphohydrolase and C-terminal Superfamily 2 (SF2) helicase domains. Here, we provide the first report of the cloning, expression, purification and in vitro functional analysis of the Cas3 protein of the Streptococcus thermophilus CRISPR4 (Ecoli subtype) system. Cas3 possesses a single-stranded DNA (ssDNA)-stimulated ATPase activity, which is coupled to unwinding of DNA/DNA and RNA/DNA duplexes. Cas3 also shows ATP-independent nuclease activity located in the HD domain with a preference for ssDNA substrates. To dissect the contribution of individual domains, Cas3 separation-of-function mutants (ATPase(+)/nuclease(-) and ATPase(-)/nuclease(+)) were obtained by site-directed mutagenesis. We propose that the Cas3 ATPase/helicase domain acts as a motor protein, which assists delivery of the nuclease activity to Cascade-crRNA complex targeting foreign DNA.}, number={7}, journal={The EMBO Journal}, publisher={Wiley-Blackwell}, author={Sinkunas, Tomas and Gasiunas, Giedrius and Fremaux, Christophe and Barrangou, Rodolphe and Horvath, Philippe and Siksnys, Virginijus}, year={2011}, month={Feb}, pages={1335–1342} }
 @article{makarova_haft_barrangou_brouns_charpentier_horvath_moineau_mojica_wolf_yakunin_et al._2011, title={Evolution and classification of the CRISPR–Cas systems}, volume={9}, DOI={10.1038/nrmicro2577}, abstractNote={The CRISPR–Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins) systems are immunity systems that are present in many bacteria and archaea. Here, Koonin and colleagues present a new classification of these systems and introduce a new nomenclature of the genes in the CRISPR–casloci that better reflects the relationships between the proteins. The CRISPR–Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins) modules are adaptive immunity systems that are present in many archaea and bacteria. These defence systems are encoded by operons that have an extraordinarily diverse architecture and a high rate of evolution for both the cas genes and the unique spacer content. Here, we provide an updated analysis of the evolutionary relationships between CRISPR–Cas systems and Cas proteins. Three major types of CRISPR–Cas system are delineated, with a further division into several subtypes and a few chimeric variants. Given the complexity of the genomic architectures and the extremely dynamic evolution of the CRISPR–Cas systems, a unified classification of these systems should be based on multiple criteria. Accordingly, we propose a 'polythetic' classification that integrates the phylogenies of the most common cas genes, the sequence and organization of the CRISPR repeats and the architecture of the CRISPR–cas loci.}, number={6}, journal={Nature Reviews Microbiology}, publisher={Springer Nature}, author={Makarova, Kira S. and Haft, Daniel H. and Barrangou, Rodolphe and Brouns, Stan J. J. and Charpentier, Emmanuelle and Horvath, Philippe and Moineau, Sylvain and Mojica, Francisco J. M. and Wolf, Yuri I. and Yakunin, Alexander F. and et al.}, year={2011}, month={May}, pages={467–477} }
 @article{barrangou_lahtinen_ibrahim_ouwehand_2011, title={Genus Lactobacillus}, DOI={10.1201/b11503-6}, journal={Lactic Acid Bacteria}, publisher={CRC Press}, author={Barrangou, Rodolphe and Lahtinen, Sampo and Ibrahim, Fandi and Ouwehand, Arthur}, year={2011}, pages={77–91} }
 @article{barrangou_horvath_2011, title={Lactic Acid Bacteria Defenses Against Phages}, DOI={10.1007/978-0-387-92771-8_19}, journal={Stress Responses of Lactic Acid Bacteria}, publisher={Springer US}, author={Barrangou, Rodolphe and Horvath, Philippe}, year={2011}, pages={459–478} }
 @article{liu_barrangou_gerner-smidt_ribot_knabel_dudley_2011, title={Novel Virulence Gene and Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Multilocus Sequence Typing Scheme for Subtyping of the Major Serovars of Salmonella enterica subsp. enterica}, volume={77}, DOI={10.1128/aem.02625-10}, abstractNote={ABSTRACT}, number={6}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Liu, F. and Barrangou, R. and Gerner-Smidt, P. and Ribot, E. M. and Knabel, S. J. and Dudley, E. G.}, year={2011}, month={Jan}, pages={1946–1956} }
 @article{loquasto_barrangou_dudley_roberts_2011, title={Short communication: The complete genome sequence of Bifidobacterium animalis subspecies animalis ATCC 25527T and comparative analysis of growth in milk with B. animalis subspecies lactis DSM 10140T}, volume={94}, DOI={10.3168/jds.2011-4499}, abstractNote={The objective of this work was to sequence the genome of Bifidobacterium animalis ssp. animalis ATCC 25527(T), the subspecies most closely related to B. animalis ssp. lactis, some strains of which are widely added to dairy foods as probiotics. The complete 1,932,963-bp genome was determined by a combination of 454-shotgun sequencing and PCR gap closing, and the completed assembly was verified by comparison with a KpnI optical map. Comparative analysis of the B. animalis ssp. animalis ATCC 25527(T) and B. animalis ssp. lactis DSM 10140(T) genomes revealed high degrees of synteny and sequence homology. Comparative genomic analysis revealed 156 and 182 genes that were unique to and absent in the B. animalis ssp. animalis genome, respectively. Among these was a set of unique clustered regularly interspaced short palindromic repeats (CRISPR)-associated genes and a novel CRISPR locus containing 30 spacers in the genome of B. animalis ssp. animalis. Although previous researchers have suggested that one of the defining phenotypic differences between B. animalis ssp. animalis and B. animalis ssp. lactis is the ability of the latter to grow in milk and milk-based media, the differential gene content did not provide insights to explain these differences. Furthermore, growth and acid production in milk and milk-based media did not differ significantly between B. animalis ssp. lactis (DSM 10140(T) and Bl04) and B. animalis ssp. animalis (ATCC 25527(T)). Growth of these strains in supplemented milk suggested that growth was limited by a lack of available low-molecular-weight nitrogen in the 3 strains examined.}, number={12}, journal={Journal of Dairy Science}, publisher={American Dairy Science Association}, author={Loquasto, J.R. and Barrangou, R. and Dudley, E.G. and Roberts, R.F.}, year={2011}, pages={5864–5870} }
 @article{liu_kariyawasam_jayarao_barrangou_gerner-smidt_ribot_knabel_dudley_2011, title={Subtyping Salmonella enterica Serovar Enteritidis Isolates from Different Sources by Using Sequence Typing Based on Virulence Genes and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)}, volume={77}, DOI={10.1128/aem.00468-11}, abstractNote={ABSTRACT}, number={13}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Liu, F. and Kariyawasam, S. and Jayarao, B. M. and Barrangou, R. and Gerner-Smidt, P. and Ribot, E. M. and Knabel, S. J. and Dudley, E. G.}, year={2011}, month={May}, pages={4520–4526} }
 @article{sapranauskas_gasiunas_fremaux_barrangou_horvath_siksnys_2011, title={The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli}, volume={39}, DOI={10.1093/nar/gkr606}, abstractNote={The CRISPR/Cas adaptive immune system provides resistance against phages and plasmids in Archaea and Bacteria. CRISPR loci integrate short DNA sequences from invading genetic elements that provide small RNA-mediated interference in subsequent exposure to matching nucleic acids. In Streptococcus thermophilus, it was previously shown that the CRISPR1/Cas system can provide adaptive immunity against phages and plasmids by integrating novel spacers following exposure to these foreign genetic elements that subsequently direct the specific cleavage of invasive homologous DNA sequences. Here, we show that the S. thermophilus CRISPR3/Cas system can be transferred into Escherichia coli and provide heterologous protection against plasmid transformation and phage infection. We show that interference is sequence-specific, and that mutations in the vicinity or within the proto-spacer adjacent motif (PAM) allow plasmids to escape CRISPR-encoded immunity. We also establish that cas9 is the sole cas gene necessary for CRISPR-encoded interference. Furthermore, mutation analysis revealed that interference relies on the Cas9 McrA/HNH- and RuvC/RNaseH-motifs. Altogether, our results show that active CRISPR/Cas systems can be transferred across distant genera and provide heterologous interference against invasive nucleic acids. This can be leveraged to develop strains more robust against phage attack, and safer organisms less likely to uptake and disseminate plasmid-encoded undesirable genetic elements.}, number={21}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={Sapranauskas, Rimantas and Gasiunas, Giedrius and Fremaux, Christophe and Barrangou, Rodolphe and Horvath, Philippe and Siksnys, Virginijus}, year={2011}, month={Aug}, pages={9275–9282} }
 @article{andersen_barrangou_abou hachem_lahtinen_goh_svensson_klaenhammer_2011, title={Transcriptional and functional analysis of galactooligosaccharide uptake by lacS in Lactobacillus acidophilus}, volume={108}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1114152108}, abstractNote={Probiotic microbes rely on their ability to survive in the gastrointestinal tract, adhere to mucosal surfaces, and metabolize available energy sources from dietary compounds, including prebiotics. Genome sequencing projects have proposed models for understanding prebiotic catabolism, but mechanisms remain to be elucidated for many prebiotic substrates. Although β-galactooligosaccharides (GOS) are documented prebiotic compounds, little is known about their utilization by lactobacilli. This study aimed to identify genetic loci inLactobacillus acidophilusNCFM responsible for the transport and catabolism of GOS. Whole-genome oligonucleotide microarrays were used to survey the differential global transcriptome during logarithmic growth ofL. acidophilusNCFM using GOS or glucose as a sole source of carbohydrate. Within the 16.6-kbpgal-lacgene cluster,lacS, a galactoside-pentose-hexuronide permease-encoding gene, was up-regulated 5.1-fold in the presence of GOS. In addition, two β-galactosidases, LacA and LacLM, and enzymes in the Leloir pathway were also encoded by genes within this locus and up-regulated by GOS stimulation. Generation of alacS-deficient mutant enabled phenotypic confirmation of the functional LacS permease not only for the utilization of lactose and GOS but also lactitol, suggesting a prominent role of LacS in the metabolism of a broad range of prebiotic β-galactosides, known to selectively modulate the beneficial gut microbiota.}, number={43}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Andersen, Joakim M. and Barrangou, Rodolphe and Abou Hachem, Maher and Lahtinen, Sampo and Goh, Yong Jun and Svensson, Birte and Klaenhammer, Todd R.}, year={2011}, month={Oct}, pages={17785–17790} }
 @article{putaala_barrangou_leyer_ouwehand_hansen_romero_rautonen_2010, title={Analysis of the human intestinal epithelial cell transcriptional response toLactobacillus acidophilus, Lactobacillus salivarius, Bifidobacterium lactisandEscherichia coli}, volume={1}, DOI={10.3920/bm2010.0003}, abstractNote={The complex microbial population residing in the human gastrointestinal tract consists of commensal, potential pathogenic and beneficial species, which are probably perceived differently by the host and consequently could be expected to trigger specific transcriptional responses. Here, we provide a comparative analysis of the global in vitro transcriptional response of human intestinal epithelial cells to Lactobacillus acidophilus NCFM™, Lactobacillus salivarius Ls-33, Bifidobacterium animalis subsp. lactis 420, and enterohaemorrhagic Escherichia coli O157:H7 (EHEC). Interestingly, L. salivarius Ls-33 DCE-induced changes were overall more similar to those of B. lactis 420 than to L. acidophilus NCFM™, which is consistent with previously observed in vivo immunomodulation properties. In the gene ontology and pathway analyses both specific and unspecific changes were observed. Common to all was the regulation of apoptosis and adipogenesis, and lipid-metabolism related regulation by the probiotics. Specific changes such as regulation of cell-cell adhesion by B. lactis 420, superoxide metabolism by L. salivarius Ls-33, and regulation of MAPK pathway by L. acidophilus NCFM™ were noted. Furthermore, fundamental differences were observed between the pathogenic and probiotic treatments in the Toll-like receptor pathway, especially for adapter molecules with a lowered level of transcriptional activation of MyD88, TRIF, IRAK1 and TRAF6 by probiotics compared to EHEC. The results in this study provide insights into the relationship between probiotics and human intestinal epithelial cells, notably with regard to strain-specific responses, and highlight the differences between transcriptional responses to pathogenic and probiotic bacteria.}, number={3}, journal={Beneficial Microbes}, publisher={Wageningen Academic Publishers}, author={Putaala, H. and Barrangou, R. and Leyer, G. and Ouwehand, A. and Hansen, E. Bech and Romero, D. and Rautonen, N.}, year={2010}, month={Sep}, pages={283–295} }
 @article{horvath_barrangou_2010, title={CRISPR/Cas, the Immune System of Bacteria and Archaea}, volume={327}, DOI={10.1126/science.1179555}, abstractNote={CRISPR Defenses}, number={5962}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Horvath, P. and Barrangou, R.}, year={2010}, month={Jan}, pages={167–170} }
 @article{duong_miller_barrangou_azcarate-peril_klaenhammer_2010, title={Construction of vectors for inducible and constitutive gene expression in Lactobacillus}, volume={4}, DOI={10.1111/j.1751-7915.2010.00200.x}, abstractNote={Summary}, number={3}, journal={Microbial Biotechnology}, publisher={Wiley-Blackwell}, author={Duong, Tri and Miller, Michael J. and Barrangou, Rodolphe and Azcarate-Peril, M. Andrea and Klaenhammer, Todd R.}, year={2010}, month={Sep}, pages={357–367} }
 @article{garneau_dupuis_villion_romero_barrangou_boyaval_fremaux_horvath_magadán_moineau_2010, title={The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA}, volume={468}, DOI={10.1038/nature09523}, abstractNote={Bacteria and Archaea have developed several defence strategies against foreign nucleic acids such as viral genomes and plasmids. Among them, clustered regularly interspaced short palindromic repeats (CRISPR) loci together with cas (CRISPR-associated) genes form the CRISPR/Cas immune system, which involves partially palindromic repeats separated by short stretches of DNA called spacers, acquired from extrachromosomal elements. It was recently demonstrated that these variable loci can incorporate spacers from infecting bacteriophages and then provide immunity against subsequent bacteriophage infections in a sequence-specific manner. Here we show that the Streptococcus thermophilus CRISPR1/Cas system can also naturally acquire spacers from a self-replicating plasmid containing an antibiotic-resistance gene, leading to plasmid loss. Acquired spacers that match antibiotic-resistance genes provide a novel means to naturally select bacteria that cannot uptake and disseminate such genes. We also provide in vivo evidence that the CRISPR1/Cas system specifically cleaves plasmid and bacteriophage double-stranded DNA within the proto-spacer, at specific sites. Our data show that the CRISPR/Cas immune system is remarkably adapted to cleave invading DNA rapidly and has the potential for exploitation to generate safer microbial strains.}, number={7320}, journal={Nature}, publisher={Springer Nature}, author={Garneau, Josiane E. and Dupuis, Marie-Ève and Villion, Manuela and Romero, Dennis A. and Barrangou, Rodolphe and Boyaval, Patrick and Fremaux, Christophe and Horvath, Philippe and Magadán, Alfonso H. and Moineau, Sylvain}, year={2010}, month={Nov}, pages={67–71} }
 @article{ventura_turroni_lima-mendez_foroni_zomer_duranti_giubellini_bottacini_horvath_barrangou_et al._2009, title={Comparative Analyses of Prophage-Like Elements Present in Bifidobacterial Genomes}, volume={75}, DOI={10.1128/aem.01112-09}, abstractNote={ABSTRACT}, number={21}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Ventura, M. and Turroni, F. and Lima-Mendez, G. and Foroni, E. and Zomer, A. and Duranti, S. and Giubellini, V. and Bottacini, F. and Horvath, P. and Barrangou, R. and et al.}, year={2009}, month={Sep}, pages={6929–6936} }
 @article{horvath_coûté-monvoisin_romero_boyaval_fremaux_barrangou_2009, title={Comparative analysis of CRISPR loci in lactic acid bacteria genomes}, volume={131}, DOI={10.1016/j.ijfoodmicro.2008.05.030}, abstractNote={Clustered regularly interspaced short palindromic repeats (CRISPR) are hypervariable loci widely distributed in bacteria and archaea, that provide acquired immunity against foreign genetic elements. Here, we investigate the occurrence of CRISPR loci in the genomes of lactic acid bacteria (LAB), including members of the Firmicutes and Actinobacteria phyla. A total of 102 complete and draft genomes across 11 genera were studied and 66 CRISPR loci were identified in 26 species. We provide a comparative analysis of the CRISPR/cas content and diversity across LAB genera and species for 37 sets of CRISPR loci. We analyzed CRISPR repeats, CRISPR spacers, leader sequences, and cas gene content, sequences and architecture. Interestingly, multiple CRISPR families were identified within Bifidobacterium, Lactobacillus and Streptococcus, and similar CRISPR loci were found in distant organisms. Overall, eight distinct CRISPR families were identified consistently across CRISPR repeats, cas gene content and architecture, and sequences of the universal cas1 gene. Since the clustering of the CRISPR families does not correlate with the classical phylogenetic tree, we hypothesize that CRISPR loci have been subjected to horizontal gene transfer and further evolved independently in select lineages, in part due to selective pressure resulting from phage predation. Globally, we provide additional insights into the origin and evolution of CRISPR loci and discuss their contribution to microbial adaptation.}, number={1}, journal={International Journal of Food Microbiology}, publisher={Elsevier BV}, author={Horvath, Philippe and Coûté-Monvoisin, Anne-Claire and Romero, Dennis A. and Boyaval, Patrick and Fremaux, Christophe and Barrangou, Rodolphe}, year={2009}, month={Apr}, pages={62–70} }
 @article{barrangou_briczinski_traeger_loquasto_richards_horvath_coute-monvoisin_leyer_rendulic_steele_et al._2009, title={Comparison of the Complete Genome Sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04}, volume={191}, DOI={10.1128/jb.00155-09}, abstractNote={ABSTRACT}, number={13}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Barrangou, R. and Briczinski, E. P. and Traeger, L. L. and Loquasto, J. R. and Richards, M. and Horvath, P. and Coute-Monvoisin, A.-C. and Leyer, G. and Rendulic, S. and Steele, J. L. and et al.}, year={2009}, month={Apr}, pages={4144–4151} }
 @misc{barrangou_azcarate-peril_altermann_duong_klaenhammer_2009, title={Compositions comprising promoter sequences and methods of use}, volume={7,495,092}, number={2009 Feb. 24}, author={Barrangou, R. and Azcarate-Peril, A. and Altermann, E. and Duong, T. and Klaenhammer, T. R.}, year={2009} }
 @article{briczinski_loquasto_barrangou_dudley_roberts_roberts_2009, title={Strain-Specific Genotyping of Bifidobacterium animalis subsp. lactis by Using Single-Nucleotide Polymorphisms, Insertions, and Deletions}, volume={75}, DOI={10.1128/aem.01430-09}, abstractNote={ABSTRACT}, number={23}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Briczinski, E. P. and Loquasto, J. R. and Barrangou, R. and Dudley, E. G. and Roberts, A. M. and Roberts, R. F.}, year={2009}, month={Oct}, pages={7501–7508} }
 @article{barrangou_horvath_2009, title={The CRISPR System Protects Microbes against Phages, Plasmids}, volume={4}, DOI={10.1128/microbe.4.224.1}, abstractNote={Many scientists believe that phages are the most abundant life form on Earth. Although phages outnumber their bacterial prey 10-fold, bacteria persist, sometimes relying on clustered regularly interspaced short palindromic repeats (CRISPRs) of DNA sequence as a defense mechanism. CRISPRs, first recognized in Escherichia coli in 1987, are found within the genomes of about 40% of bacteria and 90% of archaea tested so far.}, number={5}, journal={Microbe Magazine}, publisher={American Society for Microbiology}, author={Barrangou, Rodolphe and Horvath, Philippe}, year={2009}, month={May}, pages={224–230} }
 @article{azcarate-peril_altermann_goh_tallon_sanozky-dawes_pfeiler_o'flaherty_buck_dobson_duong_et al._2008, title={Analysis of the genome sequence of Lactobacillus gasseri ATCC 33323 reveals the molecular basis of an autochthonous intestinal organism}, volume={74}, ISSN={["1098-5336"]}, DOI={10.1128/aem.00054-08}, abstractNote={ABSTRACT}, number={15}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, publisher={American Society for Microbiology}, author={Azcarate-Peril, M. Andrea and Altermann, Eric and Goh, Yong Jun and Tallon, Richard and Sanozky-Dawes, Rosemary B. and Pfeiler, Erika A. and O'Flaherty, Sarah and Buck, B. Logan and Dobson, Alleson and Duong, Tri and et al.}, year={2008}, month={Aug}, pages={4610–4625} }
 @article{klaenhammer_altermann_pfeiler_buck_goh_o'flaherty_barrangou_duong_2008, title={Functional genomics of probiotic Lactobacilli}, volume={42}, ISSN={["0192-0790"]}, DOI={10.1097/MCG.0b013e31817da140}, abstractNote={Lactic acid bacteria (LAB) have been used in fermentation processes for millennia. Recent applications such as the use of living cultures as probiotics have significantly increased industrial interest. Related bacterial strains can differ significantly in their genotype and phenotype, and features from one bacterial strain or species cannot necessarily be applied to a related one. These strain or family-specific differences often represent unique and applicable traits. Since 2002, the complete genomes of 13 probiotic LABs have been published. The presentation will discuss these genomes and highlight probiotic traits that are predicted, or functionally linked to genetic content. We have conducted a comparative genomic analysis of 4 completely sequenced Lactobacillus strains versus 25 lactic acid bacterial genomes present in the public database at thetime of analysis. Using Differential Blast Analysis, each genome is compared with 3 other Lactobacillus and 25 other LAB genomes. Differential Blast Analysis highlighted strain-specific genes that were not represented in any other LAB used in this analysis and also identified group-specific genes shared within lactobacilli. Lactobacillus-specific genes include mucus-binding proteins involved in cell-adhesion and several transport systems for carbohydrates and amino acids. Comparative genomic analysis has identified gene targets in Lactobacillus acidophilus for functional analysis, including adhesion to mucin and intestinal epithelial cells, acid tolerance, bile tolerance, and quorum sensing. Whole genome transcriptional profiling of L. acidophilus, and isogenic mutants thereof, has revealed the impact of varying conditions (pH, bile, carbohydrates) and food matrices on the expression of genes important to probiotic-linked mechanisms.}, number={8}, journal={JOURNAL OF CLINICAL GASTROENTEROLOGY}, publisher={Ovid Technologies (Wolters Kluwer Health)}, author={Klaenhammer, Todd R. and Altermann, Eric and Pfeiler, Erika and Buck, Brock Logan and Goh, Yong-Jun and O'Flaherty, Sarah and Barrangou, Rodolphe and Duong, Tri}, year={2008}, month={Sep}, pages={S160–S162} }
 @misc{klaenhammer_altermann_barrangou_russell_duong_2008, title={Lactobacillus acidophilus nucleic acid sequences encoding carbohydrate utilization-related proteins and uses therefor}, volume={7,459,289}, number={2008 Dec. 2}, author={Klaenhammer, T. R. and Altermann, E. and Barrangou, R. and Russell, W. M. and Duong, T.}, year={2008} }
 @article{barrangou_fremaux_deveau_richards_boyaval_moineau_romero_horvath_2007, title={CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes}, volume={315}, DOI={10.1126/science.1138140}, abstractNote={
            Clustered regularly interspaced short palindromic repeats (CRISPR) are a distinctive feature of the genomes of most Bacteria and Archaea and are thought to be involved in resistance to bacteriophages. We found that, after viral challenge, bacteria integrated new spacers derived from phage genomic sequences. Removal or addition of particular spacers modified the phage-resistance phenotype of the cell. Thus, CRISPR, together with associated
            cas
            genes, provided resistance against phages, and resistance specificity is determined by spacer-phage sequence similarity.
          }, number={5819}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Barrangou, R. and Fremaux, C. and Deveau, H. and Richards, M. and Boyaval, P. and Moineau, S. and Romero, D. A. and Horvath, P.}, year={2007}, month={Mar}, pages={1709–1712} }
 @article{horvath_romero_coute-monvoisin_richards_deveau_moineau_boyaval_fremaux_barrangou_2007, title={Diversity, Activity, and Evolution of CRISPR Loci in Streptococcus thermophilus}, volume={190}, DOI={10.1128/jb.01415-07}, abstractNote={ABSTRACT}, number={4}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Horvath, P. and Romero, D. A. and Coute-Monvoisin, A.-C. and Richards, M. and Deveau, H. and Moineau, S. and Boyaval, P. and Fremaux, C. and Barrangou, R.}, year={2007}, pages={1401–1412} }
 @article{klaenhammer_azcarate-peril_altermann_barrangou_2007, title={Influence of the dairy environment on gene expression and substrate(1-3)}, volume={137}, ISSN={["0022-3166"]}, DOI={10.1093/jn/137.3.748s}, abstractNote={Lactic acid bacteria (LAB) are widely used for the industrial production of fermented dairy products and form a group of related low-GC-content gram-positive bacteria. The major species used in dairy manufacturing are Lactobacillus, Lactococcus, Streptococcus, and Leuconostoc. Traditionally most are applied as starter cultures for dairy fermentations or used as probiotic cultures, delivered in dairy vehicles. The appearance of the genomes of Lactococcus lactis, Bidifobacterium longum, Lactobacillus plantarum, L. johnsonii, L. acidophilus, 2 strains of Streptococcus thermophilus, and pending completion of many draft genomic sequences, is now promoting in-depth investigation into the comparative genetic content of LAB. Moreover, whole-genome transcriptional arrays are quickly revealing critical genes/operons that are coordinately expressed and the impact of environmental factors on expression of multiple gene sets. Comparative genomics between multiple genomes is providing insights into genes that are important in metabolic, physiological, and functional roles for different LAB in the environments they inhabit, ranging from the gastrointestinal tract to milk and acidified dairy products.}, number={3}, journal={JOURNAL OF NUTRITION}, author={Klaenhammer, Todd R. and Azcarate-Peril, M. Andrea and Altermann, Eric and Barrangou, Rodolphe}, year={2007}, month={Mar}, pages={748S–750S} }
 @article{deveau_barrangou_garneau_labonte_fremaux_boyaval_romero_horvath_moineau_2007, title={Phage Response to CRISPR-Encoded Resistance in Streptococcus thermophilus}, volume={190}, DOI={10.1128/jb.01412-07}, abstractNote={ABSTRACT}, number={4}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Deveau, H. and Barrangou, R. and Garneau, J. E. and Labonte, J. and Fremaux, C. and Boyaval, P. and Romero, D. A. and Horvath, P. and Moineau, S.}, year={2007}, pages={1390–1400} }
 @article{duong_barrangou_russell_klaenhammer_2006, title={Characterization of the tre locus and analysis of trehalose cryoprotection in Lactobacillus acidophilus NCFM}, volume={72}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.72.2.1218-1225.2006}, abstractNote={ABSTRACT}, number={2}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, publisher={American Society for Microbiology}, author={Duong, T and Barrangou, R and Russell, WM and Klaenhammer, TR}, year={2006}, month={Feb}, pages={1218–1225} }
 @article{ventura_canchaya_bernini_altermann_barrangou_mcgrath_claesson_li_leahy_walker_et al._2006, title={Comparative genomics and transcriptional analysis of prophages identified in the Genomes of Lactobacillus gasseri, Lactobacillus salivarius, and Lactobacillus casei}, volume={72}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.72.5.3130-3146.2006}, abstractNote={ABSTRACT}, number={5}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, publisher={American Society for Microbiology}, author={Ventura, Marco and Canchaya, Carlos and Bernini, Valentina and Altermann, Eric and Barrangou, Rodolphe and McGrath, Stephen and Claesson, Marcus J. and Li, Yin and Leahy, Sinead and Walker, Carey D. and et al.}, year={2006}, month={May}, pages={3130–3146} }
 @article{makarova_slesarev_wolf_sorokin_mirkin_koonin_pavlov_pavlova_karamychev_polouchine_et al._2006, title={Comparative genomics of the lactic acid bacteria}, volume={103}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.0607117103}, abstractNote={Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.}, number={42}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Makarova, K. and Slesarev, A. and Wolf, Y. and Sorokin, A. and Mirkin, B. and Koonin, E. and Pavlov, A. and Pavlova, N. and Karamychev, V. and Polouchine, N. and et al.}, year={2006}, month={Oct}, pages={15611–15616} }
 @article{barrangou_azcarate-peril_duong_conners_kelly_klaenhammer_2006, title={Global analysis of carbohydrate utilization by Lactobacillus acidophilus using cDNA microarrays}, volume={103}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.0511287103}, abstractNote={
            The transport and catabolic machinery involved in carbohydrate utilization by
            Lactobacillus acidophilus
            was characterized genetically by using whole-genome cDNA microarrays. Global transcriptional profiles were determined for growth on glucose, fructose, sucrose, lactose, galactose, trehalose, raffinose, and fructooligosaccharides. Hybridizations were carried out by using a round-robin design, and microarray data were analyzed with a two-stage mixed model ANOVA. Differentially expressed genes were visualized by hierarchical clustering, volcano plots, and contour plots. Overall, only 63 genes (3% of the genome) showed a >4-fold induction. Specifically, transporters of the phospho
            enol
            pyruvate:sugar transferase system were identified for uptake of glucose, fructose, sucrose, and trehalose, whereas ATP-binding cassette transporters were identified for uptake of raffinose and fructooligosaccharides. A member of the LacS subfamily of galactoside-pentose hexuronide translocators was identified for uptake of galactose and lactose. Saccharolytic enzymes likely involved in the metabolism of monosaccharides, disaccharides, and polysaccharides into substrates of glycolysis were also found, including enzymatic machinery of the Leloir pathway. The transcriptome appeared to be regulated by carbon catabolite repression. Although substrate-specific carbohydrate transporters and hydrolases were regulated at the transcriptional level, genes encoding regulatory proteins CcpA, Hpr, HprK/P, and EI were consistently highly expressed. Genes central to glycolysis were among the most highly expressed in the genome. Collectively, microarray data revealed that coordinated and regulated transcription of genes involved in sugar uptake and metabolism is based on the specific carbohydrate provided.
            L. acidophilus
            's adaptability to environmental conditions likely contributes to its competitive ability for limited carbohydrate sources available in the human gastrointestinal tract.
          }, number={10}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Barrangou, R and Azcarate-Peril, MA and Duong, T and Conners, SB and Kelly, RM and Klaenhammer, TR}, year={2006}, month={Mar}, pages={3816–3821} }
 @article{altermann_russell_azcarate-peril_barrangou_buck_mcauliffe_souther_dobson_duong_callanan_et al._2005, title={Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM}, volume={102}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.0409188102}, abstractNote={Lactobacillus acidophilusNCFM is a probiotic bacterium that has been produced commercially since 1972. The complete genome is 1,993,564 nt and devoid of plasmids. The average GC content is 34.71% with 1,864 predicted ORFs, of which 72.5% were functionally classified. Nine phage-related integrases were predicted, but no complete prophages were found. However, three unique regions designated as potential autonomous units (PAUs) were identified. These units resemble a unique structure and bear characteristics of both plasmids and phages. Analysis of the three PAUs revealed the presence of two R/M systems and a prophage maintenance system killer protein. A spacers interspersed direct repeat locus containing 32 nearly perfect 29-bp repeats was discovered and may provide a unique molecular signature for this organism.In silicoanalyses predicted 17 transposase genes and a chromosomal locus for lactacin B, a class II bacteriocin. Several mucus- and fibronectin-binding proteins, implicated in adhesion to human intestinal cells, were also identified. Gene clusters for transport of a diverse group of carbohydrates, including fructooligosaccharides and raffinose, were present and often accompanied by transcriptional regulators of the lacI family. For protein degradation and peptide utilization, the organism encoded 20 putative peptidases, homologs for PrtP and PrtM, and two complete oligopeptide transport systems. Nine two-component regulatory systems were predicted, some associated with determinants implicated in bacteriocin production and acid tolerance. Collectively, these features within the genome sequence ofL. acidophilusare likely to contribute to the organisms' gastric survival and promote interactions with the intestinal mucosa and microbiota.}, number={11}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Altermann, E and Russell, WM and Azcarate-Peril, MA and Barrangou, R and Buck, BL and McAuliffe, O and Souther, N and Dobson, A and Duong, T and Callanan, M and et al.}, year={2005}, month={Mar}, pages={3906–3912} }
 @article{klaenhammer_peril_barrangou_duong_altermann_2005, title={Genomic Perspectives on Probiotic Lactic Acid Bacteria}, volume={24}, ISBN={1342-1441}, DOI={10.12938/bifidus.24.31}, abstractNote={The lactic acid bacteria are Gram-positive fermentative microorganisms known primarily for their roles as starter cultures and probiotics. The food industry represents one of the largest manufacturing industries in the world and recent trends are rapidly expanding the use of probiotic cultures within functional foods. Understanding and control of lactic acid bacteria is now being revolutionized by genomic sciences and the appearance of the complete genome sequences for Bifidobacterium longum, Lactobacillus johnsonii, Lactobacillus plantarum, and draft sequences for Lactobacillus gasseri and Lactobacillus casei. This explosion of DNA sequence information, accompanied by the development of bioinformatic tools for nucleic acid and protein analysis, now allows rapid characterization of the lactic acid bacteria for their genomic content and expression profiles across the entire genome. Comparative genomics has already revealed important similarities and differences in strains, species, and genera and will likely identify key genetic features responsible for the beneficial properties ascribed to probiotic lactic acid bacteria. Practical genomics for the lactic acid bacteria promises to establish the genetic landscape, correlate genotypes with desirable phenotypes, establish genetic criteria for strain selection, improve culture stability by stress preconditioning, provide opportunities for metabolic engineering, and uncover a mechanistic basis for the beneficial activities of probiotics when delivered in various foods. This presentation will examine the genomic content of probiotic Lactobacillus cultures, compared to those lactic acid bacterial genomes that have appeared recently. In addition, expression profiling by whole genome microarrays will be used to illustrate how environmental conditions encountered during biomanufacturing, fermentation, and the gastrointestinal tract can impact gene expression and culture functionality.}, number={2}, journal={Bioscience and Microflora}, publisher={BMFH Press}, author={Klaenhammer, Todd R. and Peril, Andrea Azcarate and Barrangou, Rodolphe and Duong, Tri and Altermann, Eric}, year={2005}, pages={31–33} }
 @misc{klaenhammer_barrangou_buck_azcarate-peril_altermann_2005, title={Genomic features of lactic acid bacteria effecting bioprocessing and health}, volume={29}, ISSN={["1574-6976"]}, DOI={10.1016/j.femsre.2005.04.007}, abstractNote={The lactic acid bacteria are a functionally related group of organisms known primarily for their bioprocessing roles in food and beverages. More recently, selected members of the lactic acid bacteria have been implicated in a number of probiotic roles that impact general health and well-being. Genomic analyses of multiple members of the lactic acid bacteria, at the genus, species, and strain level, have now elucidated many genetic features that direct their fermentative and probiotic roles. This information is providing an important platform for understanding core mechanisms that control and regulate bacterial growth, survival, signaling, and fermentative processes and, in some cases, potentially underlying probiotic activities within complex microbial and host ecosystems.}, number={3}, journal={FEMS MICROBIOLOGY REVIEWS}, publisher={Wiley-Blackwell}, author={Klaenhammer, TR and Barrangou, R and Buck, BL and Azcarate-Peril, MA and Altermann, E}, year={2005}, month={Aug}, pages={393–409} }
 @article{klaenhammer_barrangou_buck_azcarate-peril_altermann_2005, title={Genomic features of lactic acid bacteria effecting bioprocessing and health}, volume={29}, DOI={10.1016/j.fmrre.2005.04.007}, abstractNote={The lactic acid bacteria are a functionally related group of organisms known primarily for their bioprocessing roles in food and beverages. More recently, selected members of the lactic acid bacteria have been implicated in a number of probiotic roles that impact general health and well-being. Genomic analyses of multiple members of the lactic acid bacteria, at the genus, species, and strain level, have now elucidated many genetic features that direct their fermentative and probiotic roles. This information is providing an important platform for understanding core mechanisms that control and regulate bacterial growth, survival, signaling, and fermentative processes and, in some cases, potentially underlying probiotic activities within complex microbial and host ecosystems.}, number={3}, journal={FEMS Microbiology Reviews}, publisher={Oxford University Press (OUP)}, author={Klaenhammer, Todd R. and Barrangou, Rodolphe and Buck, B. Logan and Azcarate-Peril, M. Andrea and Altermann, Eric}, year={2005}, month={Aug}, pages={393–409} }
 @misc{barrangou_klaenhammer_altermann_2004, title={Lactobacillus acidophilus nucleic acids encoding fructo-oligosaccharide utilization compounds and uses thereof}, volume={7,407,787}, number={2004 Jun 22}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Barrangou, R. and Klaenhammer, T. R. and Altermann, E.}, year={2004} }
 @article{pridmore_berger_desiere_vilanova_barretto_pittet_zwahlen_rouvet_altermann_barrangou_et al._2004, title={The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533}, volume={101}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.0307327101}, abstractNote={
            Lactobacillus johnsonii
            NCC 533 is a member of the acidophilus group of intestinal lactobacilli that has been extensively studied for their “probiotic” activities that include, pathogen inhibition, epithelial cell attachment, and immunomodulation. To gain insight into its physiology and identify genes potentially involved in interactions with the host, we sequenced and analyzed the 1.99-Mb genome of
            L. johnsonii
            NCC 533. Strikingly, the organism completely lacked genes encoding biosynthetic pathways for amino acids, purine nucleotides, and most cofactors. In apparent compensation, a remarkable number of uncommon and often duplicated amino acid permeases, peptidases, and phosphotransferase-type transporters were discovered, suggesting a strong dependency of NCC 533 on the host or other intestinal microbes to provide simple monomeric nutrients. Genome analysis also predicted an abundance (>12) of large and unusual cell-surface proteins, including fimbrial subunits, which may be involved in adhesion to glycoproteins or other components of mucin, a characteristic expected to affect persistence in the gastrointestinal tract (GIT). Three bile salt hydrolases and two bile acid transporters, proteins apparently critical for GIT survival, were also detected.
            In silico
            genome comparisons with the >95% complete genome sequence of the closely related
            Lactobacillus gasseri
            revealed extensive synteny punctuated by clear-cut insertions or deletions of single genes or operons. Many of these regions of difference appear to encode metabolic or structural components that could affect the organisms competitiveness or interactions with the GIT ecosystem.
          }, number={8}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Pridmore, RD and Berger, B and Desiere, F and Vilanova, D and Barretto, C and Pittet, AC and Zwahlen, MC and Rouvet, M and Altermann, E and Barrangou, R and et al.}, year={2004}, month={Feb}, pages={2512–2517} }
 @article{barrangou_altermann_hutkins_cano_klaenhammer_2003, title={Functional and comparative genomic analyses of an operon involved in fructooligosaccharide utilization by Lactobacillus acidophilus}, volume={100}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1332765100}, abstractNote={
            Lactobacillus acidophilus
            is a probiotic organism that displays
 the ability to use prebiotic compounds such as fructooligosaccharides (FOS),
 which stimulate the growth of beneficial commensals in the gastrointestinal
 tract. However, little is known about the mechanisms and genes involved in FOS
 utilization by
            Lactobacillus
            species. Analysis of the
            L.
 acidophilus
            NCFM genome revealed an
            msm
            locus composed of a
 transcriptional regulator of the
            Lac
            I family, a four-component
 ATP-binding cassette (ABC) transport system, a fructosidase, and a sucrose
 phosphorylase. Transcriptional analysis of this operon demonstrated that gene
 expression was induced by sucrose and FOS but not by glucose or fructose,
 suggesting some specificity for nonreadily fermentable sugars. Additionally,
 expression was repressed by glucose but not by fructose, suggesting catabolite
 repression via two
            cre
            -like sequences identified in the
 promoter–operator region. Insertional inactivation of the genes encoding
 the ABC transporter substrate-binding protein and the fructosidase reduced the
 ability of the mutants to grow on FOS. Comparative analysis of gene
 architecture within this cluster revealed a high degree of synteny with
 operons in
            Streptococcus mutans
            and
            Streptococcus
 pneumoniae
            . However, the association between a fructosidase and an ABC
 transporter is unusual and may be specific to
            L. acidophilus
            . This is
 a description of a previously undescribed gene locus involved in transport and
 catabolism of FOS compounds, which can promote competition of beneficial
 microorganisms in the human gastrointestinal tract.
          }, number={15}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Barrangou, R and Altermann, E and Hutkins, R and Cano, R and Klaenhammer, TR}, year={2003}, month={Jul}, pages={8957–8962} }
 @article{barrangou_yoon_breidt_fleming_klaenhammer_2002, title={Characterization of six Leuconostoc fallax bacteriophages isolated from an industrial sauerkraut fermentation}, volume={68}, ISSN={["1098-5336"]}, DOI={10.1128/aem.68.11.5452-5458.2002}, abstractNote={ABSTRACT}, number={11}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, publisher={American Society for Microbiology}, author={Barrangou, R and Yoon, SS and Breidt, F and Fleming, HP and Klaenhammer, TR}, year={2002}, month={Nov}, pages={5452–5458} }
 @article{barrangou_yoon_breidt_fleming_klaenhammer_2002, title={Identification and characterization of Leuconostoc fallax strains isolated from an industrial sauerkraut fermentation}, volume={68}, ISSN={["0099-2240"]}, DOI={10.1128/aem.68.6.2877-2884.2002}, abstractNote={ABSTRACT}, number={6}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, publisher={American Society for Microbiology}, author={Barrangou, R and Yoon, SS and Breidt, F and Fleming, HP and Klaenhammer, TR}, year={2002}, month={Jun}, pages={2877–2884} }
 @article{yoon_barrangou-poueys_breidt_klaenhammer_fleming_2002, title={Isolation and characterization of bacteriophages from fermenting sauerkraut}, volume={68}, ISSN={["0099-2240"]}, DOI={10.1128/aem.68.2.973-976.2002}, abstractNote={ABSTRACT}, number={2}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, publisher={American Society for Microbiology}, author={Yoon, SS and Barrangou-Poueys, R and Breidt, F and Klaenhammer, TR and Fleming, HP}, year={2002}, month={Feb}, pages={973–976} }
 @article{horvath_barrangou, title={Protection against Foreign DNA}, DOI={10.1128/9781555816841.ch19}, abstractNote={This chapter briefly addresses the well-characterized restriction-modification system (R-M), non-sugar-specific nucleases (SNSN), and histone-like nucleoid structuring (H-NS). It more specifically elaborates on clustered regularly interspaced short palindromic repeats (CRISPR). CRISPR/CRISPR-associated (Cas), a recently described microbial system, provides acquired immunity against phages and plasmids by targeting nucleic acids in a sequence-specific manner. CRISPR features may be exploited for typing purposes, ecological and epidemiological studies, and also for enhancing phage resistance in bacteria. R-M systems commonly act as the first line of intracellular defense against foreign DNA. Some SNSN, such as Vvn from Vibrio vulnificus and EndoI from Escherichia coli, are periplasmic and thus prevent the uptake of foreign DNA. The ubiquitous and predatory nature of phages may explain the overwhelming representation of phage sequences in CRISPR spacers, but a recent report showed that CRISPR can dramatically impact the ability of plasmids to transfer genetic material in Staphylococcus epidermidis. Also, this study experimentally confirmed that CRISPR targets DNA directly in Staphylococcus. The CRISPR RNAs (crRNAs) seem to specifically guide the Cas defense apparatus toward foreign nucleic acid molecules that match the sequence of the spacers. This study also showed that Cas3, a predicted HD nuclease fused to a DEAD-box helicase, is required for the phage-resistance phenotype. The extent of the impact of CRISPR on phage genomes is perhaps best illustrated by extensive genome recombination events observed in environmental phage populations in response to CRISPR.}, journal={Bacterial Stress Responses, Second Edition}, publisher={American Society of Microbiology}, author={Horvath, Philippe and Barrangou, Rodolphe}, pages={333–348} }