Works (237)
Updated: November 17th, 2024 22:20
2024 journal article
AI and SynBio Meet CRISPR Heralding a New Genome Editing Era
The CRISPR Journal.
Source: ORCID
Added: August 22, 2024
2024 article
Characterization of <i>Ligilactobacillus salivarius</i> CRISPR-Cas systems
Roberts, A., Spang, D., Sanozky-Dawes, R., Nethery, M. A., & Barrangou, R. (2024, July 11). (C. D. Ellermeier, Ed.). MSPHERE, Vol. 7.
Ed(s): C. Ellermeier
author keywords: Ligilactobacillus; salivarius; CRISPR; Cas
open access via doi.org (publisher)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: July 15, 2024
2024 journal article
Five Years of Progress in CRISPR Clinical Trials (2019-2024)
CRISPR JOURNAL, 7(5), 227–230.
Sources: ORCID, Web Of Science, NC State University Libraries
Added: October 22, 2024
2024 article
Surveying the State of CRISPR and Gene Editing
Barrangou, R. (2024, June 1). CRISPR JOURNAL, Vol. 7, pp. 133–134.
Sources: ORCID, Web Of Science, NC State University Libraries
Added: July 1, 2024
2023 journal article
<i>Lactobacillus acidophilus</i> Expressing Murine Rotavirus VP8 and Mucosal Adjuvants Induce Virus-Specific Immune Responses
VACCINES, 11(12).
author keywords: rotavirus; Lactobacillus acidophilus; next-generation vaccine
TL;DR:
It is indicated 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 rotav virus.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
1. No Poverty
(OpenAlex)
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 1, 2024
2023 article
Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut
Foley, M. H., Walker, M. E., Stewart, A. K., O'Flaherty, S., Gentry, E. C., Patel, S., … Theriot, C. M. (2023, March 13). NATURE MICROBIOLOGY, Vol. 3.
MeSH headings : Animals; Mice; Humans; Clostridioides difficile; Clostridioides; Bile Acids and Salts; Amidohydrolases; Clostridium Infections
TL;DR:
Insight is provided into the structural basis of BSH mechanisms that shape the BA landscape and promote colonization resistance against C. difficile in vitro and in pre-clinical in vivo models of CDI.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: April 4, 2023
2023 article
CRISPR Technology and its Many Applications with Select Examples Related to Animal Agriculture
Barrangou, R. (2023, May). JOURNAL OF ANIMAL SCIENCE, Vol. 101.
TL;DR:
The Barrangou talk will be an update on CRISPR technology and its many applications with select examples related to animal agriculture.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: March 4, 2024
2023 article
CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes
Adler, B. A., Trinidad, M. I., Bellieny-Rabelo, D., Zhang, E., Karp, H. M., Skopintsev, P., … Doudna, J. A. (2023, October 27). NUCLEIC ACIDS RESEARCH, Vol. 10.
TL;DR:
CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: October 4, 2023
2023 journal article
Genome-Wide Comparative Analysis of Lactiplantibacillus pentosus Isolates Autochthonous to Cucumber Fermentation Reveals Subclades of Divergent Ancestry
FOODS, 12(13).
author keywords: Lactiplantibacillus pentosus; comparative genomics; Lactiplantibacillus plantarum; cucumber fermentation; starter culture
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: June 23, 2023
2023 journal article
Impact of Pomegranate on Probiotic Growth, Viability, Transcriptome and Metabolism
MICROORGANISMS, 11(2).
author keywords: probiotic; prebiotic; pomegranate; lactobacilli; transcriptomic
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 7, 2023
2023 journal article
Mining microbial organisms to discover and characterize novel CRISPR-Cas systems
CURRENT OPINION IN BIOMEDICAL ENGINEERING, 27.
author keywords: Novel CRISPR-Cas; Discovery; Genome editing; Mining microbes; Mining metagenomes
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: May 18, 2023
2023 journal article
Multiplex CRISPR editing of wood for sustainable fiber production
SCIENCE, 381(6654), 216-+.
TL;DR:
This work demonstrates that genome editing can be harnessed for breeding more efficient trees, which will provide timely opportunities for sustainable forestry and a more efficient bioeconomy.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 9, 2023
2023 article
The Expanding Dissemination and Distribution Patterns of Diverse CRISPR Plasmids by Addgene
Pyhtila, B., Kasowitz, S., Leeson, R., & Barrangou, R. (2023, November 22). CRISPR JOURNAL, Vol. 11.
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: December 18, 2023
2022 article
Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing
Adler, B. A., Hessler, T., Cress, B. F., Lahiri, A., Mutalik, V. K., Barrangou, R., … Doudna, J. A. (2022, October 31). NATURE MICROBIOLOGY, Vol. 10.
MeSH headings : Gene Editing; Bacteriophages / genetics; CRISPR-Cas Systems; Escherichia coli / genetics; Phylogeny; RNA / genetics; Antiviral Agents
TL;DR:
A CRISPR-Cas13 enzyme is shown to have potent anti-phage activity that is harnessed to produce a phage genome engineering method with broad utility.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: November 1, 2022
2022 journal article
CRISPR-based engineering of phages for in situ bacterial base editing
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 119(46).
author keywords: phage engineering; CRISPR; base editing; soil microbiome
MeSH headings : Gene Editing; CRISPR-Cas Systems / genetics; Bacteriophages / genetics; Ecosystem; Soil
TL;DR:
Phage-assisted delivery, together with base editing, offers an important in situ editing approach for the genetic interrogation of microbial community members.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: November 8, 2022
2022 journal article
Clustered Regularly Interspaced Short Palindromic Repeats Genotyping of Multidrug-Resistant Salmonella Heidelberg Strains Isolated From the Poultry Production Chain Across Brazil
FRONTIERS IN MICROBIOLOGY, 13.
author keywords: antibiotic resistance; CRISPR; phylogeny; Salmonella Heidelberg; foodborne disease; WGS
TL;DR:
The 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 and emphasized the need for continuous mitigation programs to monitor the dissemination of this high-priority pathogen.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: July 11, 2022
2022 article
Functional characterization of diverse type I-F CRISPR-associated transposons
Roberts, A., Nethery, M. A., & Barrangou, R. (2022, November 17). NUCLEIC ACIDS RESEARCH, Vol. 11.
MeSH headings : CRISPR-Cas Systems; Plasmids; Endonucleases / metabolism; Escherichia coli / genetics; Escherichia coli / metabolism; DNA; RNA; CRISPR-Associated Proteins / genetics; CRISPR-Associated Proteins / metabolism
TL;DR:
This work selected a diverse set of type I-F3 CRISPR-associated transposon systems derived from Gammaproteobacteria, predicted all components essential for transposition activity, and deployed them for functionality testing within Escherichia coli, demonstrating that these systems possess a significant range of integration efficiencies with regards to temperature, transposition size, and flexible PAM requirements.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: October 19, 2022
2022 journal article
Genomic and epigenetic landscapes drive CRISPR-based genome editing in Bifidobacterium
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 119(30).
author keywords: CRISPR-Cas; bifidobacterium; genomics; epigenomics; probiotics
MeSH headings : Bifidobacterium / genetics; CRISPR-Cas Systems; Gene Editing / methods; Genome, Bacterial / genetics; Genomics; Humans; Probiotics
TL;DR:
This study adapted existing CRISPR effectors and editing strategies to generate a variety of editing outcomes in B. animalis subsp.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: July 21, 2022
2022 journal article
Metabolomic Analysis of Lactobacillus acidophilus, L. gasseri, L. crispatus, and Lacticaseibacillus rhamnosus Strains in the Presence of Pomegranate Extract
FRONTIERS IN MICROBIOLOGY, 13.
author keywords: metabolomics; Lactobacillus; probiotic; pomegranate extract; prebiotic
TL;DR:
The growth of the strains with and without the presence of POM were investigated and their carbohydrate utilization and enzyme activity profiles were identified and an untargeted metabolomic approach was utilized to quantitatively and qualitatively define the metabolite profiles of these strains.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: June 13, 2022
2022 article
Next-Generation Foods and CRISPR Engineering
Barrangou, R. (2022, August 11).
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Source: ORCID
Added: August 17, 2022
2022 article
RNA-targeting CRISPR-Cas13 Provides Broad-spectrum Phage Immunity
Adler, B. A., Hessler, T., Cress, B. F., Mutalik, V. K., Barrangou, R., Banfield, J., & Doudna, J. A. (2022, March 26). (Vol. 3). Vol. 3.
TL;DR:
It is shown that LbuCas13a enables markerless genome edits in phages with exceptionally high efficiency and precision, including edits as small as a single codon, and suggests that DNA phages are generally vulnerable to Cas13a targeting.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: March 31, 2022
2022 article
Turning CRISPR on with antibiotics
Barrangou, R., & Marraffini, L. A. (2022, January 12). CELL HOST & MICROBE, Vol. 30, pp. 12–14.
MeSH headings : Anti-Bacterial Agents / pharmacology; Bacteria / genetics; Base Sequence; CRISPR-Cas Systems; Viruses
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: February 14, 2022
2021 journal article
(Broken) Promises of Sustainable Food and Agriculture through New Biotechnologies: The CRISPR Case
CRISPR JOURNAL, 4(1), 25–31.
MeSH headings : Agriculture; Animals; Biotechnology; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; Crops, Agricultural / genetics; Food; Food Supply; Gene Editing; Livestock / genetics
TL;DR:
The CRISPR community must actively engage with 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 because without this active engagement, the promises discussed in this paper are sure to be broken.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: March 22, 2021
2021 journal article
CRISPRclassify: Repeat-Based Classification of CRISPR Loci
CRISPR JOURNAL, 4(4), 558–574.
MeSH headings : Algorithms; Area Under Curve; Base Sequence; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; Computational Biology / methods; Databases, Genetic; Gene Editing; Genetic Loci; Genome, Bacterial; Genomics / methods; Reproducibility of Results
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
4. Quality Education
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: September 7, 2021
2021 journal article
Comparative Genomic Analyses and CRISPR-Cas Characterization of Cutibacterium acnes Provide Insights Into Genetic Diversity and Typing Applications
FRONTIERS IN MICROBIOLOGY, 12.
author keywords: CRISPR; genomics; Cas; genotyping; phylogeny
TL;DR:
A comprehensive comparative analysis of 255 C. acnes genomes is presented to provide insights into the species genetic diversity and identify unique features that define various phylotypes, opening new avenues for the development of biotherapeutics to manipulate the skin microbiota.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: November 29, 2021
2021 journal article
In Vivo Transcriptome of Lactobacillus acidophilus and Colonization Impact on Murine Host Intestinal Gene Expression
MBIO, 12(1).
Ed(s): G. Huffnagle
author keywords: Lactobacillus; acidophilus; gut adaptation; in vivo gene expression; mouse colonization; probiotic
MeSH headings : Animals; Bacterial Adhesion; Bacterial Proteins / genetics; Gene Expression Profiling; Host Microbial Interactions / genetics; Immunity; Intestines / microbiology; Lactobacillus acidophilus / genetics; Lactobacillus acidophilus / physiology; Mice; Probiotics / administration & dosage; Sequence Analysis, RNA; Signal Transduction; Transcriptome
TL;DR:
Metagenomic analysis of NCFM populations postcolonization demonstrated the genomic stability of L. acidophilus as a gut transient and further established its safety as a probiotic and biotherapeutic delivery platform.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: January 26, 2021
2021 journal article
Lactobacillus bile salt hydrolase substrate specificity governs bacterial fitness and host colonization
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 118(6).
author keywords: Lactobacillus; Acidophilus; gasseri; bile salt hydrolase; bile acid
MeSH headings : Amidohydrolases / genetics; Amidohydrolases / metabolism; Ecosystem; Gastrointestinal Microbiome / genetics; Gastrointestinal Microbiome / physiology; Genetic Fitness / genetics; Host-Pathogen Interactions / genetics; Humans; Lactobacillus / enzymology; Lactobacillus / genetics; Probiotics / pharmacology; Substrate Specificity / genetics
TL;DR:
It is shown that BA type and BSH substrate preferences affect in vitro and in vivo growth of both species and that BSH enzymatic preferences and the intrinsic chemical features of various BAs determine the toxicity of these molecules during Lactobacillus growth.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 2, 2021
2021 journal article
Portable CRISPR-Cas9(N) System for Flexible Genome Engineering in Lactobacillus acidophilus, Lactobacillus gasseri, and Lactobacillus paracasei
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 87(6).
Ed(s): E. Dudley
author keywords: Lactobacillus acidophilus; CRISPR; Cas9; nickase; genome editing; probiotic; lactic acid bacteria; Lactobacillus
MeSH headings : CRISPR-Associated Protein 9; CRISPR-Cas Systems; Deoxyribonuclease I; Gene Editing / methods; Genome, Bacterial; Lactobacillus acidophilus / genetics; Lactobacillus gasseri / genetics; Lacticaseibacillus paracasei / genetics
TL;DR:
This work describes the development of a lactobacillus CRISPR-based editing system for genome manipulations in three Lactobacilli 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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 26, 2021
2021 article
Species- and site-specific genome editing in complex bacterial communities
Rubin, B. E., Diamond, S., Cress, B. F., Crits-Christoph, A., Lou, Y. C., Borges, A. L., … Doudna, J. A. (2021, December 6). NATURE MICROBIOLOGY, Vol. 12.
MeSH headings : Archaea / genetics; Bacteria / classification; CRISPR-Cas Systems; Gastrointestinal Microbiome / genetics; Gene Editing / methods; Genome, Bacterial; Humans; Infant; Microbial Consortia / genetics; RNA, Guide, Kinetoplastida; Soil Microbiology
TL;DR:
This work characterize and validate a generalizable strategy for editing the genomes of specific organisms in microbial communities, and conducts species- and site-specific edits in several bacteria, measure gene fitness in a nonmodel bacterium and enrich targeted species.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: December 13, 2021
2021 article
Todd R. Klaenhammer, an inspirational food microbiologist who leaves a lasting legacy
Barrangou, R., & Hill, C. (2021, June 1). PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol. 118.
MeSH headings : Food Microbiology / history; History, 20th Century; History, 21st Century; Humans; Lactobacillales; National Academy of Sciences, U.S.; Probiotics / history; United States
TL;DR:
Todd R. Klaenhammer dedicated his professional life to the study of bacteria of importance to food and 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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: May 20, 2021
2021 article
Toward inclusive global governance of human genome editing
Yu, H., Xue, L., Barrangou, R., Chen, S., & Huang, Y. (2021, November 23). PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol. 118.
MeSH headings : Bioethics; Biomedical Research / ethics; CRISPR-Cas Systems; Clinical Governance / ethics; Clinical Governance / standards; Gene Editing / ethics; Genome, Human; Government; Humans; Publications
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: November 18, 2021
2020 journal article
Adaptive response to iterative passages of five Lactobacillus species in simulated vaginal fluid
BMC Microbiology, 20(1).
author keywords: Lactobacillus; Vaginal; Passages; Probiotics
MeSH headings : Adaptation, Physiological / genetics; Body Fluids / chemistry; Body Fluids / microbiology; Female; Genome, Bacterial; Genomic Instability; Humans; Lactobacillus / classification; Lactobacillus / genetics; Lactobacillus / growth & development; Lactobacillus / physiology; Species Specificity; Transcriptome; Vagina / chemistry; Vagina / microbiology
TL;DR:
Insight is provided into how vaginal and non-vaginal Lactobacillus species respond and adapt to a simulated vaginal environment and trends indicate high genomic stability for all species involved, with more variability in the transcriptome especially for non-dominant species of the vaginal tract.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: ORCID
Added: November 10, 2020
2020 journal article
Applications of CRISPR-Cas systems in lactic acid bacteria
FEMS Microbiology Reviews, 44(5), 523–537.
author keywords: Lactic acid bacteria; CRISPR; Cas; genome editing; probiotics; genomics
MeSH headings : CRISPR-Cas Systems; Industrial Microbiology / trends; Lactobacillales / genetics; Microbiota / genetics
TL;DR:
CRISPR-Cas classification, overview CRISPR biology and mechanism of action, and current and future applications in lactic acid bacteria are discussed, opening new avenues for their industrial exploitation and manipulation of microbiomes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
3. Good Health and Well-being
(Web of Science)
Source: ORCID
Added: May 21, 2020
2020 article
Building a Resilient, Sustainable, and Healthier Food Supply Through Innovation and Technology
ANNUAL REVIEW OF FOOD SCIENCE AND TECHNOLOGY, VOL 12, 2021, Vol. 12, pp. 1–28.
author keywords: future foods; food production; food processing; environmental impacts; nanotechnology; gene editing; genetic engineering; artificial intelligence; robotics
MeSH headings : Agriculture; Artificial Intelligence; Biotechnology; COVID-19; Food Quality; Food Safety; Food Supply / standards; Humans; Nanotechnology; Pandemics; Robotics
TL;DR:
A perspective article, written by members of the Editorial Committee of the Annual Review of Food Science and Technology, highlights 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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: May 24, 2021
2020 article
CRISPR Shields: Fending Off Diverse Cas Nucleases with Nucleus-like Structures
Barrangou, R., & Sontheimer, E. J. (2020, March 5). MOLECULAR CELL, Vol. 77, pp. 934–936.
MeSH headings : Bacteriophages / genetics; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; DNA; RNA
TL;DR:
It is demonstrated that a nucleus-like proteinaceous structure shields phage DNA from CRISPR-associated nucleases encompassing Cascade-Cas3, Cas9, and Cas12.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: April 6, 2020
2020 journal article
Characterization and applications of Type I CRISPR-Cas systems
Biochemical Society Transactions, 48(1), 15–23.
MeSH headings : Adaptive Immunity; Animals; Bacteria / genetics; CRISPR-Associated Proteins / genetics; CRISPR-Cas Systems / genetics; CRISPR-Cas Systems / immunology; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; Gene Editing / methods; Genome, Bacterial; Genome, Human; Humans; Plasmids / genetics
TL;DR:
The features and mechanism of action of Type I CRISPR-Cas systems are described, and how endogenous systems can be reprogrammed to target the host genome and perform genome editing and transcriptional regulation by co-delivering a minimalCRISPR array together with a repair template are illustrated.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: ORCID
Added: January 11, 2020
2020 review
Combining omics technologies with CRISPR-based genome editing to study food microbes
[Review of ]. CURRENT OPINION IN BIOTECHNOLOGY, 61, 198–208.
MeSH headings : Bacteria / genetics; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; Gene Editing; Probiotics
TL;DR:
Current applications of omics technologies in food microorganisms and CRISPR-based genome editing technologies in bacteria are highlighted, and 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 is discussed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: May 8, 2020
2020 journal article
Comparative Analysis of Lactobacillus gasseri and Lactobacillus crispatus Isolated From Human Urogenital and Gastrointestinal Tracts
FRONTIERS IN MICROBIOLOGY, 10.
author keywords: probiotics; niche-specific adaptation; Lactobacillus; women's health; in vitro vaginal fluid model
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: February 17, 2020
2020 journal article
Complete Genome Sequence of Lactobacillus johnsonii NCK2677, Isolated from Mice
Microbiology Resource Announcements, 9(43).
Ed(s): D. Rasko
TL;DR:
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 is reported.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: ORCID
Added: October 22, 2020
2020 journal article
Comprehensive Mining and Characterization of CRISPR-Cas Systems in Bifidobacterium
Microorganisms, 8(5), 720.
author keywords: Bifidobacterium; CRISPR-Cas; genomics
TL;DR:
This study mined 954 publicly available Bifidobacterium genomes and identified CRIPSR-Cas systems in 57% of these strains, and characterized the CRISPR RNA, tracrRNA, and PAM sequences to provide a molecular basis for the development of new genome editing tools for a variety of applications.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Source: ORCID
Added: May 29, 2020
2020 journal article
Deletion of S-Layer Associated Ig-Like Domain Protein Disrupts the Lactobacillus acidophilus Cell Surface
FRONTIERS IN MICROBIOLOGY, 11.
author keywords: Lactobacillus; probiotic; S-layer; cell surface; S-layer associated protein; Ig-like domain
TL;DR:
Identification of similar proteins in alternative bacterial species may help pinpoint next-generation host-adapted probiotic candidates.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: April 27, 2020
2020 journal article
Genomic characterization of Lactobacillus fermentum DSM 20052
BMC Genomics, 21(1).
author keywords: Lactobacillus; Fermentum; Comparative genomics; CRISPR
MeSH headings : CRISPR-Cas Systems / genetics; Genetic Variation; Genome, Bacterial; Genomic Islands; Genomics; Interspersed Repetitive Sequences; Limosilactobacillus fermentum / classification; Limosilactobacillus fermentum / genetics; Phylogeny
TL;DR:
This study genomically characterize L. fermentum using the type strain DSM 20052 as a canonical representative of this species, enabling genomic-informed selection of strains with specific traits for commercial product formulation, and establishes a framework for the functional characterization of features of interest.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: ORCID
Added: April 30, 2020
2020 journal article
Host and body site-specific adaptation of Lactobacillus crispatus genomes
NAR Genomics and Bioinformatics, 2(1).
TL;DR:
The results demonstrated that, although a significant portion of the genomic content is conserved, human and poultry L. crispatus isolates evolved to encompass different genomic features in order to thrive in different environmental niches.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Source: ORCID
Added: January 24, 2020
2020 journal article
In Vivo Targeting of Clostridioides difficile Using Phage-Delivered CRISPR-Cas3 Antimicrobials
MBio, 11(2).
Ed(s): J. Ballard
MeSH headings : Animals; Bacteriophages / genetics; CRISPR-Associated Proteins / genetics; CRISPR-Cas Systems / genetics; Clostridioides difficile / genetics; Enterocolitis, Pseudomembranous / microbiology; Enterocolitis, Pseudomembranous / therapy; Female; Genetic Engineering; Male; Mice; Mice, Inbred C57BL
TL;DR:
The findings suggest that phage-delivered programmable CRISPR therapeutics have the potential to leverage the specificity and apparent safety of phage therapies and improve their potency and reliability for eradicating specific bacterial species within complex communities, offering a novel mechanism to treat pathogenic and/or multidrug-resistant organisms.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: ORCID
Added: March 10, 2020
2020 journal article
Reactions to the National Academies/Royal Society Report on Heritable Human Genome Editing
CRISPR JOURNAL, 3(5), 332–349.
MeSH headings : Academies and Institutes; Gene Editing / ethics; Genome, Human; Germ Cells; Human Experimentation / ethics; Humans; Research Report; Societies
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
16. Peace, Justice and Strong Institutions
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: November 24, 2020
2020 journal article
S-layer associated proteins contribute to the adhesive and immunomodulatory properties of Lactobacillus acidophilus NCFM
BMC Microbiology, 20(1).
author keywords: Lactobacillus; S-layer; Probiotics; Cell surface
MeSH headings : Bacterial Adhesion; Bacterial Proteins / chemistry; Bacterial Proteins / genetics; Bacterial Proteins / immunology; Base Sequence; Caco-2 Cells; Catalytic Domain; Computer Simulation; Epithelial Cells / cytology; Epithelial Cells / immunology; Gene Deletion; Humans; Lactobacillus acidophilus / immunology; Lactobacillus acidophilus / physiology; Phenotype; Probiotics
TL;DR:
The data presented in this study collectively links several previously uncharacterized extracellular proteins to roles in the underlying host adaptive mechanisms of L. acidophilus.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Source: ORCID
Added: August 13, 2020
2020 journal article
Sharing the CRISPR Toolbox with an Expanding Community
CRISPR JOURNAL, 3(4), 248–252.
MeSH headings : CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; Gene Editing / statistics & numerical data; Gene Editing / trends
TL;DR:
The continued adoption of CRISPR tools and constructs distributed by the nonprofit organization Addgene are discussed, the trends in the global demand for theCRISPR toolbox are highlighted, and the widespread attitude changes around open sharing are considered that are having a transformative effect on speeding up science.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: September 14, 2020
2020 article
Shutting down RNA-targeting CRISPR
Barrangou, R., & Sontheimer, E. J. (2020, July 3). SCIENCE, Vol. 369, pp. 31–32.
MeSH headings : Bacteriophages; CRISPR-Associated Proteins / genetics; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; RNA
TL;DR:
An anti-CRISPR mechanism is reported that inhibits Cas13a RNase activity, with potential utility as a CRISPR effector control switch.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 3, 2020
2020 journal article
Strain-Dependent Inhibition of Clostridioides difficile by Commensal Clostridia Carrying the Bile Acid-Inducible ( bai ) Operon
Journal of Bacteriology, 202(11).
Ed(s): L. Comstock
author keywords: 7 alpha-dehydroxylation; Clostridia; Clostridioides difficile; bile acids; cholate; deoxycholate
MeSH headings : Antibiosis; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Bile Acids and Salts / metabolism; Clostridiales / genetics; Clostridiales / physiology; Clostridioides difficile / growth & development; Clostridioides difficile / physiology; Clostridium Infections / metabolism; Clostridium Infections / microbiology; Clostridium histolyticum / genetics; Clostridium histolyticum / physiology; Humans; Operon; Species Specificity; Symbiosis
TL;DR:
Four commensal Clostridia that encode the bai operon effect C. scindens have been associated with protection against CDI, however the mechanism for this protection is unknown and competition studies revealed that C. difficile was able to outcompete the commensals in an in vitro co-culture system.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: ORCID
Added: May 9, 2020
2020 article
Strain-dependent inhibition ofClostridioides difficileby commensalClostridiaencoding the bile acid inducible(bai)operon
Reed, A. D., Nethery, M. A., Stewart, A., Barrangou, R., & Theriot, C. M. (2020, January 23).
Source: ORCID
Added: January 24, 2020
2020 journal article
Whole-genome sequencing analysis and CRISPR genotyping of rare antibiotic-resistant Salmonella enterica serovars isolated from food and related sources
FOOD MICROBIOLOGY, 93.
author keywords: Antibiotic resistance; CRISPR; Phylogeny; Salmonella serovars; Whole genome sequencing
MeSH headings : Anti-Bacterial Agents / pharmacology; Brazil; Clustered Regularly Interspaced Short Palindromic Repeats; Drug Resistance, Multiple, Bacterial / genetics; Food Microbiology; Genome, Bacterial; Genotype; Genotyping Techniques; Microbial Sensitivity Tests; Salmonella / classification; Salmonella / genetics; Salmonella / isolation & purification; Salmonella Food Poisoning; Salmonella enterica / classification; Salmonella enterica / drug effects; Salmonella enterica / genetics; Salmonella enterica / isolation & purification; Serogroup; Serotyping; Whole Genome Sequencing
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: October 5, 2020
2019 article
Applications of CRISPR Technologies Across the Food Supply Chain
ANNUAL REVIEW OF FOOD SCIENCE AND TECHNOLOGY, VOL 10, Vol. 10, pp. 133–150.
author keywords: CRISPR-Cas; genome editing; crop development; food supply chain; livestock
MeSH headings : Animals; Clustered Regularly Interspaced Short Palindromic Repeats; Crops, Agricultural / genetics; Food Supply; Gene Editing; Livestock
TL;DR:
The concept of applying CRISPR-Cas technology as a genome-editing tool for use in the food supply chain is introduced, 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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: April 22, 2019
2019 journal article
Bile salt hydrolases: Gatekeepers of bile acid metabolism and host-microbiome crosstalk in the gastrointestinal tract
PLOS PATHOGENS, 15(3).
Ed(s): L. Knoll
MeSH headings : Amidohydrolases / metabolism; Amidohydrolases / physiology; Bile Acids and Salts / metabolism; Gastrointestinal Microbiome / physiology; Gastrointestinal Tract; Host Microbial Interactions / physiology; Humans
TL;DR:
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, and there remain gaps in knowledge about the bacterial enzymes driving their composition and modification.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: April 15, 2019
2019 journal article
Bringing CRISPR to the Cinema
The CRISPR Journal, 2(4), 187–187.
MeSH headings : CRISPR-Associated Proteins; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; Gene Editing; Motion Pictures
Source: ORCID
Added: January 3, 2020
2019 journal article
CRISPR on the Move in 2019
The CRISPR Journal, 2(1), 1–2.
MeSH headings : CRISPR-Cas Systems / genetics; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; Humans; Research / trends
Source: ORCID
Added: January 3, 2020
2019 review
CRISPR-Directed Microbiome Manipulation across the Food Supply Chain
[Review of ]. TRENDS IN MICROBIOLOGY, 27(6), 489–496.
MeSH headings : CRISPR-Cas Systems; Fermentation; Food Chain; Food Microbiology; Food Supply; Gene Editing; Metabolic Engineering; Microbiota
TL;DR:
It is illustrated how the various CRISPR technologies that can alter bacterial functionalities and modulate the composition of microbial communities in foods 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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: June 4, 2019
2019 article
Collaborative networks in gene editing
Huang, Y., Porter, A., Zhang, Y., & Barrangou, R. (2019, October). NATURE BIOTECHNOLOGY, Vol. 37, pp. 1107–1109.
MeSH headings : Biomedical Research / trends; Gene Editing; Humans; International Cooperation; Leadership; Publishing / trends
TL;DR:
Of the literature on gene-editing modalities, CRISPR–Cas continues to grow, whereas publications describing meganucleases, zinc finger nucleases and transcription activator–like effector nuclease (TALENs) have been decreasing since 2016.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: November 18, 2019
2019 journal article
Comparative genomics of eight Lactobacillus buchneri strains isolated from food spoilage
BMC GENOMICS, 20(1).
author keywords: Lactobacillus buchneri; Comparative genomics; Lactic acid bacteria; CRISPR-Cas systems; Fermentation; Spoilage; Food microbiology
MeSH headings : Computational Biology / methods; Evolution, Molecular; Fermentation; Food Microbiology; Genome, Bacterial; Genomics / methods; Lactobacillus / classification; Lactobacillus / genetics; Lactobacillus / isolation & purification; Molecular Sequence Annotation; Phylogeny; Whole Genome Sequencing
TL;DR:
The findings from the comparison of eight newly-sequenced and assembled genomes against two publicly available closed reference genomes provide new insights into the genomics of L. buchneri, building a platform for future studies and identifying elements for potential strain manipulation or engineering.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: December 16, 2019
2019 review
Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants
[Review of ]. NATURE REVIEWS MICROBIOLOGY, 18(2), 67–83.
MeSH headings : Archaea / genetics; Bacteria / genetics; CRISPR-Cas Systems / genetics; CRISPR-Cas Systems / physiology; Evolution, Molecular; Gene Expression Regulation, Archaeal / physiology; Gene Expression Regulation, Bacterial / physiology
TL;DR:
An updated evolutionary classification of CRISPR–Cas systems and cas genes is provided, with an emphasis on the major developments that have occurred since the publication of the latest classification, in 2015, which includes 2 classes, 6 types and 33 subtypes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: February 27, 2020
2019 journal article
Foresight is 2020: Ten Bold Predictions for the New CRISPR Year
The CRISPR Journal, 2(6), 341–342.
MeSH headings : CRISPR-Cas Systems / genetics; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; Gene Editing / ethics; Gene Editing / methods; Humans
UN Sustainable Development Goal Categories
13. Climate Action
(OpenAlex)
Source: ORCID
Added: January 3, 2020
2019 journal article
Genome editing using the endogenous type I CRISPR-Cas system in Lactobacillus crispatus
Proceedings of the National Academy of Sciences.
author keywords: CRISPR; Cas3; type I-E; genome editing; probiotic
MeSH headings : Base Sequence; CRISPR-Cas Systems / genetics; Gene Editing; Genetic Loci; Genetic Variation; Lactobacillus crispatus / genetics; Lactobacillus crispatus / ultrastructure; Nucleotide Motifs / genetics; RNA, Guide, Kinetoplastida / genetics
TL;DR:
This approach enables flexible alteration of the formerly genetically recalcitrant species L. crispatus, with potential for probiotic enhancement, biotherapeutic engineering, and mucosal vaccine delivery, and the toolbox is expanded to include one of the most abundant and diverse systems found in nature.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2019 journal article
Outcomes and characterization of chromosomal self-targeting by native CRISPR-Cas systems in Streptococcus thermophilus
FEMS MICROBIOLOGY LETTERS, 366(9).
author keywords: CRISPR; lactic acid bacteria; Cas9; Streptococcus; genome editing
MeSH headings : Bacteriophages / genetics; CRISPR-Cas Systems; Chromosomes, Bacterial / genetics; Gene Editing; Genome, Bacterial; Homologous Recombination; Plasmids / genetics; Streptococcus thermophilus / genetics; Streptococcus thermophilus / virology
TL;DR:
Results suggest that HR contributes to the plasticity and remodeling of bacterial genomes, leading to evasion of genome targeting by CRISPR-Cas systems.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: September 3, 2019
2019 journal article
Partnering with bioRxiv
The CRISPR Journal, 2(6), 342–342.
Source: ORCID
Added: January 3, 2020
2019 journal article
Profile of Rodolphe Barrangou
Proceedings of the National Academy of Sciences, 116(32), 15754–15756.
MeSH headings : CRISPR-Cas Systems / genetics; Food Technology / history; History, 20th Century; History, 21st Century
TL;DR:
In his Inaugural Article, Rodolphe 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.
(via Semantic Scholar)
Source: ORCID
Added: January 3, 2020
2019 journal article
Recombination between phages and CRISPR-cas loci facilitates horizontal gene transfer in staphylococci
NATURE MICROBIOLOGY, 4(6), 956–963.
MeSH headings : Bacteria / genetics; Bacteriophages / genetics; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; Clustered Regularly Interspaced Short Palindromic Repeats / immunology; Endonucleases; Gene Transfer, Horizontal; Genome, Bacterial; Genome, Viral; Plasmids / genetics; Pseudomonas aeruginosa / genetics; Sequence Analysis, DNA; Staphylococcus / genetics; Staphylococcus aureus / genetics; Transduction, Genetic
TL;DR:
The data demonstrate that spacer sequences not only specify the targets of Cas nucleases but also can promote horizontal gene transfer, which can promote transfer of CRISPR elements to other bacteria in the population.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: June 17, 2019
2019 journal article
Short communication: Transcriptional response to a large genomic island deletion in the dairy starter culture Streptococcus thermophilus
JOURNAL OF DAIRY SCIENCE, 102(9), 7800–7806.
author keywords: fermentation; Streptococcus thermophilus; transcriptome; CRISPR
MeSH headings : Animals; Clustered Regularly Interspaced Short Palindromic Repeats; Fermentation; Gene Deletion; Gene Expression Regulation, Bacterial / physiology; Genomic Islands; Genomics; Lactic Acid / metabolism; Lactobacillus delbrueckii / metabolism; Milk / microbiology; Streptococcus thermophilus / genetics; Streptococcus thermophilus / metabolism; Transcriptome; Yogurt / microbiology
TL;DR:
Results suggest that deletion of a 102-kb genomic island in Strep.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
14. Life Below Water
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 26, 2019
2019 journal article
Taking CRISPR to New Heights
The CRISPR Journal, 2(3), 133–133.
MeSH headings : CRISPR-Associated Proteins; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; Gene Editing
Source: ORCID
Added: January 3, 2020
2019 journal article
Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells
NATURE BIOTECHNOLOGY, 37(12), 1493-+.
MeSH headings : CRISPR-Cas Systems / genetics; Escherichia coli / genetics; Genetic Engineering / methods; HEK293 Cells; Humans; Listeria monocytogenes / genetics; RNA, Guide, Kinetoplastida / genetics; Transcription, Genetic / genetics
TL;DR:
This study repurposes 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, and demonstrates the use of Cascade as a CRISpr-based technology for targeted eukaryotic gene regulation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: December 30, 2019
2019 journal article
The repurposing of type I-E CRISPR-Cascade for gene activation in plants
Communications Biology.
MeSH headings : Biolistics; CRISPR-Cas Systems; Chromosomes, Plant / genetics; DNA, Plant / genetics; Genes, Plant; Genetic Engineering / methods; Plasmids / genetics; Streptococcus thermophilus / genetics; Transcriptional Activation; Zea mays / embryology; Zea mays / genetics
TL;DR:
DNA targeting in Zea mays is reported using a class 1 type I-E CRISPR-Cas system from S. thermophilus and it is shown it compares favorably with Cas9 as a RNA-guided transcriptional activator.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: ORCID
Added: January 2, 2020
2019 journal article
Thinking About CRISPR: The Ethics of Human Genome Editing
The CRISPR Journal, 2(5), 247–248.
MeSH headings : CRISPR-Cas Systems / genetics; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; Gene Editing / ethics; Genome, Human / genetics; Humans
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Source: ORCID
Added: January 3, 2020
2019 journal article
Time To Let CRISPR B.E.?
The CRISPR Journal, 2(2), 67–67.
MeSH headings : Animals; CRISPR-Cas Systems / genetics; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; Genetic Engineering / methods; Humans; Nucleotides / genetics; Research / trends
Source: ORCID
Added: January 3, 2020
2018 journal article
CRISPR Craziness: A Response to the EU Court Ruling
The CRISPR Journal, 1(4), 251–252.
Source: ORCID
Added: January 3, 2020
2018 journal article
CRISPR Crossroads for Genome Editing
The CRISPR Journal, 1(6), 349–350.
Source: ORCID
Added: January 3, 2020
2018 journal article
CRISPR Visualizer: rapid identification and visualization of CRISPR loci via an automated high-throughput processing pipeline
RNA BIOLOGY, 16(4), 577–584.
author keywords: CRISPR-Cas; repeat detection; software; CRISPR spacer; crRNA
MeSH headings : Bacteria / genetics; Base Sequence; CRISPR-Cas Systems / genetics; Computational Biology; Genetic Loci; High-Throughput Nucleotide Sequencing / methods; Time Factors
TL;DR:
A high-throughput extraction pipeline coupled with a local web-based visualization tool is constructed which enables CRISPR spacer and repeat extraction, rapid visualization, graphical comparison, and progressive multiple sequence alignment and supports accelerated analysis of genomic data sets.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: May 20, 2019
2018 journal article
CRISPRdisco: An Automated Pipeline for the Discovery and Analysis of CRISPR-Cas Systems
CRISPR JOURNAL, 1(2), 171–181.
TL;DR:
An automated pipeline is developed, named CRISprdisco (CRISPR discovery), to identify CRISPR repeats and cas genes in genome assemblies, determine type and subtype, and describe system completeness, which opens new avenues to enable classification within a complex nomenclature.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science
Added: February 25, 2019
2018 review
Characterization and Repurposing of Type I and Type II CRISPR-Cas Systems in Bacteria
[Review of ]. JOURNAL OF MOLECULAR BIOLOGY, 431(1), 21–33.
author keywords: CRISPR-Cas systems; CRISPR characterization; endogenous systems; genome editing
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: February 11, 2019
2018 journal article
Characterizing the activity of abundant, diverse and active CRISPR-Cas systems in lactobacilli
Scientific Reports, 8(1).
MeSH headings : Bacteriophages / genetics; CRISPR-Cas Systems; Gene Expression Profiling; Genetic Variation; Genome, Bacterial; Lactobacillus / enzymology; Lactobacillus / genetics; Plasmids; RNA, Guide, Kinetoplastida / genetics; Recombination, Genetic
TL;DR:
The results reveal that Type II-A systems in lactobacilli are naturally active in their native host in terms of expression and efficiently targeting invasive and genomic DNA, and increase the possible Cas9 targeting space and provide multiplexing potential in native hosts and heterologous genome editing purpose.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: January 2, 2020
2018 journal article
Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems
RNA BIOLOGY, 16(4), 435–448.
MeSH headings : Bacteroides / genetics; Base Sequence; CRISPR-Cas Systems / genetics; Conserved Sequence / genetics; Evolution, Molecular; Genomics; Nucleic Acid Conformation; RNA, Bacterial / genetics; RNA, Guide, Kinetoplastida / genetics; Repetitive Sequences, Nucleic Acid / genetics; Streptococcus / genetics; Thermodynamics; Trans-Activators / genetics
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: May 20, 2019
2018 journal article
Conserved Genome Organization and Core Transcriptome of the Lactobacillus acidophilus Complex
FRONTIERS IN MICROBIOLOGY, 9.
author keywords: Lactobacillus; core genome; core transcriptome; microbial genetics; chromosome organization
TL;DR:
The 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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: October 19, 2018
2018 journal article
Cultivating CRISPR
The CRISPR Journal, 1(2), 99–100.
Source: ORCID
Added: January 3, 2020
2018 journal article
Deletion-based escape of CRISPR-Cas9 targeting in Lactobacillus gasseri
MICROBIOLOGY-SGM, 164(9), 1098–1111.
author keywords: Lactobacillus; CRISPR; Cas; Cas9; interference; spacer
MeSH headings : CRISPR-Associated Protein 9 / metabolism; Clustered Regularly Interspaced Short Palindromic Repeats; Interspersed Repetitive Sequences; Lactobacillus gasseri / genetics; Mutation; Plasmids; Recombination, Genetic; Sequence Deletion; Transformation, Bacterial
TL;DR:
It is shown that deletions of spacers within CRISPR arrays constitute a key escape mechanism to evadeCRISPR targeting, while preserving the functionality of the CRISpr-Cas system.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: December 31, 2018
2018 journal article
Enabling the Rise of a CRISPR World
The CRISPR Journal, 1(3), 205–208.
TL;DR:
This work states that 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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
3. Good Health and Well-being
(Web of Science)
Sources: NC State University Libraries, ORCID, NC State University Libraries
Added: February 18, 2019
2018 review
Engineering Components of the Lactobacillus S-Layer for Biotherapeutic Applications
[Review of ]. FRONTIERS IN MICROBIOLOGY, 9.
author keywords: Lactobacillus; probiotic; S-layer; biotherapeutic; mucosal vaccine; CRISPR
TL;DR:
The multi-faceted S-layer protein (Slp), and its use in both heterologous protein expression systems and mucosal vaccine delivery frameworks, is examined, through its diverse genetic components.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: October 16, 2018
2018 journal article
Expanding the CRISPR Landscape on a cas by cas Basis
The CRISPR Journal, 1(5), 303–303.
Source: ORCID
Added: January 3, 2020
2018 review
Harnessing CRISPR-Cas systems for precision engineering of designer probiotic lactobacilli
[Review of ]. CURRENT OPINION IN BIOTECHNOLOGY, 56, 163–171.
MeSH headings : CRISPR-Cas Systems / genetics; Drug Delivery Systems; Gene Editing; Genetic Engineering / methods; Lactobacillus / genetics; Probiotics / metabolism
TL;DR:
How the rising adoption of CRISPR-based technologies for prokaryotic engineering and tunable transcriptional regulation can be translated into next-generation development of probiotic lactobacilli with enhanced robustness and designer functionalities is discussed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: June 17, 2019
2018 journal article
Immune loss as a driver of coexistence during host-phage coevolution
ISME JOURNAL, 12(2), 585–597.
MeSH headings : Bacteria / genetics; Bacteria / immunology; Bacteriophages / physiology; Biological Evolution; CRISPR-Cas Systems; Models, Immunological
TL;DR:
It is proposed that the regular loss of immunity by the bacterial host can also produce host-phage coexistence and it is found that, while both mechanisms can produce stable coexistence, only immune loss does so robustly within realistic parameter ranges.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2018 review
Insights into the Human Virome Using CRISPR Spacers from Microbiomes
[Review of ]. VIRUSES-BASEL, 10(9).
author keywords: CRISPR-Cas systems; CRISPR spacers; virome; phages; microbiome
MeSH headings : Biodiversity; Clustered Regularly Interspaced Short Palindromic Repeats; Humans; Metagenomics; Microbiota; Viruses / classification; Viruses / genetics; Viruses / isolation & purification
TL;DR:
It is shown how the CRISPR spacer content of commensal and pathogenic bacteria can be used to determine the evidence of their phage exposure, which opens new opportunities for investigating host-virus dynamics in metagenomic data, and highlights the need for more efforts for virome sampling and sequencing.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: November 26, 2018
2018 article
Keep Calm and CRISPR On
Barrangou, R. (2018, February). CRISPR JOURNAL, Vol. 1, pp. 1–3.
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: February 25, 2019
2018 journal article
Lactobacillus gasseri CRISPR-Cas9 characterization In Vitro reveals a flexible mode of protospacer-adjacent motif recognition
PLOS ONE, 13(2).
Ed(s): S. Xu
MeSH headings : CRISPR-Cas Systems; Lactobacillus gasseri / genetics; RNA Editing
TL;DR:
This work 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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2018 journal article
MasterChef at Work: An Interview with Rodolphe Barrangou
The CRISPR Journal, 1(3), 219–222.
Source: ORCID
Added: January 3, 2020
2018 article
Mining for novel bacterial defence systems
Barrangou, R., & Oost, J. (2018, May). NATURE MICROBIOLOGY, Vol. 3, pp. 535–536.
MeSH headings : Bacteria; Genome, Bacterial
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2018 journal article
Phenotypic and genotypic diversity of Lactobacillus buchneri strains isolated from spoiled, fermented cucumber
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY, 280, 46–56.
author keywords: Lactic acid bacteria; Pickled vegetables; Spoilage organisms; Lactobacillus buchneri; Strain diversity
MeSH headings : Acetic Acid / metabolism; Bioreactors; Cucumis sativus / microbiology; Fermentation; Genotype; Lactic Acid / metabolism; Lactobacillus / classification; Lactobacillus / genetics; Lactobacillus / isolation & purification; Lactobacillus / metabolism; Propylene Glycol / metabolism; RNA, Ribosomal, 16S / genetics
TL;DR:
Describing isolates of L. buchneri purified from both industrial and experimental fermented cucumber after the onset of secondary fermentation provided the basis for further analysis of metabolic and genomic capabilities of this species to enable control of lactic acid degradation in fermented plant materials.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2018 journal article
Pomp and Circumstance: Making the Case for CRISPR
The CRISPR Journal, 1(4), 253–254.
Source: ORCID
Added: January 3, 2020
2018 article
Predicting and visualizing features of CRISPR-Cas systems
CRISPR-CAS ENZYMES, Vol. 616, pp. 1–25.
MeSH headings : Animals; Bacteria / genetics; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; Computer Simulation; Gene Editing / methods; Genomics / methods; Humans; RNA, Guide, Kinetoplastida / genetics; Software
TL;DR:
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 are described.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: December 30, 2019
2018 journal article
Pulling the genome in opposite directions to dissect gene networks
Genome Biology, 19(1).
MeSH headings : CRISPR-Associated Protein 9; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; Gene Regulatory Networks; Genome
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, NC State University Libraries, NC State University Libraries
Added: August 6, 2018
2018 journal article
Pulling the genome in opposite directions to dissect gene networks
Genome Biology, 19.
Source: NC State University Libraries
Added: August 6, 2018
2018 journal article
The Democratization of CRISPR
The CRISPR Journal, 1(3), 203–204.
Source: ORCID
Added: January 3, 2020
2018 journal article
The Lactobacillus Bile Salt Hydrolase Repertoire Reveals Niche-Specific Adaptation
MSPHERE, 3(3).
Ed(s): C. Ellermeier
author keywords: Lactobacillus; bile acid; bile salt hydrolase; gastrointestinal tract; niche; penicillin V acylase; probiotic; therapeutic
MeSH headings : Adaptation, Biological; Amidohydrolases / genetics; Genetic Variation; Genotype; Lactobacillus / classification; Lactobacillus / enzymology; Lactobacillus / genetics; Penicillin Amidase / genetics; Phylogeny; Sequence Homology
TL;DR:
The BSH repertoire across 170 sequenced species revealed that BSH-encoding lactobacilli primarily adopt the vertebrate-adapted lifestyle but not the environmental or plant-associated subsets, and will guide future mechanistic studies of BSH activity and contribute to the development and selection of Lactobacillus strains with therapeutic potential.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2018 journal article
Transcriptional and Functional Analysis of Bifidobacterium animalis subsp. lactis Exposure to Tetracycline
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 84(23).
Ed(s): V. Müller
author keywords: Bifidobacterium animalis subsp. lactis; antibiotic resistance; tetracycline; RNA sequencing; genomics; droplet digital PCR; ATP luminescence
MeSH headings : Anti-Bacterial Agents / pharmacology; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Bifidobacterium animalis / drug effects; Bifidobacterium animalis / genetics; Bifidobacterium animalis / metabolism; Clustered Regularly Interspaced Short Palindromic Repeats / drug effects; Gene Expression Regulation, Bacterial / drug effects; Genome, Bacterial / drug effects; Tetracycline / pharmacology; Tetracycline Resistance; Transcription, Genetic / drug effects
TL;DR:
The results provide high-throughput means for assessing antibiotic resistances of two highly related probiotic strains and determine the genetic network that contributes to the global tetracycline response.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: December 3, 2018
2018 journal article
Using glycolysis enzyme sequences to inform Lactobacillus phylogeny
Microbial Genomics, 4(6).
author keywords: Lactobacillus; phylogeny; glycolysis; evolution
MeSH headings : Base Composition; Evolution, Molecular; Gene Expression Regulation, Bacterial; Genetic Drift; Genome Size; Genome, Bacterial; Glycolysis / genetics; Glycolysis / physiology; Lactobacillus / classification; Lactobacillus / enzymology; Lactobacillus / genetics; Lactobacillus / metabolism; Probiotics; RNA, Ribosomal, 16S / genetics; Sequence Alignment; Species Specificity
TL;DR:
It is shown that a glycolysis-based phylogenetic tree can robustly segregate lactobacilli into distinct clusters and discern very closely related species and may constitute practical targets for evolutionary studies.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: ORCID
Added: January 3, 2020
2017 journal article
A decade of discovery: CRISPR functions and applications
NATURE MICROBIOLOGY, 2(7).
MeSH headings : Archaea / enzymology; Archaea / genetics; Bacteria / enzymology; Bacteria / genetics; CRISPR-Cas Systems; Gene Editing / history; Gene Editing / methods; History, 21st Century; Molecular Biology / history; Molecular Biology / methods
TL;DR:
A look back on the historical milestones that have paved the way for the discovery of CRISPR and its function, and the related technological applications that have emerged, with a focus on microbiology.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2017 review
Advances in Industrial Biotechnology Using CRISPR-Cas Systems
[Review of ]. TRENDS IN BIOTECHNOLOGY, 36(2), 134–146.
MeSH headings : Animals; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Biotechnology / methods; CRISPR-Associated Protein 9; CRISPR-Cas Systems; Endonucleases / genetics; Endonucleases / metabolism; Gene Editing / methods; Genetic Engineering / methods; Industrial Microbiology / methods; Metabolic Networks and Pathways / genetics; Plants / genetics; RNA, Guide, Kinetoplastida / genetics; RNA, Guide, Kinetoplastida / metabolism
TL;DR:
The fundamental characteristics of CRISPR-Cas systems are explored and how these features can be used in industrial settings are highlighted.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2017 article
CRISPR-Cas Technologies and Applications in Food Bacteria
ANNUAL REVIEW OF FOOD SCIENCE AND TECHNOLOGY, VOL 8, Vol. 8, pp. 413–437.
author keywords: probiotics; cultures; strain-typing; phage resistance; plasmid vaccination; antimicrobial; genome editing
MeSH headings : Bacteria / genetics; Bacteria / immunology; Bacterial Vaccines; Bacteriophages / genetics; CRISPR-Cas Systems; Food Industry; Food Microbiology; Gene Editing; Genes, Bacterial; Interspersed Repetitive Sequences; Probiotics
TL;DR:
The applications of CRISPR-Cas systems and tools in starter cultures and probiotics are introduced, encompassing strain-typing, phage resistance, plasmid vaccination, genome editing, and antimicrobial activity.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2017 review
CRISPR-based engineering of next-generation lactic acid bacteria
[Review of ]. CURRENT OPINION IN MICROBIOLOGY, 37, 79–87.
MeSH headings : Bifidobacterium / genetics; Bifidobacterium / physiology; CRISPR-Cas Systems; Food Microbiology / methods; Gene Editing; Humans; Lactobacillus / genetics; Lactobacillus / physiology; Metabolic Engineering; Probiotics
TL;DR:
The advent of CRISPR-based technologies has opened new avenues for the development of next-generation food microorganisms and probiotics with enhanced functionalities and can be harnessed to genetically modify probiotics and enhance their therapeutic potential to deliver vaccines or modulate the host immune response.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2017 journal article
Characterization and Exploitation of CRISPR Loci in Bifidobacterium longum
FRONTIERS IN MICROBIOLOGY, 8.
author keywords: CRISPR-Cas systems; genotyping; probiotics; Bifidobacterium longum
TL;DR:
It is suggested that CRISPR-Cas immune systems are instrumental in mounting diversified viral resistance in B. longum, and hypervariable loci can be used to gain insights into strain origin, evolution and phylogeny, and can provide discriminatory sequences to distinguish even clonal isolates.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science
Added: August 6, 2018
2017 journal article
Deletion of Lipoteichoic Acid Synthase Impacts Expression of Genes Encoding Cell Surface Proteins in Lactobacillus acidophilus
Frontiers in Microbiology, 8.
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: NC State University Libraries, ORCID, NC State University Libraries
Added: August 6, 2018
2017 article
Expanding the CRISPR Toolbox: Targeting RNA with Cas13b
Barrangou, R., & Gersbach, C. A. (2017, February 16). MOLECULAR CELL, Vol. 65, pp. 582–584.
MeSH headings : CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; Humans; RNA; RNA, Guide, Kinetoplastida / genetics
TL;DR:
In this issue of Molecular Cell, Smargon et al. 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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2017 journal article
Genome Editing of Food-Grade Lactobacilli To Develop Therapeutic Probiotics
Microbiology Spectrum, 5(5).
MeSH headings : Animals; Bacterial Infections / drug therapy; Gene Editing; Genome, Bacterial; Humans; Lactobacillus / genetics; Lactobacillus / physiology; Probiotics / chemistry; Probiotics / therapeutic use
TL;DR:
Recent advances in genetic alteration of food-grade bacteria, with a focus on CRISPR-associated enzyme genome editing, single-stranded DNA recombineering, and the modification of bacteriophages are discussed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: ORCID
Added: January 3, 2020
2017 journal article
Guest editorial: CRISPRcas9: CRISPR-Cas systems: at the cutting edge of microbiology
Current Opinion in Microbiology, 37, vii-viii.
MeSH headings : Bacteria / genetics; Bacteria / immunology; Biotechnology / trends; CRISPR-Associated Proteins / metabolism; CRISPR-Cas Systems / genetics; CRISPR-Cas Systems / immunology; Gene Editing; Microbiology / trends; Quorum Sensing
Sources: ORCID, NC State University Libraries, NC State University Libraries
Added: August 6, 2018
2017 article
Immune Loss as a Driver of Coexistence During Host-Phage Coevolution
Weissman, J. L., Holmes, R., Barrangou, R., Moineau, S., Fagan, W. F., Levin, B., & Johnson, P. L. F. (2017, February 3).
Source: ORCID
Added: January 2, 2020
2017 journal article
Investigating the Effect of Growth Phase on the Surface-Layer Associated Proteome of Lactobacillus acidophilus Using Quantitative Proteomics
FRONTIERS IN MICROBIOLOGY, 8.
author keywords: Lactobacillus; probiotic; cell surface; S-layer; quantitative proteomics
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2017 journal article
Lactobacillus acidophilus Metabolizes Dietary Plant Glucosides and Externalizes Their Bioactive Phytochemicals
MBIO, 8(6).
Ed(s): E. Martens & M. McFall-Ngai
author keywords: Lactobacillus; beta-glucoside; bioavailability; gut microbiota; phytochemical; polydatin; polyphenols; resveratrol; xenobiotic metabolism
MeSH headings : Biological Availability; Dietary Carbohydrates / metabolism; Gastrointestinal Microbiome / physiology; Glucosides / metabolism; Glucosides / pharmacology; Humans; Hydrolysis; Lactobacillus acidophilus / drug effects; Lactobacillus acidophilus / genetics; Lactobacillus acidophilus / growth & development; Lactobacillus acidophilus / metabolism; Phytochemicals / metabolism; Polyphenols / metabolism; Resveratrol; Stilbenes / metabolism
TL;DR:
This work demonstrates the growth of Lactobacillus acidophilus on mono- and diglucosyl dietary plant glycosides (PGs) possessing small aromatic aglycones and highlights an important role of lactobacilli in the bioconversion of dietary PG and presents a framework from which to derive molecular insights into their metabolism by members of the human gut microbiota.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2017 journal article
Les systèmes CRISPR-Cas comme arme contre les bactéries pathogènes
Biologie Aujourd'Hui, 211(4), 265–270.
MeSH headings : Animals; Anti-Bacterial Agents / metabolism; Bacteria / immunology; Bacteria / pathogenicity; CRISPR-Cas Systems / physiology; Cell Death / genetics; Deoxyribonucleases / genetics; Deoxyribonucleases / metabolism; Disease Resistance / genetics; Humans; Immunity, Innate / genetics
TL;DR:
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.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: January 3, 2020
2017 journal article
On the global CRISPR array behavior in class I systems
BIOLOGY DIRECT, 12.
MeSH headings : CRISPR-Cas Systems / physiology; Chromosomes, Bacterial / chemistry; Datasets as Topic; Genome, Bacterial; Models, Genetic; Poisson Distribution; Software
TL;DR:
This study establishes that bacterial Class I CRISPR array size tends to follow a geometric distribution; theseCRISPRs are not randomly distributed along the chromosome; and the CRISpr array closest to the cas genes is typically larger than loci in trans.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science
Added: August 6, 2018
2017 journal article
QnAs with Rodolphe Barrangou
Proceedings of the National Academy of Sciences, 114(28), 7183–7184.
MeSH headings : Animals; Bacteria / virology; Biotechnology / history; Biotechnology / methods; Biotechnology / trends; CRISPR-Cas Systems; Drug Resistance, Bacterial; Food Contamination; Food Microbiology; Food Technology; Genotype; History, 21st Century; Livestock; Meat; Molecular Biology
TL;DR:
Rodolphe Barrangou furnished experimental proof for the notion that CRISPR confers a form of adaptive immunity that helps bacteria fend off invading viruses, and was honored with 2017 National Academy of Sciences Award in molecular biology.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2017 journal article
Repurposing CRISPR-Cas systems as DNA-based smart antimicrobials
Cell and Gene Therapy Insights, 3(1), 63–72.
Source: ORCID
Added: January 2, 2020
2017 journal article
The S-layer Associated Serine Protease Homolog PrtX Impacts Cell Surface-Mediated Microbe-Host Interactions of Lactobacillus acidophilus NCFM
FRONTIERS IN MICROBIOLOGY, 8.
author keywords: serine protease; S-layer; S-layer associated proteins; Lactobacillus; probiotic; intestinal barrier integrity; mucin; fibronectin
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2017 review
Using CRISPR-Cas systems as antimicrobials
[Review of ]. CURRENT OPINION IN MICROBIOLOGY, 37, 155–160.
MeSH headings : Anti-Infective Agents / pharmacology; Biological Products / pharmacology; CRISPR-Cas Systems; DNA Cleavage; DNA, Bacterial / metabolism; Genetic Engineering; Microbial Viability / drug effects; Plasmids; Transformation, Bacterial
TL;DR:
This work discusses how DNA damage introduced by Cas nucleases in bacteria can efficiently and specifically lead to plasmid curing or drive cell death and establishes CRISPR-Cas systems as potent and programmable antimicrobials.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2016 review
Applications of CRISPR technologies in research and beyond
[Review of ]. NATURE BIOTECHNOLOGY, 34(9), 933–941.
TL;DR:
Programmable DNA cleavage using CRISPR–Cas9 enables efficient, site-specific genome engineering in single cells and whole organisms and is being used to expedite crop and livestock breeding, engineer new antimicrobials and control disease- carrying insects with gene drives.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2016 journal article
CRISPR Diversity and Microevolution in Clostridium difficile
GENOME BIOLOGY AND EVOLUTION, 8(9), 2841–2855.
author keywords: CRISPR-Cas; CRISPR phylogeny; CRISPR typing; BI/NAP1/RT027/ST1Type-IB
MeSH headings : CRISPR-Cas Systems; Clostridioides difficile / classification; Clostridioides difficile / genetics; Clustered Regularly Interspaced Short Palindromic Repeats; Evolution, Molecular; Phylogeny; Polymorphism, Genetic
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2016 journal article
CRISPR-Based Typing and Next-Generation Tracking Technologies
Annual Review of Food Science and Technology, 7(1), 395–411.
author keywords: CRISPR; cas; typing; epidemiology
MeSH headings : Bacteria / classification; Bacteria / genetics; CRISPR-Cas Systems / genetics; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; Clustered Regularly Interspaced Short Palindromic Repeats / physiology; Genome, Bacterial / genetics; Genotyping Techniques / methods; Genotyping Techniques / trends; Lactobacillus / classification; Lactobacillus / genetics; Salmonella / classification; Salmonella / genetics; Streptococcus thermophilus / classification; Streptococcus thermophilus / genetics
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: ORCID
Added: January 2, 2020
2016 review
CRISPR-based typing and next-generation tracking technologies
[Review of ]. Annual review of food science and technology, vol 7, 7, 395–411.
Source: NC State University Libraries
Added: August 6, 2018
2016 review
Deciphering and shaping bacterial diversity through CRISPR
[Review of ]. CURRENT OPINION IN MICROBIOLOGY, 31, 101–108.
MeSH headings : Bacteria / genetics; Bacteria / virology; Bacteriophages / genetics; CRISPR-Cas Systems / genetics; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; Genome, Bacterial / genetics; Host-Pathogen Interactions / genetics
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2016 journal article
Functional Analysis of an S-Layer-Associated Fibronectin-Binding Protein in Lactobacillus acidophilus NCFM
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 82(9), 2676–2685.
Ed(s): E. Dudley
MeSH headings : Bacterial Adhesion / physiology; Bacterial Proteins / chemistry; Bacterial Proteins / metabolism; Fibronectins / metabolism; Intestines / microbiology; Lactobacillus acidophilus / chemistry; Lactobacillus acidophilus / genetics; Lactobacillus acidophilus / metabolism; Membrane Glycoproteins / metabolism; Mutation; Phylogeny; Protein Binding
TL;DR:
To investigate the functional role of LBA0191 (designated FbpB) in L. acidophilus NCFM, an fbpB-deficient strain was constructed and a mutant with a deletion of fBPB lost the ability to adhere to mucin and fibronectin in vitro.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2016 journal article
Genotyping by PCR and High-Throughput Sequencing of Commercial Probiotic Products Reveals Composition Biases
FRONTIERS IN MICROBIOLOGY, 7.
author keywords: probiotics; labeling; testing and assessment; Lactobacillus; Bifidobacterium; multiplex PCR; taxonomy; high-throughput nucleotide sequencing
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2016 journal article
Guide RNAs: A Glimpse at the Sequences that Drive CRISPR–Cas Systems
Cold Spring Harbor Protocols, 2016(7), pdb.top090902.
MeSH headings : CRISPR-Cas Systems; Gene Editing / methods; RNA, Guide, Kinetoplastida / genetics; RNA, Guide, Kinetoplastida / metabolism; Streptococcus pyogenes / enzymology
TL;DR:
The biological significance of Type II CRISPR-Cas elements, including the tracrRNA, crRNA, Cas9, and protospacer-adjacent motif (PAM), are discussed, and the native function of these elements is looked at to understand how they can be engineered, enhanced, and optimized for genome editing applications.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2016 journal article
Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems
MOLECULAR CELL, 62(1), 137–147.
MeSH headings : Bacillus / chemistry; Bacillus / metabolism; CRISPR-Associated Proteins / chemistry; CRISPR-Associated Proteins / genetics; CRISPR-Cas Systems; Escherichia coli / chemistry; Escherichia coli / metabolism; Francisella / chemistry; Francisella / metabolism; High-Throughput Screening Assays / methods; Protein Structure, Tertiary; Streptococcus thermophilus / chemistry; Streptococcus thermophilus / metabolism
TL;DR:
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 to accelerate ability to understand and exploit the multitude of CRISPR-Cas systems in nature.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2016 journal article
Phylogenetic Analysis of the Bifidobacterium Genus Using Glycolysis Enzyme Sequences
FRONTIERS IN MICROBIOLOGY, 7.
author keywords: Bifidobacterium; glycolysis; phylogeny; probiotic; evolution
TL;DR:
It is shown 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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2016 journal article
Prediction and Validation of Native and Engineered Cas9 Guide Sequences
Cold Spring Harbor Protocols, 2016(7), pdb.prot086785.
MeSH headings : Bacterial Proteins / metabolism; CRISPR-Associated Protein 9; Endonucleases / metabolism; Gene Editing / methods; RNA, Guide, Kinetoplastida / genetics; RNA, Guide, Kinetoplastida / metabolism; Streptococcus pyogenes / enzymology
TL;DR:
How to predict tracrRNA sequences and suggest a method for designing single guide RNAs containing only critical structural modules are discussed, which is crucial for determining potential targets for Cas9.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2015 journal article
Advances in CRISPR-Cas9 genome engineering: lessons learned from RNA interference
NUCLEIC ACIDS RESEARCH, 43(7), 3407–3419.
MeSH headings : Animals; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; Genetic Engineering; Genome; RNA Interference
TL;DR:
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 is examined.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2015 review
An updated evolutionary classification of CRISPR-Cas systems
[Review of ]. Nature Reviews. Microbiology, 13(11), 722–736.
Source: NC State University Libraries
Added: August 6, 2018
2015 journal article
An updated evolutionary classification of CRISPR–Cas systems
Nature Reviews Microbiology, 13(11), 722–736.
MeSH headings : Archaea / genetics; Bacteria / genetics; CRISPR-Cas Systems / genetics; Evolution, Molecular; Genome, Archaeal; Genome, Bacterial; Phylogeny
TL;DR:
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 is presented.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Crossref, NC State University Libraries
Added: January 2, 2020
2015 journal article
CRISPR Immunity Drives Rapid Phage Genome Evolution in Streptococcus thermophilus
MBIO, 6(2).
MeSH headings : Adaptation, Biological; CRISPR-Cas Systems; Evolution, Molecular; Genome, Viral; Host-Parasite Interactions; Mutation Rate; Polymorphism, Single Nucleotide; Recombination, Genetic; Streptococcus thermophilus / genetics; Streptococcus thermophilus / virology
TL;DR:
CRISPR immunity drives the accumulation of phage genome rearrangements (which enable longer phage survival) and escape mutations, establishing CRISPR as one of the fundamental drivers of phages evolution.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2015 journal article
CRISPR-Based Technologies and the Future of Food Science
Journal of Food Science, 80(11), R2367–R2372.
author keywords: CRISPR; genome; microbiology
MeSH headings : Bacteria / genetics; Bacteria / virology; Bacteriophages; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; Fermentation; Food Technology; Humans; Probiotics
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
3. Good Health and Well-being
(Web of Science)
Source: ORCID
Added: January 2, 2020
2015 journal article
CRISPR-based screening of genomic island excision events in bacteria
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112(26), 8076–8081.
author keywords: CRISPR; lactic acid bacteria; transposons; IS-elements; Cas9
MeSH headings : Clustered Regularly Interspaced Short Palindromic Repeats; Gene Deletion; Genome, Bacterial; Homeostasis; Homologous Recombination; Streptococcus thermophilus / genetics; Streptococcus thermophilus / growth & development
TL;DR:
This study shows that CRISPR-Cas systems can be directed to target and delete genomic islands that are flanked by insertion-sequence elements and devoid of essential genes, and established that self-targeting CRISpr-cas systems may direct significant evolution of bacterial genomes on a population level, influencing genome homeostasis and remodeling.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
14. Life Below Water
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2015 journal article
Conserved S-Layer-Associated Proteins Revealed by Exoproteomic Survey of S-Layer-Forming Lactobacilli
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 82(1), 134–145.
Ed(s): H. Nojiri
MeSH headings : Bacterial Proteins / chemistry; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Lactobacillus / chemistry; Lactobacillus / classification; Lactobacillus / genetics; Lactobacillus / metabolism; Lactobacillus acidophilus / chemistry; Lactobacillus acidophilus / genetics; Lactobacillus acidophilus / metabolism; Membrane Glycoproteins / chemistry; Membrane Glycoproteins / genetics; Membrane Glycoproteins / metabolism; Molecular Sequence Data; Phylogeny; Proteomics
TL;DR:
Proteomic complexity and differences in the cell surface properties between S-layer- and non-S- layer-forming lactobacilli reveal the potential for SLAPs to mediate intimate probiotic interactions and signaling with the host intestinal mucosa.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2015 journal article
Diversity of CRISPR-Cas immune systems and molecular machines
Genome Biology, 16(1).
MeSH headings : Adaptive Immunity / genetics; Animals; Bacteria / genetics; Bacteria / immunology; CRISPR-Cas Systems / genetics; CRISPR-Cas Systems / immunology; DNA / genetics; Genetic Engineering / methods; Genetic Variation / genetics; Genetic Variation / immunology; Humans; RNA Editing / genetics
TL;DR:
A plethora of CRISPR molecular machines occur broadly in prokaryotic genomes, with a diversity of Cas nucleases that can be repurposed for various applications.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: ORCID
Added: January 2, 2020
2015 review
Diversity of CRISPR-Cas immune systems and molecular machines
[Review of ]. Genome Biology, 16.
Source: NC State University Libraries
Added: August 6, 2018
2015 journal article
Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera
NATURE COMMUNICATIONS, 6.
MeSH headings : Biotechnology; Genome, Bacterial; Lactobacillus / enzymology; Lactobacillus / genetics; Leuconostoc / genetics; Pediococcus / genetics; Phylogeny; Sequence Analysis, DNA
TL;DR:
The genome sequences of 213 different Lactobacilli strains and associated genera are reported, and new insight is provided into phylogenomic organization and adaptive immunity elements in this bacteria family, presenting a robust phylogenomic framework of existing species and for classifying new species.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2015 review
Exploiting CRISPR-Cas immune systems for genome editing in bacteria
[Review of ]. CURRENT OPINION IN BIOTECHNOLOGY, 37, 61–68.
MeSH headings : CRISPR-Cas Systems; DNA Repair; DNA, Bacterial / genetics; Genome, Bacterial; Humans; Immune System; Protein Engineering
TL;DR:
It is envisioned that CRISPR-Cas technologies will play a key role in the development of next-generation industrial bacteria, and the application of single stranded DNA recombineering combined with CRISpr-Cas selection to edit the genome of a probiotic organism is highlighted.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2015 review
Harnessing CRISPR-Cas systems for bacterial genome editing
[Review of ]. TRENDS IN MICROBIOLOGY, 23(4), 225–232.
author keywords: genome editing; CRISPR-Cas; Cas9
MeSH headings : Bacteria / genetics; CRISPR-Cas Systems / genetics; Clustered Regularly Interspaced Short Palindromic Repeats; DNA Repair; Genetic Engineering / methods; Genome, Bacterial; Homeostasis / genetics; Mutation; Phenotype
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2015 journal article
JFS Special Issue: 75 years of advancing food science, and preparing for the next 75 CRISPR-based technologies and the future of food science
Journal of Food Science, 80(11), R2367–2372.
Source: NC State University Libraries
Added: August 6, 2018
2015 journal article
Metagenomic reconstructions of bacterial CRISPR loci constrain population histories
ISME JOURNAL, 10(4), 858–870.
MeSH headings : Bacteria / classification; Bacteria / genetics; Bacteria / virology; Bacteriophages / genetics; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; Metagenomics; Plasmids
TL;DR:
Metagenomics is used to study the stability and dynamics of the type I-E CRISPR-Cas locus of Leptospirillum group II bacteria in biofilms sampled over 5 years from an acid mine drainage (AMD) system and suggest long-term coexistence of Leptonospirillo group II with AMDV1 and periods whenAMDV1 was less dominant.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2015 journal article
Microbial Ecology of Watery Kimchi
JOURNAL OF FOOD SCIENCE, 80(5), M1031–M1038.
author keywords: high-throughput sequencing; microbial ecology; watery kimchi
MeSH headings : DNA, Bacterial / chemistry; DNA, Bacterial / classification; DNA, Bacterial / isolation & purification; DNA, Ribosomal / chemistry; Enterobacteriaceae / classification; Enterobacteriaceae / genetics; Enterobacteriaceae / isolation & purification; Fermentation; Food Microbiology; Lactobacillus / classification; Proteobacteria / classification; Proteobacteria / genetics; Proteobacteria / isolation & purification; RNA, Ribosomal, 16S / genetics; Raphanus / microbiology; Sequence Analysis, DNA; Temperature; Vegetables / microbiology
TL;DR:
Differences in biochemistry and microbial ecology that can result from preparation method and fermentation conditions of the kimchi may impact safety and quality and quality (homolactic fermentation can be undesirable, if too much acid is produced) of the product.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2015 journal article
Occurrence and Diversity of CRISPR-Cas Systems in the Genus Bifidobacterium
PLOS ONE, 10(7).
Ed(s): C. Riedel
MeSH headings : Bifidobacterium / genetics; CRISPR-Cas Systems / genetics; Chromosomes, Bacterial / genetics; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; DNA / genetics; Evolution, Molecular; Genetic Variation / genetics; Genome, Bacterial / genetics; Prophages / genetics
TL;DR:
It is 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, which may shed light on evolutionary processes and strain divergence.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2015 journal article
Occurrence and activity of a type II CRISPR-Cas system in Lactobacillus gasseri
MICROBIOLOGY-SGM, 161, 1752–1761.
MeSH headings : Base Sequence; CRISPR-Cas Systems / genetics; Clustered Regularly Interspaced Short Palindromic Repeats; Gene Order; Genome, Bacterial; Lactobacillus / genetics; Molecular Sequence Data; Plasmids / genetics
TL;DR:
The distribution and function of a native type II-A CRISPR-Cas system in the commensal species L. gasseri is reported, which 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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2015 review
The Bacterial Origins of the CRISPR Genome-Editing Revolution
[Review of ]. HUMAN GENE THERAPY, 26(7), 413–424.
MeSH headings : Animals; Archaea / genetics; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; Genetic Engineering / economics; Genetic Engineering / trends; Genome, Bacterial; Humans
TL;DR:
The biological and mechanistic basis for these remarkable immune systems, and how their engineered derivatives are revolutionizing basic and clinical research are described.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2015 review
The roles of CRISPR-Cas systems in adaptive immunity and beyond
[Review of ]. CURRENT OPINION IN IMMUNOLOGY, 32, 36–41.
MeSH headings : Archaea / immunology; Bacteria / immunology; Bacterial Physiological Phenomena; Biological Evolution; CRISPR-Cas Systems / physiology; Gene Expression Regulation, Bacterial; Genome, Bacterial; Transcription, Genetic
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2014 article
A CRISPR design for next-generation antimicrobials
GENOME BIOLOGY, Vol. 15.
MeSH headings : Animals; Anti-Infective Agents / administration & dosage; CRISPR-Cas Systems; Drug Resistance, Microbial / genetics; Enterohemorrhagic Escherichia coli / genetics; Gene Targeting; RNA, Guide, Kinetoplastida / genetics; Ribonucleases / genetics
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2014 article
Bacteriophage exclusion, a new defense system
Barrangou, R., & Oost, J. (2015, January 14). EMBO JOURNAL, Vol. 34, pp. 134–135.
MeSH headings : Bacillus subtilis / virology; Bacteriophages / genetics; Bacteriophages / pathogenicity; DNA Methylation; DNA Modification Methylases / genetics; Genome, Microbial; Virulence / genetics
TL;DR:
Bacteriophage exclusion (BREX) is unveiled as a novel, widespread bacteriophages resistance system that provides innate immunity against virulent and temperate phage in bacteria.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
10. Reduced Inequalities
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2014 review
CRISPR-Cas Systems: Prokaryotes Upgrade to Adaptive Immunity
[Review of ]. MOLECULAR CELL, 54(2), 234–244.
MeSH headings : Adaptive Immunity / genetics; Bacteriophages / immunology; CRISPR-Associated Proteins / immunology; Clustered Regularly Interspaced Short Palindromic Repeats / immunology; DNA, Bacterial / chemistry; Inverted Repeat Sequences; Prokaryotic Cells / immunology; Prokaryotic Cells / virology
TL;DR:
CRISPR-Cas shares functional features with the mammalian adaptive immune system, while also exhibiting characteristics of Lamarckian evolution and can be repurposed for numerous DNA targeting applications including transcriptional control.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2014 article
Cas9 Targeting and the CRISPR Revolution
Barrangou, R. (2014, May 16). SCIENCE, Vol. 344, pp. 707–708.
MeSH headings : Clustered Regularly Interspaced Short Palindromic Repeats; DNA Cleavage; Gene Targeting / methods; Genetic Engineering / methods; RNA, Guide, Kinetoplastida / genetics; Streptococcus pyogenes / genetics
TL;DR:
This work has shown that genome editing technology based on the prokaryotic CRISPR–Cas9 system is completely revolutionizing genome engineering and has already started to supplant incumbent genome editing technologies, such as TALENs and ZFNs.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2014 journal article
Characterization and evolution of Salmonella CRISPR-Cas systems
MICROBIOLOGY-SGM, 161, 374–386.
TL;DR:
Salmonella CRISPR-Cas systems are no longer immunogenic; rather, their impressive conservation indicates they may have an alternative function in Salmonella, and 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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2014 article
Functions and Applications of RNA-Guided CRISPR-Cas Immune Systems
Barrangou, R., & Horvath, P. (2014, October). Encyclopedia of Molecular Cell Biology and Molecular Medicine.
TL;DR:
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.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2014 journal article
Genomic Encyclopedia of Type Strains of the Genus Bifidobacterium
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 80(20), 6290–6302.
MeSH headings : Animals; Bifidobacterium / genetics; Bifidobacterium / metabolism; Bifidobacterium / physiology; Biological Evolution; Clustered Regularly Interspaced Short Palindromic Repeats; Computer Simulation; Gastrointestinal Tract / microbiology; Genome, Bacterial; Molecular Sequence Data; Phylogeny; Sequence Analysis, DNA; Species Specificity
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2014 journal article
Guide RNA Functional Modules Direct Cas9 Activity and Orthogonality
MOLECULAR CELL, 56(2), 333–339.
MeSH headings : Bacterial Proteins / chemistry; CRISPR-Associated Protein 9; CRISPR-Associated Proteins / chemistry; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; DNA / chemistry; DNA Cleavage; Endonucleases / chemistry; Genetic Engineering / methods; HEK293 Cells; Humans; Nucleic Acid Conformation; RNA, Guide, Kinetoplastida / chemistry; RNA, Guide, Kinetoplastida / genetics; RNA, Guide, Kinetoplastida / ultrastructure
TL;DR:
Six conserved modules within native crRNA:tracrRNA duplexes and single guide RNAs that direct Cas9 endonuclease activity are identified and characterized and it is shown the bulge and nexus are necessary for DNA cleavage and the nexus and hairpins are instrumental in defining orthogonality between systems.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2014 journal article
Microbiology: Bacteria get vaccinated
Nature, 513(7517), 175–176.
MeSH headings : Adaptive Immunity / immunology; Bacteriophages / immunology; CRISPR-Cas Systems / immunology; Streptococcus thermophilus / immunology
TL;DR:
Infection by defective bacterial viruses that cannot replicate has now been found to be the key feature enabling bacteria to rapidly develop adaptive immunity against functional viruses.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, NC State University Libraries, NC State University Libraries
Added: August 6, 2018
2014 journal article
Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR-Cas Systems
MBIO, 5(1).
MeSH headings : CRISPR-Cas Systems; DNA, Bacterial / genetics; DNA, Bacterial / metabolism; Escherichia coli / genetics; Genome, Bacterial; Hydrolysis; Microbial Viability
TL;DR:
It is demonstrated that genome targeting with CRISPR-Cas systems can be employed for the sequence-specific and titratable removal of individual bacterial strains and species and may open new avenues for the development of “smart” antibiotics that circumvent multidrug resistance and differentiate between pathogenic and beneficial microorganisms.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science
Added: August 6, 2018
2014 article
Protection against Foreign DNA
Horvath, P., & Barrangou, R. Bacterial Stress Responses, Second Edition, pp. 333–348.
TL;DR:
This study experimentally confirmed that CRISPR targets DNA directly in Staphylococcus, and showed that Cas3, a predicted HD nuclease fused to a DEAD-box helicase, is required for the phage-resistance phenotype.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: ORCID
Added: January 2, 2020
2014 journal article
Short communication: Determination of Salmonella clustered regularly interspaced short palindromic repeats (CRISPR) diversity on dairy farms in Wisconsin and Minnesota
Journal of Dairy Science, 97(10), 6370–6377.
author keywords: salmonellosis; cow; clustered regularly interspaced short palindromic repeats (CRISPR)
MeSH headings : Animals; Base Sequence; Cattle; Cattle Diseases / epidemiology; Cattle Diseases / microbiology; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; Dairying; Feces / microbiology; Female; Genetic Variation; Genotype; Humans; Minnesota / epidemiology; Molecular Sequence Data; Salmonella / genetics; Salmonella / isolation & purification; Salmonella Food Poisoning / epidemiology; Salmonella Food Poisoning / microbiology; Salmonella Infections, Animal / epidemiology; Salmonella Infections, Animal / microbiology; Sequence Analysis, DNA; Serogroup; Wisconsin / epidemiology
TL;DR:
The results indicate that Salmonella strains present in smaller dairy herds (<500 head) are specific to that farm and new Salmonellosis strains may emerge over time.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2014 journal article
The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp enterica
PEERJ, 2.
author keywords: Salmonella; Horizontal gene transfer; Evolution; CRISPR; Outbreak; Phylogeny; Whole genome sequencing; Typing
TL;DR:
A novel clustering approach based onCRISPR spacer content is developed, but it is found that typing based on CRISPRs was less accurate than the MLST-based alternative; typed based on WGS data was the most accurate.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
10. Reduced Inequalities
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2014 journal article
The three major types of CRISPR-Cas systems function independently in CRISPR RNA biogenesis in Streptococcus thermophilus
MOLECULAR MICROBIOLOGY, 93(1), 98–112.
MeSH headings : Bacterial Proteins / metabolism; CRISPR-Cas Systems; Models, Genetic; RNA, Bacterial / metabolism; Sequence Analysis, RNA; Streptococcus thermophilus / genetics; Streptococcus thermophilus / metabolism
TL;DR:
Investigation of the features and biogenesis of the CRISPR (cr)RNAs in Streptococcus thermophilus (Sth) strain DGCC7710 indicates that multipleCRISPR‐Cas systems can function independently in crRNA biogenesis within a given organism.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2014 article
Unraveling the potential of CRISPR-Cas9 for gene therapy
Barrangou, R., & May, A. P. (2015, March). EXPERT OPINION ON BIOLOGICAL THERAPY, Vol. 15, pp. 311–314.
author keywords: Cas9; CRISPR; gene therapy; genome editing
MeSH headings : Animals; CRISPR-Cas Systems / genetics; DNA Repair / genetics; Genetic Therapy / methods; Genetic Therapy / trends; Genome; Humans
TL;DR:
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 and has opened new avenues for the investigation of genetic diseases in general, and for gene therapy applications in particular.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2013 journal article
A Snapshot into the Metabolism of Isomalto-oligosaccharides in Probiotic Bacteria
Journal of Applied Glycoscience, 60(2), 95–100.
TL;DR:
Genetic, transcriptomic, enzymatic, and biophysical analyses are used to explore IMO utilization routes in probiotic lactobacilli and bifidobacteria as represented by Lactobacillus acidophilus NCFM and BifidOBacterium animalis subsp.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2013 journal article
Antibiotic Resistance in Salmonella enterica Serovar Typhimurium Associates with CRISPR Sequence Type
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 57(9), 4282–4289.
TL;DR:
CRISPR-MVLST is a promising subtyping method for monitoring the farm-to-fork spread of antibiotic resistance in S. Typhimurium and its subpopulations are being transmitted through the food system.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2013 journal article
Association of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Elements with Specific Serotypes and Virulence Potential of Shiga Toxin-Producing Escherichia coli
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 80(4), 1411–1420.
MeSH headings : Cluster Analysis; Clustered Regularly Interspaced Short Palindromic Repeats; DNA, Bacterial / chemistry; DNA, Bacterial / genetics; Genotype; Molecular Sequence Data; Sequence Analysis, DNA; Serotyping; Shiga-Toxigenic Escherichia coli / classification; Shiga-Toxigenic Escherichia coli / genetics; Shiga-Toxigenic Escherichia coli / pathogenicity; Virulence Factors / genetics
TL;DR:
There was no association identified between the presence of subtype I-E cas and virulence genes, but the total number of spacers had a negative correlation with potential pathogenicity, and the relationship between the CRISPR-cas system and potential virulence needs to be determined on a broader scale.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2013 journal article
Bifidobacterium animalis subsp lactis ATCC 27673 Is a Genomically Unique Strain within Its Conserved Subspecies
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 79(22), 6903–6910.
MeSH headings : Base Composition; Bifidobacterium / classification; Bifidobacterium / genetics; Bifidobacterium / isolation & purification; Clustered Regularly Interspaced Short Palindromic Repeats; Comparative Genomic Hybridization; DNA, Bacterial / genetics; Genome, Bacterial; Genomic Islands; Molecular Sequence Data; Open Reading Frames; Sequence Analysis, DNA
TL;DR:
This study revealed that ATCC 27673 is a strain of B. animalis subsp.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
14. Life Below Water
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2013 book
Source: ORCID
Added: January 2, 2020
2013 review
CRISPR-Cas systems and RNA-guided interference
[Review of ]. WILEY INTERDISCIPLINARY REVIEWS-RNA, 4(3), 267–278.
MeSH headings : Archaea / genetics; Archaea / virology; Bacteria / genetics; Bacteria / virology; Gene Transfer, Horizontal; Interspersed Repetitive Sequences; Plasmids; RNA, Small Interfering / genetics; RNA, Small Interfering / metabolism; RNA, Untranslated / genetics; RNA, Untranslated / metabolism; Recombination, Genetic; Repetitive Sequences, Nucleic Acid; Viruses / genetics
TL;DR:
A number of studies have shown that CRISPR‐mediated immunity can readily increase the breadth and depth of virus resistance in bacteria and archaea and applications of crRNA‐guided interference are discussed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2013 journal article
CRISPR-MVLST subtyping of Salmonella enterica subsp. enterica serovars Typhimurium and Heidelberg and application in identifying outbreak isolates
BMC Microbiology, 13(1), 254.
author keywords: CRISPR subtyping; CRISPR-MVLST; Molecular subtyping; Salmonella Heidelberg; Salmonella Typhimurium
MeSH headings : DNA, Bacterial / chemistry; DNA, Bacterial / genetics; Disease Outbreaks; Electrophoresis, Gel, Pulsed-Field; Foodborne Diseases / epidemiology; Foodborne Diseases / microbiology; Humans; Molecular Sequence Data; Molecular Typing / methods; Salmonella Infections / epidemiology; Salmonella Infections / microbiology; Salmonella enterica / classification; Salmonella enterica / genetics; Salmonella enterica / isolation & purification; Sequence Analysis, DNA; United States
TL;DR:
Pulsed-field Gel Electrophoresis (PFGE) and a recently developed molecular subtyping approach termed CRISPR-MVLST that exploits the hypervariable nature of virulence genes and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) to subtype clinical S. Typhimurium and S. Heidelberg isolates are analyzed.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2013 journal article
Complete Genome Sequence of Probiotic Strain Lactobacillus acidophilus La-14
Genome Announcements, 1(3), e00376–13-e00376–13.
TL;DR:
Globally, 111 single nucleotide polymorphisms (SNPs) were observed throughout the genome of Lactobacillus acidophilus strain La-14 and a 416-bp deletion in the LA14_1146 sugar ABC transporter was identified.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: ORCID
Added: January 2, 2020
2013 journal article
Genomic impact of CRISPR immunization against bacteriophages
BIOCHEMICAL SOCIETY TRANSACTIONS, 41(6), 1383–1391.
author keywords: adaptation; bacteriophage; clustered regularly interspaced short palindromic repeats; (CRISPR)-CRISPR-associated (Cas) system; draft genome; evolution
MeSH headings : Bacteriophages / immunology; Base Sequence; CRISPR-Cas Systems / genetics; CRISPR-Cas Systems / immunology; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; Clustered Regularly Interspaced Short Palindromic Repeats / immunology; Genome, Bacterial / genetics; Molecular Sequence Data; Mutation / genetics; Streptococcus thermophilus / genetics; Streptococcus thermophilus / immunology
TL;DR:
The genome sequence of a BIM (bacteriophage-insensitive mutant) derived from the DGCC7710 model organism is determined, and it is determined that building CRISPR-encoded immunity does not significantly affect the genome, which allows the maintenance of important functional properties in isogenicCRISPR mutants.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2013 journal article
In vitro reconstitution of Cascade-mediated CRISPR immunity in Streptococcus thermophilus
The EMBO Journal, 32(3), 385–394.
author keywords: DNA interference; DNA-dependent ATPase; nuclease
MeSH headings : Adaptive Immunity / immunology; Adenosine Triphosphate / metabolism; Base Sequence; Chromatography, High Pressure Liquid; Cloning, Molecular; DNA Cleavage; DNA Helicases / metabolism; Denaturing Gradient Gel Electrophoresis; Electrophoretic Mobility Shift Assay; In Vitro Techniques; Mass Spectrometry; Molecular Sequence Data; Plasmids / metabolism; RNA, Bacterial / genetics; RNA, Bacterial / immunology; Repetitive Sequences, Nucleic Acid / genetics; Repetitive Sequences, Nucleic Acid / immunology; Ribonucleoproteins / immunology; Ribonucleoproteins / metabolism; Rosaniline Dyes; Sequence Analysis, DNA; Streptococcus thermophilus / enzymology; Streptococcus thermophilus / immunology; Streptococcus thermophilus / virology
TL;DR:
It is shown 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, establishing a molecular basis for CRISPR immunity in St‐CRISPR4‐Cas and other Type I systems.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2013 journal article
Lactobacillus buchneri Genotyping on the Basis of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Locus Diversity
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 80(3), 994–1001.
MeSH headings : Clustered Regularly Interspaced Short Palindromic Repeats; DNA, Bacterial / chemistry; DNA, Bacterial / genetics; Food Microbiology; Genetic Variation; Genotype; Lactobacillus / classification; Lactobacillus / genetics; Lactobacillus / isolation & purification; Molecular Sequence Data; Molecular Typing / methods; Sequence Analysis, DNA
TL;DR:
Findings suggest that type II-A CRISPR-Cas systems are valuable for genotyping of L. buchneri, a species relevant for commercial silage, bioethanol, and vegetable fermentations.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2013 journal article
Phylogenetic Diversity of the Enteric Pathogen Salmonella enterica subsp enterica Inferred from Genome-Wide Reference-Free SNP Characters
GENOME BIOLOGY AND EVOLUTION, 5(11), 2109–2123.
author keywords: H antigens; serovar; O antigens; CRISPR; lineage-through-time plot; comparative method
MeSH headings : Base Sequence; Clustered Regularly Interspaced Short Palindromic Repeats; Evolution, Molecular; Gene Transfer, Horizontal; Genome, Bacterial; Molecular Sequence Data; O Antigens / genetics; Phylogeny; Polymorphism, Single Nucleotide; Salmonella enterica / classification; Salmonella enterica / genetics
TL;DR:
This study shows the ability to extract reference-free SNPs from a large set of genomes and then to use these SNPs for phylogenetic reconstruction, an important step forward for bacterial disease tracking and in efficiently elucidating the evolutionary history of highly clonal organisms.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2013 journal article
RNA-guided genome editing à la carte
Cell Research, 23(6), 733–734.
MeSH headings : CRISPR-Cas Systems / genetics; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; DNA Restriction Enzymes; Endonucleases; Genetic Engineering; Humans; Plasmids / genetics; RNA / genetics; RNA / metabolism; RNA Editing / genetics; RNA, Guide, Kinetoplastida / genetics; RNA, Small Interfering / genetics; Viruses / genetics
TL;DR:
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.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2013 review
Recent insight into oligosaccharide uptake and metabolism in probiotic bacteria
[Review of ]. BIOCATALYSIS AND BIOTRANSFORMATION, 31(4), 226–235.
author keywords: Prebiotic; oligosaccharide uptake; ATP-binding cassette transport system; phosphotransferase system; transcriptional analysis
TL;DR:
It is 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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
10. Reduced Inequalities
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2013 journal article
Strong bias in the bacterial CRISPR elements that confer immunity to phage
Nature Communications, 4, 1430.
MeSH headings : Autoimmunity / genetics; Bacteriophages / physiology; Biological Evolution; DNA, Intergenic / genetics; Genetic Loci / genetics; Genome, Viral / genetics; High-Throughput Nucleotide Sequencing; Host-Pathogen Interactions / genetics; Immunity / genetics; Inverted Repeat Sequences / genetics; Open Reading Frames / genetics; Polymorphism, Single Nucleotide / genetics; Streptococcus thermophilus / genetics; Streptococcus thermophilus / immunology; Streptococcus thermophilus / virology
TL;DR:
A strong and reproducible bias in the phage genome locations from which spacers derive is detected, suggesting selection for specific spacers based on location and effectiveness in CRISPR–Cas systems.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2013 journal article
Subtyping of Salmonella enterica Serovar Newport Outbreak Isolates by CRISPR-MVLST and Determination of the Relationship between CRISPR-MVLST and PFGE Results
JOURNAL OF CLINICAL MICROBIOLOGY, 51(7), 2328–2336.
MeSH headings : Cluster Analysis; DNA Fingerprinting / methods; DNA, Bacterial / chemistry; DNA, Bacterial / genetics; Electrophoresis, Gel, Pulsed-Field / methods; Genotype; Humans; Molecular Epidemiology / methods; Molecular Sequence Data; Multilocus Sequence Typing / methods; Salmonella enterica / classification; Salmonella enterica / genetics
TL;DR:
The data show that CRISPR-MVLST could be a complementary approach to PFGE subtyping for S. Newport and suggest that bothSubtyping approaches have high discriminatory abilities with a potential for clustering cases with common exposures.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2013 journal article
The Evolutionary Divergence of Shiga Toxin-Producing Escherichia coli Is Reflected in Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Spacer Composition
Applied and Environmental Microbiology, 79(18), 5710–5720.
MeSH headings : Cluster Analysis; Clustered Regularly Interspaced Short Palindromic Repeats; DNA, Bacterial / chemistry; DNA, Bacterial / genetics; Evolution, Molecular; False Negative Reactions; False Positive Reactions; Genetic Variation; Molecular Sequence Data; Real-Time Polymerase Chain Reaction / methods; Sensitivity and Specificity; Sequence Analysis, DNA; Shiga-Toxigenic Escherichia coli / classification; Shiga-Toxigenic Escherichia coli / genetics; United States
TL;DR:
Conservation of CRISPR arrays among isolates expressing the same flagellar antigen, specifically, H7, H2, and H11, suggested that these isolates share an ancestor and provided an explanation for the false positives previously observed in the qPCR results.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: January 2, 2020
2013 journal article
The Population and Evolutionary Dynamics of Phage and Bacteria with CRISPR–Mediated Immunity
PLoS Genetics, 9(3), e1003312.
Ed(s): D. Hughes
MeSH headings : Bacteriophages / genetics; Bacteriophages / immunology; Base Sequence; Biological Evolution; DNA, Intergenic / genetics; Genetics, Population; Immunity / genetics; Interspersed Repetitive Sequences / genetics; Models, Theoretical; Molecular Sequence Data; Mutation; Sequence Analysis, DNA; Streptococcus thermophilus / genetics; Streptococcus thermophilus / immunology; Streptococcus thermophilus / virology
TL;DR:
It is postulated that the invasion of phage into populations of BIMs resistant by the acquisition of one (but not two) spacers and the establishment of a BIM–CEM arms race than predicted from existing assumptions about phage infection and CRISPR–cas immunity can be attributed to the phages infection-associated production of enzymes or other compounds.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2013 journal article
The combination of CRISPR-MVLST and PFGE provides increased discriminatory power for differentiating human clinical isolates of Salmonella enterica subsp. enterica serovar Enteritidis
Food Microbiology, 34(1), 164–173.
author keywords: Salmonella Enteritidis; CRISPR-MVLST; Molecular subtyping
MeSH headings : Bacterial Typing Techniques / methods; Electrophoresis, Gel, Pulsed-Field / methods; Feces / microbiology; Humans; Inverted Repeat Sequences; Molecular Sequence Data; Phylogeny; Polymerase Chain Reaction / methods; Salmonella Infections / microbiology; Salmonella enteritidis / classification; Salmonella enteritidis / genetics; Salmonella enteritidis / isolation & purification; Urine / microbiology
TL;DR:
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.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2013 journal article
Transcriptional analysis of oligosaccharide utilization by Bifidobacterium lactis Bl-04
BMC GENOMICS, 14(1).
author keywords: Bifidobacterium lactis; Transcriptomics; ABC transporter; GPH transporter; Prebiotics; Glycoside hydrolase
MeSH headings : Bifidobacterium / drug effects; Bifidobacterium / genetics; Cell Membrane / drug effects; Cell Membrane / metabolism; Data Mining; Gene Expression Profiling; Genetic Variation / genetics; Genomics; Multigene Family / genetics; Oligosaccharides / pharmacology; Prebiotics; Transcription, Genetic / drug effects; Up-Regulation / drug effects
TL;DR:
This study identified the differential gene expression for utilization of potential prebiotics highlighting the extensive capabilities of Bifidobacterium lactis Bl-04 to utilize oligosaccharides.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: ORCID, Web Of Science
Added: August 6, 2018
2013 journal article
crRNA and tracrRNA guide Cas9-mediated DNA interference in Streptococcus thermophilus
RNA BIOLOGY, 10(5), 841–851.
author keywords: CRISPR; DNA silencing; Type II CRISPR-Cas systems
MeSH headings : Bacterial Proteins / chemistry; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Base Sequence; CRISPR-Associated Proteins / chemistry; CRISPR-Associated Proteins / genetics; CRISPR-Associated Proteins / metabolism; Clustered Regularly Interspaced Short Palindromic Repeats; DNA / genetics; Escherichia coli / genetics; Escherichia coli / metabolism; Molecular Sequence Data; RNA, Bacterial / chemistry; RNA, Bacterial / genetics; RNA, Bacterial / metabolism; Ribonuclease III / chemistry; Ribonuclease III / genetics; Ribonuclease III / metabolism; Sequence Alignment; Streptococcus pyogenes / genetics; Streptococcus pyogenes / metabolism; Streptococcus thermophilus / genetics; Streptococcus thermophilus / metabolism
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2012 journal article
Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation
BMC Genomics, 13(1), 533.
author keywords: Lactobacillus casei; Lactic acid bacteria; Comparative genomics; Pan-genome; Supragenome; Evolution; Adaptation
MeSH headings : Adaptation, Physiological / genetics; Biological Evolution; Cluster Analysis; Gene Transfer, Horizontal; Genome, Bacterial; Genomic Islands; Lacticaseibacillus casei / genetics; Phylogeny
TL;DR:
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.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2012 article
Applications of the Versatile CRISPR-Cas Systems
CRISPR-Cas Systems, pp. 267–286.
Source: ORCID
Added: January 2, 2020
2012 article
Applications of the Versatile CRISPR-Cas Systems
CRISPR-Cas Systems, pp. 267–286.
TL;DR:
The ability to readily transfer functional CRISPR-Cas systems across even distant bacteria, and re-program their endonuclease activity make them amenable to genetic engineering and useful for genome editing.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2012 book
TL;DR:
Applications of the versatile CRISPR-Cas systems in microbial community context and their implications for genotyping and regulation of physiological processes are studied.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2012 journal article
CRISPR: New Horizons in Phage Resistance and Strain Identification
Annual Review of Food Science and Technology, 3(1), 143–162.
author keywords: bacteriophage; cas gene; interference; typing; immunity; starter culture
MeSH headings : Bacteriophages / classification; Bacteriophages / genetics; Bacteriophages / physiology; Fermentation; Food Microbiology / trends; Genes, Viral; Gram-Positive Bacteria / classification; Gram-Positive Bacteria / genetics; Gram-Positive Bacteria / metabolism; Gram-Positive Bacteria / virology; Inverted Repeat Sequences; Lysogeny; RNA Interference; RNA, Small Interfering
TL;DR:
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.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2012 journal article
Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria
Proceedings of the National Academy of Sciences, 109(39), E2579–E2586.
author keywords: nuclease; site-directed mutagenesis; RNA interference; DNA interference
MeSH headings : Bacterial Proteins / genetics; Bacterial Proteins / metabolism; DNA Breaks, Double-Stranded; DNA Breaks, Single-Stranded; Endonucleases / genetics; Endonucleases / metabolism; RNA, Bacterial / genetics; RNA, Bacterial / metabolism; Ribonucleoproteins / genetics; Ribonucleoproteins / metabolism; Streptococcus thermophilus / enzymology; Streptococcus thermophilus / genetics
TL;DR:
It is demonstrated 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, paving the way for engineering of universal programmable RNA-guided DNA endonucleases.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2012 journal article
Complete Genome Sequences of Probiotic Strains Bifidobacterium animalis subsp. lactis B420 and Bi-07
Journal of Bacteriology, 194(15), 4131–4132.
MeSH headings : Bifidobacterium / genetics; Bifidobacterium / isolation & purification; DNA, Bacterial / chemistry; DNA, Bacterial / genetics; Genome, Bacterial; INDEL Mutation; Molecular Sequence Data; Polymorphism, Single Nucleotide; Probiotics; Repetitive Sequences, Nucleic Acid; Sequence Analysis, DNA
TL;DR:
Comparative genomic analysis with the type strain DSMZ10140 revealed 40 to 55 single nucleotide polymorphisms and an indel in a clustered regularly interspaced short palindromic repeat (CRISPR) locus that provide a molecular basis for strain typing within the two main phylogenetic groups of this monomorphic species.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2012 journal article
Persisting Viral Sequences Shape Microbial CRISPR-based Immunity
PLoS Computational Biology, 8(4), e1002475.
Ed(s): C. Mering
MeSH headings : Computer Simulation; Genetics, Population; Immunogenetic Phenomena / physiology; Inverted Repeat Sequences / physiology; Models, Genetic; Models, Immunological; Virus Physiological Phenomena
TL;DR:
A population genetic mathematical model of CRISPR-virus coevolution with six years of metagenomic sequencing is combined to link the recoverable genomic dynamics ofCRISPR loci to the unknown population dynamics of virus and host in natural communities.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: January 2, 2020
2012 journal article
Phage mutations in response to CRISPR diversification in a bacterial population
Environmental Microbiology, 15(2), 463–470.
MeSH headings : Bacteriophages / genetics; Bacteriophages / physiology; Base Sequence; Biological Evolution; DNA, Intergenic / genetics; Genetic Variation; Genome, Viral / genetics; Humans; Molecular Sequence Data; Mutation; Polymorphism, Single Nucleotide; Streptococcus thermophilus / genetics; Streptococcus thermophilus / virology
TL;DR:
The sequential fixation or near fixation of these single mutations indicates selection events so severe that single phage genotypes ultimately gave rise to all surviving lineages and potentially carried traits unrelated to immunity to fixation, suggesting a strong selective advantage for the phage that mutated in this region.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: January 2, 2020
2012 journal article
Phage-Induced Expression of CRISPR-Associated Proteins Is Revealed by Shotgun Proteomics in Streptococcus thermophilus
PLoS ONE, 7(5), e38077.
Ed(s): H. Bruggemann
MeSH headings : Bacterial Proteins / genetics; Bacteriophages / physiology; Genetic Loci / genetics; Inverted Repeat Sequences / genetics; Proteomics; Streptococcus thermophilus / cytology; Streptococcus thermophilus / genetics; Streptococcus thermophilus / virology; Time Factors; Transcriptome / genetics
TL;DR:
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, providing novel insights into the proteomic response of S. thermophilus, specifically CRISPR-associated proteins, upon phage 2972 infection.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2012 journal article
RNA-mediated programmable DNA cleavage
Nature Biotechnology, 30(9), 836–838.
MeSH headings : Bacteriophages / immunology; DNA Breaks, Double-Stranded; DNA Cleavage; Deoxyribonucleases, Type II Site-Specific / metabolism; Inverted Repeat Sequences; RNA / metabolism; Streptococcus pyogenes / enzymology
TL;DR:
Genome engineering has a new tool—endonucleases involved in bacterial adaptive immunity that can be reprogrammed with customizable small, noncoding RNAs.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Source: ORCID
Added: January 2, 2020
2012 journal article
Transcriptional Analysis of Prebiotic Uptake and Catabolism by Lactobacillus acidophilus NCFM
PLOS ONE, 7(9).
Ed(s): C. Gibas
MeSH headings : ATP-Binding Cassette Transporters / metabolism; Cellobiose / pharmacology; Gene Expression Regulation, Bacterial / drug effects; Glucans / pharmacology; Isomaltose / analogs & derivatives; Isomaltose / pharmacology; Lactobacillus acidophilus / drug effects; Lactobacillus acidophilus / enzymology; Lactobacillus acidophilus / metabolism; Oligosaccharides / pharmacology; Phosphoenolpyruvate Sugar Phosphotransferase System / metabolism; Prebiotics; Raffinose / pharmacology; Sugar Alcohols / pharmacology
TL;DR:
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, highlighting the broad oligosaccharide metabolic repertoire of L. acidophillus NCFM.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science
Added: August 6, 2018
2011 journal article
CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation
Annual Review of Genetics, 45(1), 273–297.
author keywords: coevolution; immunity; interference; RNAi; bacteriophage
MeSH headings : Adaptive Immunity; Archaea / chemistry; Archaea / genetics; Archaea / immunology; Archaea / virology; Bacteria / chemistry; Bacteria / genetics; Bacteria / immunology; Bacteria / virology; Bacterial Proteins / chemistry; Bacterial Proteins / genetics; Bacterial Proteins / immunology; Bacteriophages / genetics; Bacteriophages / immunology; CRISPR-Associated Proteins; Computational Biology; Endodeoxyribonucleases / chemistry; Endodeoxyribonucleases / genetics; Escherichia coli Proteins; Evolution, Molecular; Gene Expression Regulation, Archaeal; Gene Expression Regulation, Bacterial; Genetic Loci; Plasmids / immunology; RNA Interference; RNA Processing, Post-Transcriptional; RNA, Archaeal / chemistry; RNA, Archaeal / genetics; RNA, Archaeal / immunology; RNA, Bacterial / chemistry; RNA, Bacterial / genetics; RNA, Bacterial / immunology; RNA, Small Untranslated / chemistry; RNA, Small Untranslated / genetics; RNA, Small Untranslated / immunology; Transcription, Genetic; Virus Diseases / genetics; Virus Diseases / immunology; Virus Diseases / virology
TL;DR:
Exciting breakthroughs in understanding the mechanisms of the CRISPR-Cas system and its potential for biotechnological applications and understanding evolutionary dynamics are discussed.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2011 journal article
Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system
The EMBO Journal, 30(7), 1335–1342.
author keywords: Cas3; CRISPR; Ecoli subtype; site-directed mutagenesis; Streptococcus thermophilus
MeSH headings : Adenosine Triphosphate / metabolism; Cloning, Molecular; DNA Helicases / genetics; DNA Helicases / metabolism; DNA Mutational Analysis; DNA, Bacterial / chemistry; DNA, Bacterial / genetics; DNA, Single-Stranded / metabolism; Escherichia coli / genetics; Gene Expression; Models, Biological; Molecular Sequence Data; Mutagenesis, Site-Directed; Plasmids; Repetitive Sequences, Nucleic Acid; Sequence Analysis, DNA; Streptococcus thermophilus / enzymology; Streptococcus thermophilus / genetics
TL;DR:
It is proposed 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.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2011 journal article
Evolution and classification of the CRISPR–Cas systems
Nature Reviews Microbiology, 9(6), 467–477.
MeSH headings : Adaptive Immunity / genetics; Archaea / genetics; Archaeal Proteins / classification; Archaeal Proteins / genetics; Bacterial Proteins / classification; Bacterial Proteins / genetics; Genome, Bacterial; Phylogeny; Repetitive Sequences, Nucleic Acid
TL;DR:
An updated analysis of the evolutionary relationships between CRISPR–Cas systems and Cas proteins is provided and a 'polythetic' classification that integrates the phylogenies of the most common cas genes, the sequence and organization of theCRISPR repeats and the architecture of the CRISpr–cas loci is proposed.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2011 article
Genus Lactobacillus
Lactic Acid Bacteria, pp. 77–91.
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Source: ORCID
Added: January 2, 2020
2011 article
Lactic Acid Bacteria Defenses Against Phages
Stress Responses of Lactic Acid Bacteria, pp. 459–478.
TL;DR:
This chapter highlights the most broadly used phage-resistance systems in LAB, with an emphasis on the novel CRISPR/Cas system, which provides acquired adaptive immunity against phages by targeting viral nucleic acid in a sequence-specific manner.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2011 journal article
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
Applied and Environmental Microbiology, 77(6), 1946–1956.
MeSH headings : Alleles; Cluster Analysis; DNA, Bacterial / genetics; Electrophoresis, Gel, Pulsed-Field; Molecular Sequence Data; Multilocus Sequence Typing / methods; Polymerase Chain Reaction; Polymorphism, Genetic / genetics; Salmonella enterica / classification; Salmonella enterica / genetics; Virulence / genetics
TL;DR:
The novel MLST scheme described in the present study accurately differentiated outbreak strains/clones of the major serovars of Salmonella, and therefore, it shows promise for subtyping this important food-borne pathogen during investigations of outbreaks.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2011 journal article
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
Journal of Dairy Science, 94(12), 5864–5870.
author keywords: Bifidobacterium animalis ssp animalis; genome; growth in milk; clustered regularly interspaced short palindromic repeats (CRISPR)
MeSH headings : Animals; Base Sequence; Bifidobacterium / genetics; Bifidobacterium / growth & development; DNA, Intergenic / genetics; Genome, Bacterial / genetics; Inverted Repeat Sequences / genetics; Milk / microbiology; Molecular Sequence Data; Sequence Alignment; Sequence Analysis, DNA / methods; Sequence Homology, Nucleic Acid
Source: ORCID
Added: January 2, 2020
2011 journal article
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)
Applied and Environmental Microbiology, 77(13), 4520–4526.
MeSH headings : Animals; Chickens; Cluster Analysis; DNA, Bacterial / chemistry; DNA, Bacterial / genetics; Disease Outbreaks; Eggs; Environmental Microbiology; Food Microbiology; Genotype; Humans; Inverted Repeat Sequences; Molecular Sequence Data; Molecular Typing / methods; Salmonella Infections / microbiology; Salmonella Infections, Animal / microbiology; Salmonella enteritidis / classification; Salmonella enteritidis / genetics; Salmonella enteritidis / isolation & purification; Sequence Analysis, DNA; United States / epidemiology; Virulence Factors / genetics
TL;DR:
A sequence typing scheme based on virulence genes and clustered regularly interspaced short palindromic repeats (CRISPR) identified three persistent and predominate STs circulating among U.S. human clinical isolates and chicken, egg, and hen house environmental isolates in Pennsylvania, and a potential environment-specific sequence type.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2011 journal article
The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli
Nucleic Acids Research, 39(21), 9275–9282.
MeSH headings : Bacterial Proteins / chemistry; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Bacteriophage lambda / genetics; Base Sequence; Cloning, Molecular; DNA, Bacterial / chemistry; Escherichia coli / genetics; Escherichia coli / immunology; Escherichia coli / virology; Immunity; Molecular Sequence Data; Mutation; Nucleotide Motifs; Plasmids / genetics; Protein Structure, Tertiary; Repetitive Sequences, Nucleic Acid; Streptococcus thermophilus / genetics; Transformation, Bacterial
TL;DR:
The results show that active CRISPR/Cas systems can be transferred across distant genera and provide heterologous interference against invasive nucleic acids and 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.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2011 journal article
Transcriptional and functional analysis of galactooligosaccharide uptake by lacS in Lactobacillus acidophilus
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108(43), 17785–17790.
author keywords: lactose permease; catabolite repression element
MeSH headings : DNA, Complementary / genetics; Gene Expression Regulation, Bacterial / physiology; Lactobacillus acidophilus / genetics; Lactobacillus acidophilus / metabolism; Membrane Transport Proteins / metabolism; Microarray Analysis; Oligonucleotide Array Sequence Analysis; Oligosaccharides / pharmacokinetics; Prebiotics; Reverse Transcriptase Polymerase Chain Reaction; beta-Galactosidase / genetics; beta-Galactosidase / metabolism
TL;DR:
P phenotypic confirmation of the functional LacS permease not only for the utilization of lactose and GOS but also lactitol is confirmed, 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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science
Added: August 6, 2018
2010 journal article
Analysis of the human intestinal epithelial cell transcriptional response toLactobacillus acidophilus, Lactobacillus salivarius, Bifidobacterium lactisandEscherichia coli
Beneficial Microbes, 1(3), 283–295.
author keywords: probiotics; Escherichia coli; microarray; cell line models; epithelial cells
MeSH headings : Bifidobacterium / physiology; Cell Line; Epithelial Cells / drug effects; Epithelial Cells / metabolism; Epithelial Cells / microbiology; Escherichia coli / physiology; Gene Expression Profiling; Gene Expression Regulation / drug effects; Humans; Intestinal Mucosa / metabolism; Intestines / cytology; Intestines / drug effects; Intestines / microbiology; Lactobacillus / physiology; Models, Biological; Probiotics / pharmacology; Signal Transduction; Transcriptional Activation / drug effects
TL;DR:
Insight is provided into the relationship between probiotics and human intestinal epithelial cells, notably with regard to strain-specific responses, and the differences between transcriptional responses to pathogenic and probiotic bacteria are highlighted.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2010 journal article
CRISPR/Cas, the Immune System of Bacteria and Archaea
Science, 327(5962), 167–170.
MeSH headings : Archaea / genetics; Archaea / immunology; Archaea / virology; Archaeal Proteins / metabolism; Bacteria / genetics; Bacteria / immunology; Bacteria / virology; Bacterial Proteins / metabolism; Bacteriophages / genetics; Bacteriophages / physiology; Base Sequence; Conserved Sequence; Gene Transfer, Horizontal; Genes, Archaeal; Genes, Bacterial; Genetic Loci; Genome, Archaeal; Genome, Bacterial; Genome, Viral; Mutation; Plasmids; RNA Interference; RNA, Archaeal / genetics; RNA, Archaeal / metabolism; RNA, Bacterial / genetics; RNA, Bacterial / metabolism; Repetitive Sequences, Nucleic Acid
TL;DR:
Clustered regularly interspaced short palindromic repeats (CRISPR) form peculiar genetic loci, which provide acquired immunity against viruses and plasmids by targeting nucleic acid in a sequence-specific manner.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2010 journal article
Construction of vectors for inducible and constitutive gene expression in Lactobacillus
Microbial Biotechnology, 4(3), 357–367.
MeSH headings : Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Gene Expression; Gene Expression Regulation, Bacterial; Genetic Vectors / genetics; Genetic Vectors / metabolism; Lactobacillus / genetics; Lactobacillus / metabolism; Operon; Plasmids / genetics; Plasmids / metabolism
TL;DR:
Development of these expression vectors could support several novel applications, including the expression of enzymes, proteins, vaccines and biotherapeutics by intestinal lactobacilli.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, NC State University Libraries
Added: August 6, 2018
2010 journal article
The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA
Nature, 468(7320), 67–71.
MeSH headings : Bacteriophages / genetics; Bacteriophages / metabolism; Base Sequence; DNA, Intergenic / genetics; DNA, Intergenic / metabolism; DNA, Viral / genetics; DNA, Viral / metabolism; Drug Resistance, Bacterial / genetics; Genetic Loci / genetics; Genetic Loci / immunology; Interspersed Repetitive Sequences / genetics; Molecular Sequence Data; Mutation; Plasmids / genetics; Plasmids / metabolism; RNA, Bacterial / genetics; RNA, Bacterial / immunology; Streptococcus thermophilus / genetics; Streptococcus thermophilus / immunology; Streptococcus thermophilus / virology
TL;DR:
In vivo evidence is provided that the Streptococcus thermophilus CRISPR1/Cas system can also naturally acquire spacers from a self-replicating plasmid containing an antibiotic-resistance gene, leading toplasmid loss.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2009 journal article
Comparative Analyses of Prophage-Like Elements Present in Bifidobacterial Genomes
Applied and Environmental Microbiology, 75(21), 6929–6936.
MeSH headings : Bifidobacterium / genetics; Bifidobacterium / virology; Computational Biology; DNA, Bacterial / genetics; Gene Expression Profiling; Gene Order; Genome, Bacterial; Phylogeny; Prophages / genetics; Sequence Homology
TL;DR:
The genetic organization, phylogenetic relationships, and, in some cases, transcription profiles and inducibility of 19 prophage-like elements present on the individual chromosomes of nine bifidobacterial strains, which represent six different species are investigated.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2009 journal article
Comparison of the Complete Genome Sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04
Journal of Bacteriology, 191(13), 4144–4151.
MeSH headings : Bifidobacterium / genetics; Genome, Bacterial / genetics; Molecular Sequence Data; Polymorphism, Single Nucleotide / genetics; Sequence Analysis, DNA / methods
TL;DR:
The high degree of genome conservation observed between the two strains in terms of size, organization, and sequence is indicative of a genomically monomorphic subspecies and explains the inability to differentiate the strains by standard techniques such as pulsed-field gel electrophoresis.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: January 2, 2020
2009 patent
Compositions comprising promoter sequences and methods of use
Source: NC State University Libraries
Added: August 6, 2018
2009 journal article
Strain-Specific Genotyping of Bifidobacterium animalis subsp. lactis by Using Single-Nucleotide Polymorphisms, Insertions, and Deletions
Applied and Environmental Microbiology, 75(23), 7501–7508.
MeSH headings : Animals; Bacterial Proteins / genetics; Bacterial Typing Techniques / methods; Bifidobacterium / classification; Bifidobacterium / genetics; Cluster Analysis; Culture Media / chemistry; DNA Fingerprinting / methods; Genotype; Glucose / metabolism; Membrane Transport Proteins / genetics; Mutagenesis, Insertional; Point Mutation; Polymorphism, Genetic; Sequence Analysis, DNA; Sequence Deletion
TL;DR:
The presence of a nonsynonymous SNP within the gene encoding a putative glucose uptake protein was found to correlate with the ability of certain strains to transport glucose and to grow rapidly in a medium containing glucose as the sole carbon source.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2009 journal article
The CRISPR System Protects Microbes against Phages, Plasmids
Microbe Magazine, 4(5), 224–230.
TL;DR:
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.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2008 article
Analysis of the genome sequence of Lactobacillus gasseri ATCC 33323 reveals the molecular basis of an autochthonous intestinal organism
Azcarate-Peril, M. A., Altermann, E., Goh, Y. J., Tallon, R., Sanozky-Dawes, R. B., Pfeiler, E. A., … Klaenhammer, T. R. (2008, August). APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Vol. 74, pp. 4610–4625.
MeSH headings : Adult; Bacterial Adhesion / genetics; Bacterial Adhesion / physiology; Bacterial Proteins / genetics; Child; DNA Primers; Gastrointestinal Tract / microbiology; Genes, Bacterial; Genome, Bacterial; Humans; Infant, Newborn; Intestines / microbiology; Lactobacillus / genetics; Lactobacillus / isolation & purification; Lactobacillus / pathogenicity; Open Reading Frames
TL;DR:
The results from this study indicated high intraspecies variability from a genome encoding traits important for survival and retention in the gastrointestinal tract.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: ORCID, Web Of Science
Added: August 6, 2018
2008 journal article
Comparative analysis of CRISPR loci in lactic acid bacteria genomes
International Journal of Food Microbiology, 131(1), 62–70.
author keywords: Clustered regularly interspaced short palindromic repeats (CRISPR); Lactic acid bacteria; Cas gene; Phage; Horizontal gene transfer
TL;DR:
It is hypothesized 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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: January 2, 2020
2008 article
Functional genomics of probiotic Lactobacilli
Klaenhammer, T. R., Altermann, E., Pfeiler, E., Buck, B. L., Goh, Y.-J., O'Flaherty, S., … Duong, T. (2008, September). JOURNAL OF CLINICAL GASTROENTEROLOGY, Vol. 42, pp. S160–S162.
author keywords: Lactobacillus acidophilus; Lactobacillus johnsonii; Lactobacillus plantarum; Lactobacillus gasseri; genomics; probiotic cultures; lactic acid bacteria
MeSH headings : Animals; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Evolution, Molecular; Genome, Bacterial; Genomics; Humans; Lactobacillus / classification; Lactobacillus / genetics; Lactobacillus / metabolism; Lactobacillus / physiology; Probiotics / metabolism; Species Specificity
TL;DR:
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 is conducted.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2008 patent
Lactobacillus acidophilus nucleic acid sequences encoding carbohydrate utilization-related proteins and uses therefor
Source: NC State University Libraries
Added: August 6, 2018
2007 journal article
CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes
Science, 315(5819), 1709–1712.
MeSH headings : DNA, Bacterial / genetics; DNA, Intergenic / genetics; Evolution, Molecular; Genes, Bacterial; Genome, Viral; Molecular Sequence Data; Mutation; Polymorphism, Single Nucleotide; Repetitive Sequences, Nucleic Acid; Streptococcus Phages / genetics; Streptococcus Phages / physiology; Streptococcus thermophilus / genetics; Streptococcus thermophilus / virology; Viral Plaque Assay; Virus Replication
TL;DR:
It is found that, after viral challenge, bacteria integrated new spacers derived from phage genomic sequences, and CRISPR provided resistance against phages, and resistance specificity is determined by spacer-phage sequence similarity.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2007 journal article
Diversity, Activity, and Evolution of CRISPR Loci in Streptococcus thermophilus
Journal of Bacteriology, 190(4), 1401–1412.
MeSH headings : Base Sequence; DNA, Bacterial / chemistry; DNA, Bacterial / genetics; DNA, Intergenic / chemistry; DNA, Intergenic / genetics; Evolution, Molecular; Genetic Variation; Genome, Bacterial; Models, Molecular; Nucleic Acid Conformation; Phylogeny; Repetitive Sequences, Nucleic Acid / genetics; Sequence Analysis, DNA; Streptococcus thermophilus / classification; Streptococcus thermophilus / genetics
TL;DR:
A novel Streptococcus thermophilus locus is characterized, and its ability to integrate novel spacers in response to bacteriophage is experimentally demonstrated, and it is hypothesized that the level of diversity is correlated with relative CRISPR activity and proposed that the activity is highest for CRISpr1, followed by CRIS PR3, while CRISP2 may be degenerate.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2007 article
Influence of the dairy environment on gene expression and substrate(1-3)
Klaenhammer, T. R., Azcarate-Peril, M. A., Altermann, E., & Barrangou, R. (2007, March). JOURNAL OF NUTRITION, Vol. 137, pp. 748S–750S.
MeSH headings : Animals; Cattle; Dairy Products; Dairying; Environment; Gene Expression Regulation, Bacterial; Lactobacillaceae / genetics; Lactobacillaceae / metabolism; Probiotics
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2007 journal article
Phage Response to CRISPR-Encoded Resistance in Streptococcus thermophilus
Journal of Bacteriology, 190(4), 1390–1400.
MeSH headings : Base Sequence; DNA, Bacterial / genetics; DNA, Intergenic / genetics; DNA, Viral / genetics; Genome, Bacterial / genetics; Genome, Viral / genetics; Host-Pathogen Interactions; Models, Genetic; Molecular Sequence Data; Repetitive Sequences, Nucleic Acid / genetics; Sequence Homology, Nucleic Acid; Streptococcus Phages / genetics; Streptococcus Phages / physiology; Streptococcus thermophilus / genetics; Streptococcus thermophilus / virology
TL;DR:
It is shown through the analyses of 20 mutant phages that virulent phages are rapidly evolving through single nucleotide mutations as well as deletions, in response to CRISPR1.
(via Semantic Scholar)
Source: ORCID
Added: January 2, 2020
2006 journal article
Characterization of the tre locus and analysis of trehalose cryoprotection in Lactobacillus acidophilus NCFM
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 72(2), 1218–1225.
MeSH headings : Amino Acid Sequence; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Base Sequence; Cryoprotective Agents / metabolism; Cryoprotective Agents / pharmacology; DNA, Bacterial / genetics; Disaccharidases / genetics; Disaccharidases / metabolism; Fermentation; Genes, Bacterial; Lactobacillus acidophilus / drug effects; Lactobacillus acidophilus / genetics; Lactobacillus acidophilus / metabolism; Molecular Sequence Data; Mutagenesis, Insertional; Mutation; Phosphoenolpyruvate Sugar Phosphotransferase System / genetics; Phosphoenolpyruvate Sugar Phosphotransferase System / metabolism; Repressor Proteins / genetics; Repressor Proteins / metabolism; Trehalose / metabolism; Trehalose / pharmacology
TL;DR:
Analysis of the Lactobacillus acidophilus NCFM genome revealed a putative trehalose utilization locus, which was found to be significantly reduced in the transporter mutant but unaffected in the hydrolase mutant, suggesting that intracellular transport and hydrolysis contribute significantly to cryoprotection.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2006 journal article
Comparative genomics and transcriptional analysis of prophages identified in the Genomes of Lactobacillus gasseri, Lactobacillus salivarius, and Lactobacillus casei
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 72(5), 3130–3146.
MeSH headings : Animals; Base Sequence; Genome, Bacterial; Genome, Viral; Genomics; Humans; Lactobacillus / genetics; Lactobacillus / virology; Lacticaseibacillus casei / virology; Molecular Sequence Data; Phylogeny; Prophages / classification; Prophages / genetics; Prophages / isolation & purification; Prophages / metabolism; Sequence Analysis, DNA; Siphoviridae / classification; Siphoviridae / genetics; Siphoviridae / isolation & purification; Siphoviridae / metabolism; Transcription, Genetic; Viral Proteins / genetics; Viral Proteins / metabolism
TL;DR:
Phylogenetic investigation of these newly described prophage sequences revealed that they have not followed an evolutionary development similar to that of their bacterial hosts and that they show a high degree of diversity, even within a species.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2006 journal article
Comparative genomics of the lactic acid bacteria
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103(42), 15611–15616.
author keywords: evolutionary genomics; fermentation
MeSH headings : Animals; Bacterial Proteins / classification; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Biological Evolution; Food Microbiology; Gene Transfer, Horizontal; Genome, Bacterial; Genomics; Lactic Acid / metabolism; Lactobacillus / classification; Lactobacillus / genetics; Phylogeny; Streptococcaceae / classification; Streptococcaceae / genetics
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2006 journal article
Global analysis of carbohydrate utilization by Lactobacillus acidophilus using cDNA microarrays
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103(10), 3816–3821.
author keywords: ATP-binding cassette; carbon catabolite repression; fructooligosaccharide; galactoside-pentose hexuronide
MeSH headings : ATP-Binding Cassette Transporters / genetics; ATP-Binding Cassette Transporters / metabolism; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Carbohydrate Metabolism / genetics; Gastrointestinal Tract / microbiology; Gene Expression Profiling; Genes, Bacterial; Humans; Lactobacillus acidophilus / genetics; Lactobacillus acidophilus / metabolism; Models, Biological; Oligonucleotide Array Sequence Analysis; Phosphoenolpyruvate Sugar Phosphotransferase System / genetics; Reverse Transcriptase Polymerase Chain Reaction
TL;DR:
The transport and catabolic machinery involved in carbohydrate utilization by Lactobacillus acidophilus was characterized genetically by using whole-genome cDNA microarrays, and genes central to glycolysis were among the most highly expressed in the genome.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2005 journal article
Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102(11), 3906–3912.
author keywords: adhesion; stress response; proteolytic system; sugar metabolism; in silico analysis
MeSH headings : Bacterial Adhesion / genetics; Bacteriocins / genetics; Bacteriophages / genetics; Bacteriophages / pathogenicity; Carbohydrate Metabolism; Computational Biology; Genome, Bacterial; Lactobacillus acidophilus / genetics; Lactobacillus acidophilus / metabolism; Lactobacillus acidophilus / virology; Molecular Sequence Data; Peptide Hydrolases / genetics; Prophages / genetics; Sequence Analysis, DNA; Transposases / genetics
TL;DR:
These features within the genome sequence of L. acidophilus are likely to contribute to the organisms' gastric survival and promote interactions with the intestinal mucosa and microbiota.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2005 journal article
Genomic Perspectives on Probiotic Lactic Acid Bacteria
Bioscience and Microflora, 24(2), 31–33.
TL;DR:
The genomic content of probiotic Lactobacillus cultures is examined, compared to those lactic acid bacterial genomes that have appeared recently, to illustrate how environmental conditions encountered during biomanufacturing, fermentation, and the gastrointestinal tract can impact gene expression and culture functionality.
(via Semantic Scholar)
Sources: NC State University Libraries, ORCID, NC State University Libraries
Added: August 6, 2018
2005 review
Genomic features of lactic acid bacteria effecting bioprocessing and health
[Review of ]. FEMS MICROBIOLOGY REVIEWS, 29(3), 393–409.
author keywords: lactic acid bacteria; genomics; bioprocessing; probiotics; comparative genomics; functional genomics
MeSH headings : Food Microbiology; Genome, Bacterial; Genomics; Health; Humans; Lactobacillus / genetics; Lactobacillus / growth & development; Lactobacillus / physiology; Lactococcus / genetics; Lactococcus / growth & development; Lactococcus / physiology; Probiotics
TL;DR:
Genomic analyses of multiple members of the lactic acid bacteria have now elucidated many genetic features that direct their fermentative and probiotic roles, providing an important platform for understanding core mechanisms that control and regulate bacterial growth, survival, signaling, and fermentative processes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2005 journal article
Genomic features of lactic acid bacteria effecting bioprocessing and health
FEMS Microbiology Reviews, 29(3), 393–409.
Source: ORCID
Added: January 2, 2020
2004 patent
Lactobacillus acidophilus nucleic acids encoding fructo-oligosaccharide utilization compounds and uses thereof
Washington, DC: U.S. Patent and Trademark Office.
Source: NC State University Libraries
Added: August 6, 2018
2004 journal article
The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 101(8), 2512–2517.
MeSH headings : Biological Transport; Cell Adhesion; Energy Metabolism; Fimbriae, Bacterial / genetics; Genes, Bacterial / genetics; Genome, Bacterial; Humans; Intestinal Mucosa / microbiology; Lactobacillus / genetics; Lactobacillus / metabolism; Lactobacillus / pathogenicity; Molecular Sequence Data; Operon / genetics
TL;DR:
Genome analysis predicted an abundance 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).
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2003 journal article
Functional and comparative genomic analyses of an operon involved in fructooligosaccharide utilization by Lactobacillus acidophilus
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 100(15), 8957–8962.
MeSH headings : ATP-Binding Cassette Transporters / genetics; ATP-Binding Cassette Transporters / metabolism; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Base Sequence; Biological Transport, Active; Chromosome Mapping; DNA, Bacterial / genetics; Escherichia coli Proteins / genetics; Escherichia coli Proteins / metabolism; Genome, Bacterial; Lac Repressors; Lactobacillus acidophilus / genetics; Lactobacillus acidophilus / metabolism; Molecular Sequence Data; Multigene Family; Mutation; Oligosaccharides / metabolism; Operon; Phenotype; Phylogeny; Repressor Proteins / genetics; Repressor Proteins / metabolism; Sequence Homology, Nucleic Acid; Species Specificity
TL;DR:
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.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2002 journal article
Characterization of six Leuconostoc fallax bacteriophages isolated from an industrial sauerkraut fermentation
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 68(11), 5452–5458.
MeSH headings : Bacteriophages / genetics; Bacteriophages / growth & development; Bacteriophages / isolation & purification; Bacteriophages / metabolism; Bacteriophages / ultrastructure; DNA Fingerprinting; DNA, Viral / analysis; Fermentation; Genome, Viral; Leuconostoc / virology; Polymorphism, Restriction Fragment Length; Random Amplified Polymorphic DNA Technique; Viral Proteins / analysis
TL;DR:
Bacteriophages active against Leuconostoc fallax strains are likely to contribute to the microbial ecology of sauerkraut fermentation and could be responsible for some of the variability observed in this type of fermentation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science
Added: August 6, 2018
2002 journal article
Identification and characterization of Leuconostoc fallax strains isolated from an industrial sauerkraut fermentation
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 68(6), 2877–2884.
MeSH headings : Brassica / microbiology; Cell Culture Techniques; DNA, Intergenic / analysis; Fermentation; Industry; Leuconostoc / genetics; Leuconostoc / isolation & purification; Plant Extracts; Polymerase Chain Reaction; RNA, Ribosomal, 16S / analysis; RNA, Ribosomal, 16S / genetics; Random Amplified Polymorphic DNA Technique
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science
Added: August 6, 2018
2002 journal article
Isolation and characterization of bacteriophages from fermenting sauerkraut
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 68(2), 973–976.
MeSH headings : Bacteriophages / classification; Bacteriophages / isolation & purification; Brassica; Fermentation; Food-Processing Industry / instrumentation; Food-Processing Industry / methods; Lactobacillus / virology; Leuconostoc / virology; Myoviridae / classification; Myoviridae / isolation & purification; Siphoviridae / classification; Siphoviridae / isolation & purification
TL;DR:
The first report of bacteriophage isolated from commercial vegetable fermentations is presented, and these phages were active against fermentation isolates and selected Leuconostoc mesenteroides and Lactobacillus plantarum strains, including a starter culture.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science
Added: August 6, 2018
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