@article{hornstein_charles_franklin_edwards_vintila_kleiner_sederoff_2024, title={<i>IPD3</i>, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host <i>Arabidopsis</i> when restored long after its evolutionary loss}, volume={114}, ISSN={["1573-5028"]}, url={https://doi.org/10.1007/s11103-024-01422-3}, DOI={10.1007/s11103-024-01422-3}, abstractNote={Abstract}, number={2}, journal={PLANT MOLECULAR BIOLOGY}, author={Hornstein, Eli D. and Charles, Melodi and Franklin, Megan and Edwards, Brianne and Vintila, Simina and Kleiner, Manuel and Sederoff, Heike}, year={2024}, month={Apr} }
 @article{awan_bartlett_blakeley-ruiz_richie_theriot_kleiner_2024, title={Dietary protein from different sources escapes host digestion and is differentially modified by the microbiota}, url={https://doi.org/10.1101/2024.06.26.600830}, DOI={10.1101/2024.06.26.600830}, abstractNote={Protein is an essential macronutrient and variations in its source and quantity have been shown to impact long-term health outcomes. Differential health impacts of dietary proteins from various sources are likely driven by differences in their digestibility by the host and subsequent availability to the intestinal microbiota. However, our current understanding regarding the fate of dietary proteins from different sources in the gut, specifically how component proteins within these sources interact with the host and the gut microbiota, is limited. To determine which dietary proteins are efficiently digested by the host and which proteins escape host digestion and are used by the gut microbiota, we used high-resolution mass spectrometry to quantify the proteins that make up different dietary protein sources before and after digestion in germ-free and conventionally raised mice. Contrary to expectation, we detected proteins from all sources in fecal samples of both germ-free and conventional mice suggesting that even protein sources with a high digestive efficiency make it in part to the colon where they can serve as a substrate for the microbiota. Additionally, we found clear patterns where specific component proteins of the dietary protein sources were used as a preferred substrate by the microbiota or were not as accessible to the microbiota. We found that specific proteins with functions that could impact host health and physiology were differentially enriched in germ-free or conventionally raised mice. These findings reveal large differences in the fate of dietary protein from various sources in the gut that could explain some of their differential health impacts.}, author={Awan, Ayesha and Bartlett, Alexandria and Blakeley-Ruiz, J. Alfredo and Richie, Tanner and Theriot, Casey M. and Kleiner, Manuel}, year={2024}, month={Jun} }
 @article{parnell_pal_awan_vintila_houdinet_hawkes_balint-kurti_wagner_kleiner_2024, title={Effective Seed Sterilization Methods Require Optimization Across Maize Genotypes}, url={https://doi.org/10.1094/PBIOMES-12-23-0137-R}, DOI={10.1094/PBIOMES-12-23-0137-R}, journal={Phytobiomes Journal}, author={Parnell, J. Jacob and Pal, Gaurav and Awan, Ayesha and Vintila, Simina and Houdinet, Gabriella and Hawkes, Christine V. and Balint-Kurti, Peter J. and Wagner, Maggie R. and Kleiner, Manuel}, year={2024}, month={Jul} }
 @article{ratinskaia_malavin_zvi-kedem_vintila_kleiner_rubin-blum_2024, title={Metabolically-versatile Ca. Thiodiazotropha symbionts of the deep-sea lucinid clam Lucinoma kazani have the genetic potential to fix nitrogen}, volume={4}, ISSN={["2730-6151"]}, DOI={10.1093/ismeco/ycae076}, abstractNote={Abstract Lucinid clams are one of the most diverse and widespread symbiont-bearing animal groups in both shallow and deep-sea chemosynthetic habitats. Lucinids harbor Ca. Thiodiazotropha symbionts that can oxidize inorganic and organic substrates such as hydrogen sulfide and formate to gain energy. The interplay between these key metabolic functions, nutrient uptake and biotic interactions in Ca. Thiodiazotropha is not fully understood. We collected Lucinoma kazani individuals from next to a deep-sea brine pool in the eastern Mediterranean Sea, at a depth of 1150 m and used Oxford Nanopore and Illumina sequencing to obtain high-quality genomes of their Ca. Thiodiazotropha gloverae symbiont. The genomes served as the basis for transcriptomic and proteomic analyses to characterize the in situ gene expression, metabolism and physiology of the symbionts. We found genes needed for N2 fixation in the deep-sea symbiont’s genome, which, to date, were only found in shallow-water Ca. Thiodiazotropha. However, we did not detect the expression of these genes and thus the potential role of nitrogen fixation in this symbiosis remains to be determined. We also found the high expression of carbon fixation and sulfur oxidation genes, which indicates chemolithoautotrophy as the key physiology of Ca. Thiodiazotropha. However, we also detected the expression of pathways for using methanol and formate as energy sources. Our findings highlight the key traits these microbes maintain to support the nutrition of their hosts and interact with them.}, number={1}, journal={ISME COMMUNICATIONS}, author={Ratinskaia, Lina and Malavin, Stas and Zvi-Kedem, Tal and Vintila, Simina and Kleiner, Manuel and Rubin-Blum, Maxim}, year={2024}, month={Jun} }
 @article{ratinskaia_malavin_zvi-kedem_vintila_kleiner_rubin-blum_2024, title={Metabolically-versatileCa.Thiodiazotropha symbionts of the deep-sea lucinid clamLucinoma kazanihave the genetic potential to fix nitrogen}, url={https://doi.org/10.1101/2024.04.05.588213}, DOI={10.1101/2024.04.05.588213}, abstractNote={Abstract}, author={Ratinskaia, Lina and Malavin, Stas and Zvi-Kedem, Tal and Vintila, Simina and Kleiner, Manuel and Rubin-Blum, Maxim}, year={2024}, month={Apr} }
 @article{petrone_bartlett_jiang_korenek_vintila_tenekjian_yancy_david_kleiner_2024, title={Metaproteomics and DNA metabarcoding as tools to assess dietary intake in humans}, url={https://doi.org/10.1101/2024.04.09.588275}, DOI={10.1101/2024.04.09.588275}, abstractNote={Abstract}, author={Petrone, Brianna L. and Bartlett, Alexandria and Jiang, Sharon and Korenek, Abigail and Vintila, Simina and Tenekjian, Christine and Yancy, William S., Jr. and David, Lawrence A. and Kleiner, Manuel}, year={2024}, month={Apr} }
 @article{maier_gin_callahan_sheriff_duerkop_kleiner_2024, title={Pseudo-pac site sequences used by phage P22 in generalized transduction of <i>Salmonella</i>}, volume={20}, ISSN={["1553-7374"]}, url={https://doi.org/10.1371/journal.ppat.1012301}, DOI={10.1371/journal.ppat.1012301}, abstractNote={Salmonella enterica Serovar Typhimurium ( Salmonella ) and its bacteriophage P22 are a model system for the study of horizontal gene transfer by generalized transduction. Typically, the P22 DNA packaging machinery initiates packaging when a short sequence of DNA, known as the pac site, is recognized on the P22 genome. However, sequences similar to the pac site in the host genome, called pseudo-pac sites, lead to erroneous packaging and subsequent generalized transduction of Salmonella DNA. While the general genomic locations of the Salmonella pseudo-pac sites are known, the sequences themselves have not been determined. We used visualization of P22 sequencing reads mapped to host Salmonella genomes to define regions of generalized transduction initiation and the likely locations of pseudo-pac sites. We searched each genome region for the sequence with the highest similarity to the P22 pac site and aligned the resulting sequences. We built a regular expression (sequence match pattern) from the alignment and used it to search the genomes of two P22-susceptible Salmonella strains—LT2 and 14028S—for sequence matches. The final regular expression successfully identified pseudo-pac sites in both LT2 and 14028S that correspond with generalized transduction initiation sites in mapped read coverages. The pseudo-pac site sequences identified in this study can be used to predict locations of generalized transduction in other P22-susceptible hosts or to initiate generalized transduction at specific locations in P22-susceptible hosts with genetic engineering. Furthermore, the bioinformatics approach used to identify the Salmonella pseudo-pac sites in this study could be applied to other phage—host systems.}, number={6}, journal={PLOS PATHOGENS}, author={Maier, Jessie L. and Gin, Craig and Callahan, Benjamin and Sheriff, Emma K. and Duerkop, Breck A. and Kleiner, Manuel}, editor={Secor, PatrickEditor}, year={2024}, month={Jun} }
 @article{michellod_bien_birgel_violette_kleiner_fearn_zeidler_gruber-vodicka_dubilier_liebeke_2023, title={De novo phytosterol synthesis in animals}, volume={380}, ISSN={["1095-9203"]}, url={https://doi.org/10.1126/science.add7830}, DOI={10.1126/science.add7830}, abstractNote={
            Sterols are vital for nearly all eukaryotes. Their distribution differs in plants and animals, with phytosterols commonly found in plants whereas most animals are dominated by cholesterol. We show that sitosterol, a common sterol of plants, is the most abundant sterol in gutless marine annelids. Using multiomics, metabolite imaging, heterologous gene expression, and enzyme assays, we show that these animals synthesize sitosterol de novo using a noncanonical C-24 sterol methyltransferase (C
            24
            -SMT). This enzyme is essential for sitosterol synthesis in plants, but not known from most bilaterian animals. Our phylogenetic analyses revealed that C
            24
            -SMTs are present in representatives of at least five animal phyla, indicating that the synthesis of sterols common to plants is more widespread in animals than currently known.
          }, number={6644}, journal={SCIENCE}, author={Michellod, Dolma and Bien, Tanja and Birgel, Daniel and Violette, Marlene and Kleiner, Manuel and Fearn, Sarah and Zeidler, Caroline and Gruber-Vodicka, Harald R. and Dubilier, Nicole and Liebeke, Manuel}, year={2023}, month={May}, pages={520–526} }
 @article{parnell_pal_awan_vintila_houdinet_hawkes_balint-kurti_wagner_kleiner_2023, title={Effective seed sterilization methods require optimization across maize genotypes}, url={https://doi.org/10.1101/2023.12.14.571779}, DOI={10.1101/2023.12.14.571779}, abstractNote={Abstract}, author={Parnell, J. Jacob and Pal, Gaurav and Awan, Ayesha and Vintila, Simina and Houdinet, Gabriella and Hawkes, Christine V. and Balint-Kurti, Peter J. and Wagner, Maggie R. and Kleiner, Manuel}, year={2023}, month={Dec} }
 @article{swift_kolp_carmichael_ford_hansen_sikes_kleiner_wagner_2023, title={Environmental legacy effects impact maize growth and microbiome assembly under drought stress}, url={https://doi.org/10.1101/2023.04.11.536405}, DOI={10.1101/2023.04.11.536405}, abstractNote={Abstract}, author={Swift, Joel F. and Kolp, Matthew R. and Carmichael, Amanda and Ford, Natalie E. and Hansen, Paige M. and Sikes, Benjamin A. and Kleiner, Manuel and Wagner, Maggie R.}, year={2023}, month={Apr} }
 @article{parnell_vintila_tang_wagner_kleiner_2023, title={Evaluation of ready-to-use freezer stocks of a synthetic microbial community for maize root colonization}, volume={12}, ISSN={["2165-0497"]}, url={https://doi.org/10.1128/spectrum.02401-23}, DOI={10.1128/spectrum.02401-23}, abstractNote={ABSTRACT}, journal={MICROBIOLOGY SPECTRUM}, author={Parnell, J. Jacob and Vintila, Simina and Tang, Clara and Wagner, Maggie R. and Kleiner, Manuel}, editor={Hockett, Kevin LorenEditor}, year={2023}, month={Dec} }
 @article{parnell_vintila_tang_wagner_kleiner_2023, title={Evaluation of ready-to-use freezer stocks of a synthetic microbial community for maize root colonization}, url={https://doi.org/10.1101/2023.05.10.540175}, DOI={10.1101/2023.05.10.540175}, abstractNote={Abstract}, author={Parnell, J. Jacob and Vintila, Simina and Tang, Clara and Wagner, Maggie R. and Kleiner, Manuel}, year={2023}, month={May} }
 @article{bartlett_blakeley-ruiz_richie_theriot_kleiner_2023, title={Large Quantities of Bacterial DNA and Protein in Common Dietary Protein Source Used in Microbiome Studies}, url={https://doi.org/10.1101/2023.12.07.570621}, DOI={10.1101/2023.12.07.570621}, abstractNote={Abstract}, author={Bartlett, Alexandria and Blakeley-Ruiz, J. Alfredo and Richie, Tanner and Theriot, Casey M. and Kleiner, Manuel}, year={2023}, month={Dec} }
 @article{kleiner_polerecky_lott_bergin_häusler_liebeke_wentrup_musat_kuypers_dubilier_2023, title={Mechanism of high energy efficiency of carbon fixation by sulfur-oxidizing symbionts revealed by single-cell analyses and metabolic modeling}, url={https://doi.org/10.1101/2023.11.25.568684}, DOI={10.1101/2023.11.25.568684}, abstractNote={Summary}, author={Kleiner, M. and Polerecky, L. and Lott, C. and Bergin, C. and Häusler, S. and Liebeke, M. and Wentrup, C. and Musat, N. and Kuypers, M. M. M. and Dubilier, N.}, year={2023}, month={Nov} }
 @article{zvi-kedem_vintila_kleiner_tchernov_rubin-blum_2023, title={Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels}, url={https://doi.org/10.1101/2023.02.09.527947}, DOI={10.1101/2023.02.09.527947}, abstractNote={Abstract}, author={Zvi-Kedem, Tal and Vintila, Simina and Kleiner, Manuel and Tchernov, Dan and Rubin-Blum, Maxim}, year={2023}, month={Feb} }
 @article{zvi-kedem_vintila_kleiner_tchernov_rubin-blum_2023, title={Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels}, volume={3}, ISSN={["2730-6151"]}, DOI={10.1038/s43705-023-00254-4}, abstractNote={Abstract}, number={1}, journal={ISME COMMUNICATIONS}, author={Zvi-Kedem, Tal and Vintila, Simina and Kleiner, Manuel and Tchernov, Dan and Rubin-Blum, Maxim}, year={2023}, month={May} }
 @article{hornstein_charles_franklin_edwards_vintila_kleiner_sederoff_2023, title={Re-engineering a lost trait:IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss}, url={https://doi.org/10.1101/2023.03.06.531368}, DOI={10.1101/2023.03.06.531368}, abstractNote={Abstract}, author={Hornstein, Eli D. and Charles, Melodi and Franklin, Megan and Edwards, Brianne and Vintila, Simina and Kleiner, Manuel and Sederoff, Heike}, year={2023}, month={Mar} }
 @article{kleiner_kouris_violette_d'angelo_liu_korenek_tolic_sachsenberg_mccalder_lipton_et al._2023, title={Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes}, volume={11}, ISSN={["2049-2618"]}, DOI={10.1186/s40168-022-01454-1}, abstractNote={Abstract}, number={1}, journal={MICROBIOME}, author={Kleiner, Manuel and Kouris, Angela and Violette, Marlene and D'Angelo, Grace and Liu, Yihua and Korenek, Abigail and Tolic, Nikola and Sachsenberg, Timo and McCalder, Janine and Lipton, Mary S. S. and et al.}, year={2023}, month={Feb} }
 @article{blakeley-ruiz_kleiner_2022, title={Considerations for constructing a protein sequence database for metaproteomics}, volume={20}, ISSN={["2001-0370"]}, url={http://dx.doi.org/10.1016/j.csbj.2022.01.018}, DOI={10.1016/j.csbj.2022.01.018}, abstractNote={Mass spectrometry-based metaproteomics has emerged as a prominent technique for interrogating the functions of specific organisms in microbial communities, in addition to total community function. Identifying proteins by mass spectrometry requires matching mass spectra of fragmented peptide ions to a database of protein sequences corresponding to the proteins in the sample. This sequence database determines which protein sequences can be identified from the measurement, and as such the taxonomic and functional information that can be inferred from a metaproteomics measurement. Thus, the construction of the protein sequence database directly impacts the outcome of any metaproteomics study. Several factors, such as source of sequence information and database curation, need to be considered during database construction to maximize accurate protein identifications traceable to the species of origin. In this review, we provide an overview of existing strategies for database construction and the relevant studies that have sought to test and validate these strategies. Based on this review of the literature and our experience we provide a decision tree and best practices for choosing and implementing database construction strategies.}, journal={COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL}, publisher={Elsevier BV}, author={Blakeley-Ruiz, J. Alfredo and Kleiner, Manuel}, year={2022}, pages={937–952} }
 @article{michellod_bien_birgel_jensen_kleiner_fearn_zeidler_gruber-vodicka_dubilier_liebeke_2022, title={De novo phytosterol synthesis in animals}, volume={4}, url={https://doi.org/10.1101/2022.04.22.489198}, DOI={10.1101/2022.04.22.489198}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Michellod, Dolma and Bien, Tanja and Birgel, Daniel and Jensen, Marlene and Kleiner, Manuel and Fearn, Sarah and Zeidler, Caroline and Gruber-Vodicka, Harald R and Dubilier, Nicole and Liebeke, Manuel}, year={2022}, month={Apr} }
 @misc{bartlett_kleiner_2022, title={Dietary protein and the intestinal microbiota: An understudied relationship}, volume={25}, ISSN={["2589-0042"]}, DOI={10.1016/j.isci.2022.105313}, abstractNote={Diet has a profound impact on the microbial community in the gastrointestinal tract, the intestinal microbiota, to the benefit or detriment of human health. To understand the influence of diet on the intestinal microbiota, research has focused on individual macronutrients. Some macronutrients (e.g. fiber) have been studied in great detail and have been found to strongly influence the intestinal microbiota. The relationship between dietary protein, a vital macronutrient, and the intestinal microbiota has gone largely unexplored. Emerging evidence suggests that dietary protein strongly impacts intestinal microbiota composition and function and that protein-microbiota interactions can have critical impacts on host health. In this review, we focus on recent studies investigating the impact of dietary protein quantity and source on the intestinal microbiota and resulting host health consequences. We highlight major open questions critical to understanding health outcomes mediated by interactions between dietary protein and the microbiota.}, number={11}, journal={ISCIENCE}, author={Bartlett, Alexandria and Kleiner, Manuel}, year={2022}, month={Nov} }
 @article{beck_kleiner_garrell_2022, title={Elucidating Plant-Microbe-Environment Interactions Through Omics-Enabled Metabolic Modelling Using Synthetic Communities}, volume={13}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2022.910377}, abstractNote={With a growing world population and increasing frequency of climate disturbance events, we are in dire need of methods to improve plant productivity, resilience, and resistance to both abiotic and biotic stressors, both for agriculture and conservation efforts. Microorganisms play an essential role in supporting plant growth, environmental response, and susceptibility to disease. However, understanding the specific mechanisms by which microbes interact with each other and with plants to influence plant phenotypes is a major challenge due to the complexity of natural communities, simultaneous competition and cooperation effects, signalling interactions, and environmental impacts. Synthetic communities are a major asset in reducing the complexity of these systems by simplifying to dominant components and isolating specific variables for controlled experiments, yet there still remains a large gap in our understanding of plant microbiome interactions. This perspectives article presents a brief review discussing ways in which metabolic modelling can be used in combination with synthetic communities to continue progress toward understanding the complexity of plant-microbe-environment interactions. We highlight the utility of metabolic models as applied to a community setting, identify different applications for both flux balance and elementary flux mode simulation approaches, emphasize the importance of ecological theory in guiding data interpretation, and provide ideas for how the integration of metabolic modelling techniques with big data may bridge the gap between simplified synthetic communities and the complexity of natural plant-microbe systems.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Beck, Ashley E. and Kleiner, Manuel and Garrell, Anna-Katharina}, year={2022}, month={Jun} }
 @article{salvato_vintila_finkel_dangl_kleiner_2022, title={Evaluation of Protein Extraction Methods for Metaproteomic Analyses of Root-Associated Microbes}, volume={35}, ISSN={["1943-7706"]}, url={https://doi.org/10.1094/MPMI-05-22-0116-TA}, DOI={10.1094/MPMI-05-22-0116-TA}, abstractNote={ Metaproteomics is a powerful tool for the characterization of metabolism, physiology, and functional interactions in microbial communities, including plant-associated microbiota. However, the metaproteomic methods that have been used to study plant-associated microbiota are very laborious and require large amounts of plant tissue, hindering wider application of these methods. We optimized and evaluated different protein extraction methods for metaproteomics of plant-associated microbiota in two different plant species ( Arabidopsis and maize). Our main goal was to identify a method that would work with low amounts of input material (40 to 70 mg) and that would maximize the number of identified microbial proteins. We tested eight protocols, each comprising a different combination of physical lysis method, extraction buffer, and cell-enrichment method on roots from plants grown with synthetic microbial communities. We assessed the performance of the extraction protocols by liquid chromatography-tandem mass spectrometry–based metaproteomics and found that the optimal extraction method differed between the two species. For Arabidopsis roots, protein extraction by beating whole roots with small beads provided the greatest number of identified microbial proteins and improved the identification of proteins from gram-positive bacteria. For maize, vortexing root pieces in the presence of large glass beads yielded the greatest number of microbial proteins identified. Based on these data, we recommend the use of these two methods for metaproteomics with Arabidopsis and maize. Furthermore, detailed descriptions of the eight tested protocols will enable future optimization of protein extraction for metaproteomics in other dicot and monocot plants. }, number={11}, journal={MOLECULAR PLANT-MICROBE INTERACTIONS}, author={Salvato, Fernanda and Vintila, Simina and Finkel, Omri M. and Dangl, Jeffery L. and Kleiner, Manuel}, year={2022}, month={Nov}, pages={977–988} }
 @article{sato_wippler_wentrup_ansorge_sadowski_gruber-vodicka_dubilier_kleiner_2022, title={Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium}, volume={10}, ISSN={["2049-2618"]}, DOI={10.1186/s40168-022-01372-2}, abstractNote={Abstract}, number={1}, journal={MICROBIOME}, author={Sato, Yui and Wippler, Juliane and Wentrup, Cecilia and Ansorge, Rebecca and Sadowski, Miriam and Gruber-Vodicka, Harald and Dubilier, Nicole and Kleiner, Manuel}, year={2022}, month={Oct} }
 @article{smith_salvato_garikipati_kleiner_septer_2021, title={Activation of the Type VI Secretion System in the Squid Symbiont Vibrio fischeri Requires the Transcriptional Regulator TasR and the Structural Proteins TssM and TssA}, volume={203}, ISSN={["1098-5530"]}, DOI={10.1128/JB.00399-21}, abstractNote={
            Interbacterial weapons like the T6SS are often located on mobile genetic elements, and their expression is highly regulated. We found that two conserved structural proteins are required for T6SS expression in
            Vibrio fischeri
            .
          }, number={21}, journal={JOURNAL OF BACTERIOLOGY}, author={Smith, Stephanie and Salvato, Fernanda and Garikipati, Aditi and Kleiner, Manuel and Septer, Alecia N.}, year={2021}, month={Nov} }
 @article{hinzke_kleiner_meister_schlueter_hentschker_pane-farre_hildebrandt_felbeck_sievert_bonn_et al._2021, title={Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis}, volume={10}, ISSN={["2050-084X"]}, url={https://europepmc.org/articles/PMC7787665}, DOI={10.7554/elife.58371}, abstractNote={The hydrothermal vent tubewormRiftia pachyptilahosts a single 16S rRNA phylotype of intracellular sulfur-oxidizing symbionts, which vary considerably in cell morphology and exhibit a remarkable degree of physiological diversity and redundancy, even in the same host. To elucidate whether multiple metabolic routes are employed in the same cells or rather in distinct symbiont subpopulations, we enriched symbionts according to cell size by density gradient centrifugation. Metaproteomic analysis, microscopy, and flow cytometry strongly suggest thatRiftiasymbiont cells of different sizes represent metabolically dissimilar stages of a physiological differentiation process: While small symbionts actively divide and may establish cellular symbiont-host interaction, large symbionts apparently do not divide, but still replicate DNA, leading to DNA endoreduplication. Moreover, in large symbionts, carbon fixation and biomass production seem to be metabolic priorities. We propose that this division of labor between smaller and larger symbionts benefits the productivity of the symbiosis as a whole.}, journal={ELIFE}, publisher={eLife Sciences Publications, Ltd}, author={Hinzke, Tjorven and Kleiner, Manuel and Meister, Mareike and Schlueter, Rabea and Hentschker, Christian and Pane-Farre, Jan and Hildebrandt, Petra and Felbeck, Horst and Sievert, Stefan M. and Bonn, Florian and et al.}, year={2021}, month={Jan} }
 @article{bossche_kunath_schallert_schaepe_abraham_armengaud_arntzen_bassignani_benndorf_fuchs_et al._2021, title={Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows}, volume={12}, ISSN={["2041-1723"]}, DOI={10.1038/s41467-021-27542-8}, abstractNote={Abstract}, number={1}, journal={NATURE COMMUNICATIONS}, author={Bossche, Tim and Kunath, Benoit J. and Schallert, Kay and Schaepe, Stephanie S. and Abraham, Paul E. and Armengaud, Jean and Arntzen, Magnus O. and Bassignani, Ariane and Benndorf, Dirk and Fuchs, Stephan and et al.}, year={2021}, month={Dec} }
 @article{jensen_wippler_kleiner_2021, title={Evaluation of RNAlater as a Field-Compatible Preservation Method for Metaproteomic Analyses of Bacterium-Animal Symbioses}, volume={9}, ISSN={["2165-0497"]}, url={https://doi.org/10.1128/Spectrum.01429-21}, DOI={10.1128/Spectrum.01429-21}, abstractNote={Metaproteomics, the large-scale identification and quantification of proteins from microbial communities, provide direct insights into the phenotypes of microorganisms on the molecular level. To ensure the integrity of the metaproteomic data, samples need to be preserved immediately after sampling to avoid changes in protein abundance patterns.}, number={2}, journal={MICROBIOLOGY SPECTRUM}, publisher={American Society for Microbiology}, author={Jensen, Marlene and Wippler, Juliane and Kleiner, Manuel}, editor={Gralnick, Jeffrey A.Editor}, year={2021}, month={Oct} }
 @article{jensen_wippler_kleiner_2021, title={Evaluation of RNAlater™ as a field-compatible preservation method for metaproteomic analyses of bacteria-animal symbioses}, volume={6}, url={https://doi.org/10.1101/2021.06.16.448770}, DOI={10.1101/2021.06.16.448770}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Jensen, Marlene and Wippler, Juliane and Kleiner, Manuel}, year={2021}, month={Jun} }
 @article{mordant_kleiner_2021, title={Evaluation of Sample Preservation and Storage Methods for Metaproteomics Analysis of Intestinal Microbiomes}, volume={9}, ISSN={["2165-0497"]}, url={https://doi.org/10.1128/Spectrum.01877-21}, DOI={10.1128/Spectrum.01877-21}, abstractNote={Metaproteomics is a powerful tool to study the intestinal microbiome. By identifying and quantifying a large number of microbial, dietary, and host proteins in microbiome samples, metaproteomics provides direct evidence of the activities and functions of microbial community members.}, number={3}, journal={MICROBIOLOGY SPECTRUM}, publisher={American Society for Microbiology}, author={Mordant, Angie and Kleiner, Manuel}, editor={Khursigara, Cezar M.Editor}, year={2021}, month={Dec} }
 @article{sato_wippler_wentrup_ansorge_sadowski_gruber-vodicka_dubilier_kleiner_2021, title={Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium}, volume={1}, url={https://doi.org/10.1101/2021.01.30.428904}, DOI={10.1101/2021.01.30.428904}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Sato, Yui and Wippler, Juliane and Wentrup, Cecilia and Ansorge, Rebecca and Sadowski, Miriam and Gruber-Vodicka, Harald and Dubilier, Nicole and Kleiner, Manuel}, year={2021}, month={Jan} }
 @misc{salvato_hettich_kleiner_2021, title={Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes}, volume={17}, ISSN={["1553-7374"]}, url={https://doi.org/10.1371/journal.ppat.1009245}, DOI={10.1371/journal.ppat.1009245}, abstractNote={Host-associated microbial communities (microbiomes) play critical roles in human, animal, and plant health and development. However, interactions between the host, members of the microbiome, and invading pathogens are in most cases still poorly understood. Such interactions are multidimensional [1] and can alter the taxonomic composition and/or the functional metabolic activities of the microbiome in response to disease or treatment conditions. For example, after 2 days of antibiotic treatment, the mouse gut microbiome is altered and more susceptible to invasion by the pathogen Clostridioides difficile [2]. Studies of these multidimensional interactions have been fueled by the ability to use high-throughput sequencing of phylogenetic marker genes to profile microbial community composition and shotgun metagenomics to profile functional potential [3]. However, many protein-coding genes predicted from metagenomes are not necessarily expressed under a given condition, and thus, it is difficult to assess the activities and functional interactions in microbial communities based on DNA sequencing data alone [4]. The physiological and pathological processes expressed in these communities under specific conditions are better reflected by the abundances of transcripts or proteins [5,6]. In this Pearl, we provide a brief introduction to metaproteomics, which is a tool for the large-scale analysis of proteins in microbiomes that allows researchers to address a diversity of questions related to functions and interactions in microbiomes [7]. The term “metaproteomics” was first used in 2004 for “the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time” [8], and since then, a large array of metaproteomics approaches have been developed [7]. Our objective in this Pearl is to highlight what we feel are 5 essential elements to be considered for a metaproteomics research campaign and to introduce nonexpert readers to the topic without going into too much technical detail.}, number={2}, journal={PLOS PATHOGENS}, publisher={Public Library of Science (PLoS)}, author={Salvato, Fernanda and Hettich, Robert L. and Kleiner, Manuel}, editor={Hogan, Deborah A.Editor}, year={2021}, month={Feb} }
 @article{mankowski_kleiner_erséus_leisch_sato_volland_hüttel_wentrup_woyke_wippler_et al._2021, title={Highly variable fidelity drives symbiont community composition in an obligate symbiosis}, volume={4}, url={https://doi.org/10.1101/2021.04.28.441735}, DOI={10.1101/2021.04.28.441735}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Mankowski, Anna and Kleiner, Manuel and Erséus, Christer and Leisch, Nikolaus and Sato, Yui and Volland, Jean-Marie and Hüttel, Bruno and Wentrup, Cecilia and Woyke, Tanja and Wippler, Juliane and et al.}, year={2021}, month={Apr} }
 @article{maggie sogin_kleiner_borowski_gruber-vodicka_dubilier_2021, title={Life in the Dark: Phylogenetic and Physiological Diversity of Chemosynthetic Symbioses}, volume={75}, ISSN={["1545-3251"]}, DOI={10.1146/annurev-micro-051021-123130}, abstractNote={Possibly the last discovery of a previously unknown major ecosystem on Earth was made just over half a century ago, when researchers found teaming communities of animals flourishing two and a half kilometers below the ocean surface at hydrothermal vents. We now know that these highly productive ecosystems are based on nutritional symbioses between chemosynthetic bacteria and eukaryotes and that these chemosymbioses are ubiquitous in both deep-sea and shallow-water environments. The symbionts are primary producers that gain energy from the oxidation of reduced compounds, such as sulfide and methane, to fix carbon dioxide or methane into biomass to feed their hosts. This review outlines how the symbiotic partners have adapted to living together. We first focus on the phylogenetic and metabolic diversity of these symbioses and then highlight selected research directions that could advance our understanding of the processes that shaped the evolutionary and ecological success of these associations.}, journal={ANNUAL REVIEW OF MICROBIOLOGY, VOL 75, 2021}, author={Maggie Sogin, E. and Kleiner, Manuel and Borowski, Christian and Gruber-Vodicka, Harald R. and Dubilier, Nicole}, year={2021}, pages={695–718} }
 @article{wagner_tang_salvato_clouse_bartlett_vintila_phillips_sermons_hoffmann_balint-kurti_et al._2021, title={Microbe-dependent heterosis in maize}, volume={118}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.2021965118}, DOI={10.1073/pnas.2021965118}, abstractNote={Significance}, number={30}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Wagner, Maggie R. and Tang, Clara and Salvato, Fernanda and Clouse, Kayla M. and Bartlett, Alexandria and Vintila, Simina and Phillips, Laura and Sermons, Shannon and Hoffmann, Mark and Balint-Kurti, Peter J. and et al.}, year={2021}, month={Jul} }
 @article{ataeian_vadlamani_haines_mosier_dong_kleiner_strous_hawley_2021, title={Proteome and strain analysis of cyanobacterium Candidatus "Phormidium alkaliphilum" reveals traits for success in biotechnology}, volume={24}, ISSN={["2589-0042"]}, url={https://doi.org/10.1016/j.isci.2021.103405}, DOI={10.1016/j.isci.2021.103405}, abstractNote={Cyanobacteria encompass a diverse group of photoautotrophic bacteria with important roles in nature and biotechnology. Here we characterized Candidatus "Phormidium alkaliphilum," an abundant member in alkaline soda lake microbial communities globally. The complete, circular whole-genome sequence of Ca. "P. alkaliphilum" was obtained using combined Nanopore and Illumina sequencing of a Ca. "P. alkaliphilum" consortium. Strain-level diversity of Ca. "P. alkaliphilum" was shown to contribute to photobioreactor robustness under different operational conditions. Comparative genomics of closely related species showed that adaptation to high pH was not attributed to specific genes. Proteomics at high and low pH showed only minimal changes in gene expression, but higher productivity in high pH. Diverse photosystem antennae proteins, and high-affinity terminal oxidase, compared with other soda lake cyanobacteria, appear to contribute to the success of Ca. "P. alkaliphilum" in photobioreactors and biotechnology applications.}, number={12}, journal={ISCIENCE}, publisher={Elsevier BV}, author={Ataeian, Maryam and Vadlamani, Agasteswar and Haines, Marianne and Mosier, Damon and Dong, Xiaoli and Kleiner, Manuel and Strous, Marc and Hawley, Alyse K.}, year={2021}, month={Dec} }
 @article{kleiner_kouris_jensen_grace_liu_korenek_tolić_sachsenberg_mccalder_lipton_et al._2021, title={Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes}, volume={3}, url={https://doi.org/10.1101/2021.03.29.437612}, DOI={10.1101/2021.03.29.437612}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Kleiner, Manuel and Kouris, Angela and Jensen, Marlene and Grace, D’Angelo and Liu, Yihua and Korenek, Abigail and Tolić, Nikola and Sachsenberg, Timo and McCalder, Janine and Lipton, Mary S. and et al.}, year={2021}, month={Mar} }
 @article{ponnudurai_heiden_sayavedra_hinzke_kleiner_hentschker_felbeck_sievert_schlüter_becher_et al._2020, title={Comparative proteomics of related symbiotic mussel species reveals high variability of host–symbiont interactions}, url={https://doi.org/10.1038/s41396-019-0517-6}, DOI={10.1038/s41396-019-0517-6}, abstractNote={Abstract}, journal={The ISME Journal}, author={Ponnudurai, Ruby and Heiden, Stefan E and Sayavedra, Lizbeth and Hinzke, Tjorven and Kleiner, Manuel and Hentschker, Christian and Felbeck, Horst and Sievert, Stefan M and Schlüter, Rabea and Becher, Dörte and et al.}, year={2020}, month={Feb} }
 @article{speare_smith_salvato_kleiner_septer_2020, title={Environmental Viscosity Modulates Interbacterial Killing during Habitat Transition}, volume={11}, ISSN={["2150-7511"]}, DOI={10.1128/mBio.03060-19}, abstractNote={
            Bacteria often engage in interference competition to gain access to an ecological niche, such as a host. However, little is known about how the physical environment experienced by free-living or host-associated bacteria influences such competition. We used the bioluminescent squid symbiont
            Vibrio fischeri
            to study how environmental viscosity impacts bacterial competition. Our results suggest that upon transition from a planktonic environment to a host-like environment,
            V. fischeri
            cells activate their type VI secretion system, a contact-dependent interbacterial nanoweapon, to eliminate natural competitors. This work shows that competitor cells form aggregates under host-like conditions, thereby facilitating the contact required for killing, and reveals how
            V. fischeri
            regulates a key competitive mechanism in response to the physical environment.
          }, number={1}, journal={MBIO}, author={Speare, Lauren and Smith, Stephanie and Salvato, Fernanda and Kleiner, Manuel and Septer, Alecia N.}, year={2020} }
 @article{sato_wippler_wentrup_dubilier_kleiner_2020, title={High-Quality Draft Genome Sequences of Two Deltaproteobacterial Endosymbionts, Delta1a and Delta1b, from the Uncultured Sva0081 Clade, Assembled from Metagenomes of the Gutless Marine Worm Olavius algarvensis}, volume={9}, ISSN={["2576-098X"]}, DOI={10.1128/MRA.00276-20}, abstractNote={
            Here, we present high-quality metagenome-assembled genome sequences of two closely related deltaproteobacterial endosymbionts from the gutless marine worm
            Olavius algarvensis
            (Annelida). The first is an improved draft genome sequence of the previously described sulfate-reducing symbiont Delta1. The second is from a closely related, recently discovered symbiont of
            O. algarvensis
            .
          }, number={16}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Sato, Yui and Wippler, Juliane and Wentrup, Cecilia and Dubilier, Nicole and Kleiner, Manuel}, year={2020}, month={Apr} }
 @article{sato_wippler_wentrup_woyke_dubilier_kleiner_2020, title={High-Quality Draft Genome Sequences of the Uncultured Delta3 Endosymbiont (Deltaproteobacteria) Assembled from Metagenomes of the Gutless Marine Worm Olavius algarvensis}, volume={9}, ISBN={2576-098X}, DOI={10.1128/MRA.00704-20.}, abstractNote={Here, we present two high-quality, draft metagenome-assembled genomes of deltaproteobacterial OalgDelta3 endosymbionts from the gutless marine worm  Olavius algarvensis  Their 16S rRNA gene sequences share 98% identity with Delta3 endosymbionts of related host species  Olavius ilvae  (GenBank accession no. AJ620501) and  Inanidrilus exumae  (GenBank accession no. FM202060), for which no symbiont genomes are available.}, number={31}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Sato, Yui and Wippler, Juliane and Wentrup, Cecilia and Woyke, Tanja and Dubilier, Nicole and Kleiner, Manuel}, year={2020}, month={Jul} }
 @article{sato_wippler_wentrup_woyke_dubilier_kleiner_2020, title={High-Quality Draft Genome Sequences of the Uncultured Delta3 Endosymbiont (Deltaproteobacteria) Assembled from Metagenomes of the Gutless Marine Worm Olavius algarvensis}, volume={9}, ISSN={["2576-098X"]}, url={https://doi.org/10.1128/MRA.00704-20}, DOI={10.1128/MRA.00704-20}, abstractNote={Here, we present two high-quality, draft metagenome-assembled genomes of deltaproteobacterial OalgDelta3 endosymbionts from the gutless marine worm Olavius algarvensis. Their 16S rRNA gene sequences share 98% identity with Delta3 endosymbionts of related host species Olavius ilvae (GenBank accession no. AJ620501) and Inanidrilus exumae (GenBank accession no. FM202060), for which no symbiont genomes are available. ABSTRACT Here, we present two high-quality, draft metagenome-assembled genomes of deltaproteobacterial OalgDelta3 endosymbionts from the gutless marine worm Olavius algarvensis. Their 16S rRNA gene sequences share 98% identity with Delta3 endosymbionts of related host species Olavius ilvae (GenBank accession no. AJ620501) and Inanidrilus exumae (GenBank accession no. FM202060), for which no symbiont genomes are available.}, number={31}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, publisher={American Society for Microbiology}, author={Sato, Yui and Wippler, Juliane and Wentrup, Cecilia and Woyke, Tanja and Dubilier, Nicole and Kleiner, Manuel}, editor={Stewart, Frank J.Editor}, year={2020}, month={Jul} }
 @article{assie_leisch_meier_gruber-vodicka_tegetmeyer_meyerdierks_kleiner_hinzke_joye_saxton_et al._2020, title={Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)}, volume={14}, ISSN={["1751-7370"]}, url={https://doi.org/10.1038/s41396-019-0508-7}, DOI={10.1038/s41396-019-0508-7}, abstractNote={Abstract}, number={1}, journal={ISME JOURNAL}, author={Assie, Adrien and Leisch, Nikolaus and Meier, Dimitri V and Gruber-Vodicka, Harald and Tegetmeyer, Halina E. and Meyerdierks, Anke and Kleiner, Manuel and Hinzke, Tjorven and Joye, Samantha and Saxton, Matthew and et al.}, year={2020}, month={Jan}, pages={104–122} }
 @article{hinzke_kleiner_meister_schlüter_hentschker_pané-farré_hildebrandt_felbeck_sievert_bonn_et al._2020, title={Metabolic differences between symbiont subpopulations in the deep-sea tubeworm Riftia pachyptila}, volume={4}, url={https://doi.org/10.1101/2020.04.08.032177}, DOI={10.1101/2020.04.08.032177}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Hinzke, Tjorven and Kleiner, Manuel and Meister, Mareike and Schlüter, Rabea and Hentschker, Christian and Pané-Farré, Jan and Hildebrandt, Petra and Felbeck, Horst and Sievert, Stefan M. and Bonn, Florian and et al.}, year={2020}, month={Apr} }
 @article{wagner_tang_salvato_clouse_bartlett_sermons_hoffmann_balint-kurti_kleiner_2020, title={Microbe-dependent heterosis in maize}, volume={5}, url={https://doi.org/10.1101/2020.05.05.078766}, DOI={10.1101/2020.05.05.078766}, abstractNote={ABSTRACT}, publisher={Cold Spring Harbor Laboratory}, author={Wagner, Maggie R. and Tang, Clara and Salvato, Fernanda and Clouse, Kayla M. and Bartlett, Alexandria and Sermons, Shannon and Hoffmann, Mark and Balint-Kurti, Peter J. and Kleiner, Manuel}, year={2020}, month={May} }
 @article{kleiner_bushnell_sanderson_hooper_duerkop_2020, title={Microbial DNA on the move: sequencing based detection and analysis of transduced DNA in pure cultures and microbial communities}, volume={1}, url={https://doi.org/10.1101/2020.01.15.908442}, DOI={10.1101/2020.01.15.908442}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Kleiner, Manuel and Bushnell, Brian and Sanderson, Kenneth E. and Hooper, Lora V. and Duerkop, Breck A.}, year={2020}, month={Jan} }
 @article{kleiner_bushnell_sanderson_hooper_duerkop_2020, title={Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities}, volume={8}, ISSN={["2049-2618"]}, url={https://europepmc.org/articles/PMC7667829}, DOI={10.1186/s40168-020-00935-5}, abstractNote={Abstract}, number={1}, journal={MICROBIOME}, publisher={Springer Science and Business Media LLC}, author={Kleiner, Manuel and Bushnell, Brian and Sanderson, Kenneth E. and Hooper, Lora V. and Duerkop, Breck A.}, year={2020}, month={Nov} }
 @article{zorz_sharp_kleiner_gordon_pon_dong_strous_2019, title={A shared core microbiome in soda lakes separated by large distances}, volume={10}, ISSN={["2041-1723"]}, DOI={10.1038/s41467-019-12195-5}, abstractNote={Abstract}, journal={NATURE COMMUNICATIONS}, author={Zorz, Jackie K. and Sharp, Christine and Kleiner, Manuel and Gordon, Paul M. K. and Pon, Richard T. and Dong, Xiaoli and Strous, Marc}, year={2019}, month={Sep} }
 @article{jaeckle_seah_tietjen_leisch_liebeke_kleiner_berg_gruber-vodicka_2019, title={Chemosynthetic symbiont with a drastically reduced genome serves as primary energy storage in the marine flatworm Paracatenula}, volume={116}, ISSN={["1091-6490"]}, url={https://doi.org/10.1073/pnas.1818995116}, DOI={10.1073/pnas.1818995116}, abstractNote={
            Hosts of chemoautotrophic bacteria typically have much higher biomass than their symbionts and consume symbiont cells for nutrition. In contrast to this, chemoautotrophic
            Candidatus
            Riegeria symbionts in mouthless
            Paracatenula
            flatworms comprise up to half of the biomass of the consortium. Each species of
            Paracatenula
            harbors a specific
            Ca
            . Riegeria, and the endosymbionts have been vertically transmitted for at least 500 million years. Such prolonged strict vertical transmission leads to streamlining of symbiont genomes, and the retained physiological capacities reveal the functions the symbionts provide to their hosts. Here, we studied a species of
            Paracatenula
            from Sant’Andrea, Elba, Italy, using genomics, gene expression, imaging analyses, as well as targeted and untargeted MS. We show that its symbiont,
            Ca
            . R. santandreae has a drastically smaller genome (1.34 Mb) than the symbiont´s free-living relatives (4.29–4.97 Mb) but retains a versatile and energy-efficient metabolism. It encodes and expresses a complete intermediary carbon metabolism and enhanced carbon fixation through anaplerosis and accumulates massive intracellular inclusions such as sulfur, polyhydroxyalkanoates, and carbohydrates. Compared with symbiotic and free-living chemoautotrophs,
            Ca
            . R. santandreae’s versatility in energy storage is unparalleled in chemoautotrophs with such compact genomes. Transmission EM as well as host and symbiont expression data suggest that
            Ca
            . R. santandreae largely provisions its host via outer-membrane vesicle secretion. With its high share of biomass in the symbiosis and large standing stocks of carbon and energy reserves, it has a unique role for bacterial symbionts—serving as the primary energy storage for its animal host.
          }, number={17}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Jaeckle, Oliver and Seah, Brandon K. B. and Tietjen, Malin and Leisch, Nikolaus and Liebeke, Manuel and Kleiner, Manuel and Berg, Jasmine S. and Gruber-Vodicka, Harald R.}, year={2019}, month={Apr}, pages={8505–8514} }
 @article{rubin-blum_dubilier_kleiner_2019, title={Genetic evidence for two carbon fixation pathways (the Calvin-Benson-Bassham Cycle and the Reverse Tricarboxylic Acid Cycle) in symbiotic and free-living bacteria}, volume={4}, ISSN={["2379-5042"]}, url={https://doi.org/10.1128/mSphere.00394-18}, DOI={10.1128/msphere.00394-18}, abstractNote={Primary production on Earth is dependent on autotrophic carbon fixation, which leads to the incorporation of carbon dioxide into biomass. Multiple metabolic pathways have been described for autotrophic carbon fixation, but most autotrophic organisms were assumed to have the genes for only one of these pathways. Our finding of a cultivable bacterium with two carbon fixation pathways in its genome, the rTCA and the CBB cycle, opens the possibility to study the potential benefits of having these two pathways and the interplay between them. Additionally, this will allow the investigation of the unusual and potentially very efficient mechanism of electron flow that could drive the rTCA cycle in these autotrophs. Such studies will deepen our understanding of carbon fixation pathways and could provide new avenues for optimizing carbon fixation in biotechnological applications.}, number={1}, journal={mSphere}, publisher={American Society for Microbiology}, author={Rubin-Blum, M. and Dubilier, N. and Kleiner, M.}, editor={Hallam, Steven J.Editor}, year={2019}, pages={e00394–18} }
 @article{hinzke_kleiner_breusing_felbeck_häsler_sievert_schlüter_rosenstiel_reusch_schweder_et al._2019, title={Host-Microbe Interactions in the Chemosynthetic Riftia pachyptila Symbiosis.}, volume={10}, url={https://europepmc.org/articles/PMC6918071}, DOI={10.1128/mBio.02243-19}, abstractNote={
            All animals are associated with microorganisms; hence, host-microbe interactions are of fundamental importance for life on earth. However, we know little about the molecular basis of these interactions. Therefore, we studied the deep-sea
            Riftia pachyptila
            symbiosis, a model association in which the tubeworm host is associated with only one phylotype of endosymbiotic bacteria and completely depends on this sulfur-oxidizing symbiont for nutrition. Using a metaproteomics approach, we identified both metabolic interaction processes, such as substrate transfer between the two partners, and interactions that serve to maintain the symbiotic balance, e.g., host efforts to control the symbiont population or symbiont strategies to modulate these host efforts. We suggest that these interactions are essential principles of mutualistic animal-microbe associations.
          }, number={6}, journal={mBio}, publisher={American Society for Microbiology}, author={Hinzke, Tjorven and Kleiner, Manuel and Breusing, Corinna and Felbeck, Horst and Häsler, Robert and Sievert, Stefan M. and Schlüter, Rabea and Rosenstiel, Philip and Reusch, Thorsten B. H. and Schweder, Thomas and et al.}, editor={Distel, Daniel and Ruby, Edward G.Editors}, year={2019}, month={Dec} }
 @article{hinzke_kleiner_breusing_felbeck_häsler_sievert_schlüter_rosenstiel_reusch_schweder_et al._2019, title={Host-microbe interactions in the chemosyntheticRiftia pachyptilasymbiosis}, volume={5}, url={https://doi.org/10.1101/651323}, DOI={10.1101/651323}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Hinzke, Tjorven and Kleiner, Manuel and Breusing, Corinna and Felbeck, Horst and Häsler, Robert and Sievert, Stefan M. and Schlüter, Rabea and Rosenstiel, Philip and Reusch, Thorsten B. H. and Schweder, Thomas and et al.}, year={2019}, month={May} }
 @article{kleiner_2019, title={Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities}, volume={4}, ISSN={["2379-5077"]}, url={https://doi.org/10.1128/mSystems.00115-19}, DOI={10.1128/mSystems.00115-19}, abstractNote={Metaproteomics is the large-scale identification and quantification of proteins from microbial communities and thus provides direct insight into the phenotypes of microorganisms on the molecular level. Initially, metaproteomics was mainly used to assess the “expressed” metabolism and physiology of microbial community members.}, number={3}, journal={MSYSTEMS}, publisher={American Society for Microbiology}, author={Kleiner, Manuel}, year={2019} }
 @article{hinzke_kouris_hughes_strous_kleiner_2019, title={More Is Not Always Better: Evaluation of 1D and 2D-LC-MS/MS Methods for Metaproteomics}, volume={10}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2019.00238}, abstractNote={Metaproteomics, the study of protein expression in microbial communities, is a versatile tool for environmental microbiology. Achieving sufficiently high metaproteome coverage to obtain a comprehensive picture of the activities and interactions in microbial communities is one of the current challenges in metaproteomics. An essential step to maximize the number of identified proteins is peptide separation via liquid chromatography (LC) prior to mass spectrometry (MS). Thorough optimization and comparison of LC methods for metaproteomics are, however, currently lacking. Here, we present an extensive development and test of different 1D and 2D-LC approaches for metaproteomic peptide separations. We used fully characterized mock community samples to evaluate metaproteomic approaches with very long analytical columns (50 and 75 cm) and long gradients (up to 12 h). We assessed a total of over 20 different 1D and 2D-LC approaches in terms of number of protein groups and unique peptides identified, peptide spectrum matches (PSMs) generated, the ability to detect proteins of low-abundance species, the effect of technical replicate runs on protein identifications and method reproducibility. We show here that, while 1D-LC approaches are faster and easier to set up and lead to more identifications per minute of runtime, 2D-LC approaches allow for a higher overall number of identifications with up to >10,000 protein groups identified. We also compared the 1D and 2D-LC approaches to a standard GeLC workflow, in which proteins are pre-fractionated via gel electrophoresis. This method yielded results comparable to the 2D-LC approaches, however with the drawback of a much increased sample preparation time. Based on our results, we provide recommendations on how to choose the best LC approach for metaproteomics experiments, depending on the study aims.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Hinzke, Tjorven and Kouris, Angela and Hughes, Rebecca-Ayme and Strous, Marc and Kleiner, Manuel}, year={2019}, month={Feb} }
 @article{seah_antony_huettel_zarzycki_borzyskowski_erb_kouris_kleiner_liebeke_dubilier_et al._2019, title={Sulfur-Oxidizing Symbionts without Canonical Genes for Autotrophic CO2 Fixation}, volume={10}, ISSN={["2150-7511"]}, url={https://doi.org/10.1128/mBio.01112-19}, DOI={10.1128/mBio.01112-19}, abstractNote={
            Many animals and protists depend on symbiotic sulfur-oxidizing bacteria as their main food source. These bacteria use energy from oxidizing inorganic sulfur compounds to make biomass autotrophically from CO
            2
            , serving as primary producers for their hosts. Here we describe a clade of nonautotrophic sulfur-oxidizing symbionts, “
            Candidatus
            Kentron,” associated with marine ciliates. They lack genes for known autotrophic pathways and have a carbon stable isotope fingerprint heavier than other symbionts from similar habitats. Instead, they have the potential to oxidize sulfur to fuel the uptake of organic compounds for heterotrophic growth, a metabolic mode called chemolithoheterotrophy that is not found in other symbioses. Although several symbionts have heterotrophic features to supplement primary production, in Kentron they appear to supplant it entirely.
          }, number={3}, journal={MBIO}, publisher={American Society for Microbiology}, author={Seah, Brandon K. B. and Antony, Chakkiath Paul and Huettel, Bruno and Zarzycki, Jan and Borzyskowski, Lennart Schada and Erb, Tobias J. and Kouris, Angela and Kleiner, Manuel and Liebeke, Manuel and Dubilier, Nicole and et al.}, editor={Giovannoni, Stephen J.Editor}, year={2019} }
 @article{seah_antony_huettel_zarzycki_borzyskowski_erb_kouris_kleiner_liebeke_dubilier_et al._2019, title={Sulfur-oxidizing symbionts without canonical genes for autotrophic CO2fixation}, volume={2}, url={https://doi.org/10.1101/540435}, DOI={10.1101/540435}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Seah, Brandon K. B. and Antony, Chakkiath Paul and Huettel, Bruno and Zarzycki, Jan and Borzyskowski, Lennart Schada and Erb, Tobias J. and Kouris, Angela and Kleiner, Manuel and Liebeke, Manuel and Dubilier, Nicole and et al.}, year={2019}, month={Feb} }
 @article{gruber-vodicka_leisch_kleiner_hinzke_liebeke_mcfall-ngai_hadfield_dubilier_2019, title={TheTrichoplaxmicrobiome: the simplest animal lives in an intimate symbiosis with two intracellular bacteria}, volume={3}, url={https://doi.org/10.1101/568287}, DOI={10.1101/568287}, abstractNote={Summary paragraph}, publisher={Cold Spring Harbor Laboratory}, author={Gruber-Vodicka, Harald R. and Leisch, Nikolaus and Kleiner, Manuel and Hinzke, Tjorven and Liebeke, Manuel and McFall-Ngai, Margaret and Hadfield, Michael G. and Dubilier, Nicole}, year={2019}, month={Mar} }
 @article{gruber-vodicka_leisch_kleiner_hinzke_liebeke_mcfall-ngai_hadfield_dubilier_2019, title={Two intracellular and cell type-specific bacterial symbionts in the placozoan Trichoplax H2}, volume={4}, ISSN={["2058-5276"]}, DOI={10.1038/s41564-019-0475-9}, abstractNote={Abstract}, number={9}, journal={NATURE MICROBIOLOGY}, author={Gruber-Vodicka, Harald R. and Leisch, Nikolaus and Kleiner, Manuel and Hinzke, Tjorven and Liebeke, Manuel and McFall-Ngai, Margaret and Hadfield, Michael G. and Dubilier, Nicole}, year={2019}, month={Sep}, pages={1465–1474} }
 @article{kleiner_dong_hinzke_wippler_thorson_mayer_strous_2018, title={A metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities}, volume={1}, url={https://doi.org/10.1101/245290}, DOI={10.1101/245290}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Kleiner, Manuel and Dong, Xiaoli and Hinzke, Tjorven and Wippler, Juliane and Thorson, Erin and Mayer, Bernhard and Strous, Marc}, year={2018}, month={Jan} }
 @article{petersen_kemper_gruber-vodicka_cardini_van der geest_kleiner_bulgheresi_mußmann_herbold_seah_et al._2018, title={Author Correction: Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation}, volume={3}, ISSN={2058-5276}, url={http://dx.doi.org/10.1038/S41564-018-0196-5}, DOI={10.1038/S41564-018-0196-5}, abstractNote={In this Article, the completeness and number of contigs for draft genomes from two individuals of Laxus oneistus are incorrect in the main text, although the correct information is included in Table 1. The original and corrected versions of the relevant sentence are shown in the correction notice.}, number={8}, journal={Nature Microbiology}, publisher={Springer Science and Business Media LLC}, author={Petersen, Jillian M. and Kemper, Anna and Gruber-Vodicka, Harald and Cardini, Ulisse and van der Geest, Matthijs and Kleiner, Manuel and Bulgheresi, Silvia and Mußmann, Marc and Herbold, Craig and Seah, Brandon K. B. and et al.}, year={2018}, month={Jun}, pages={961–961} }
 @article{hinzke_kleiner_markert_2018, series={Methods in Molecular Biology}, title={Centrifugation-based enrichment of bacterial cell populations for metaproteomic studies on bacteria-invertebrate symbioses}, volume={1841}, DOI={10.1007/978-1-4939-8695-8_22}, abstractNote={Owing to high sample complexity, metaproteomic investigations on bacteria–animal symbioses with two or more uncultured partners can be challenging. A selective isolation or enrichment of distinct (sub-)populations within those consortia can solve this problem. Subsequent discrete proteomic analyses benefit from increased sample purity and higher proteome coverage for each of the individual organisms. Here, we describe centrifugation-based methods that allow for a separation of the host and its bacterial symbiont population(s), or even for an enrichment of distinct symbiotic cell cycle stages in the deep-sea mussels Bathymodiolus azoricus and B. thermophilus, the gutless oligochaete Olavius algarvensis and the deep-sea tube worm Riftia pachyptila, respectively.}, journal={Springer}, author={Hinzke, T. and Kleiner, M. and Markert, S.}, editor={Becher, D.Editor}, year={2018}, pages={319–334}, collection={Methods in Molecular Biology} }
 @article{zorz_kozlowski_stein_strous_kleiner_2018, title={Comparative Proteomics of Three Species of Ammonia-Oxidizing Bacteria.}, url={http://europepmc.org/abstract/med/29867847}, DOI={10.3389/fmicb.2018.00938}, abstractNote={Ammonia-oxidizing bacteria (AOB) are important members of terrestrial, marine, and industrial microbial communities and play a fundamental role in the Nitrogen cycle within these systems. They are responsible for the first step of nitrification, ammonia oxidation to nitrite. Although AOB are widespread and essential to environmental and industrial systems, where they regularly experience fluctuations in ammonia availability, no comparative studies of the physiological response of diverse AOB species at the protein level exist. In the present study, we used 1D-LC-MS/MS proteomics to compare the metabolism and physiology of three species of ammonia AOB, Nitrosomonas europaea, Nitrosospira multiformis, and Nitrosomonas ureae, under ammonia replete and ammonia starved conditions. Additionally, we compared the expression of orthologous genes to determine the major differences in the proteome composition of the three species. We found that approximately one-third of the predicted proteome was expressed in each species and that proteins for the key metabolic processes, ammonia oxidation and carbon fixation, were among the most abundant. The red copper protein, nitrosocyanin was highly abundant in all three species hinting toward its possible role as a central metabolic enzyme in AOB. The proteomic data also allowed us to identify pyrophosphate-dependent 6-phosphofructokinase as the potential enzyme replacing the Calvin-Benson-Bassham cycle enzyme Fructose-1,6-bisphosphatase missing in N. multiformis and N. ureae. Additionally, between species, there were statistically significant differences in the expression of many abundant proteins, including those related to nitrogen metabolism (nitrite reductase), motility (flagellin), cell growth and division (FtsH), and stress response (rubrerythrin). The three species did not exhibit a starvation response at the proteome level after 24 h of ammonia starvation, however, the levels of the RuBisCO enzyme were consistently reduced after the starvation period, suggesting a decrease in capacity for biomass accumulation. This study presents the first published proteomes of N. ureae and N. multiformis, and the first comparative proteomics study of ammonia-oxidizing bacteria, which gives new insights into consistent metabolic features and differences between members of this environmentally and industrially important group.}, journal={Frontiers in microbiology}, author={Zorz, JK and Kozlowski, JA and Stein, LY and Strous, M and Kleiner, M}, year={2018} }
 @article{assié_leisch_meier_gruber-vodicka_tegetmeyer_meyerdirks_kleiner_hinzke_joye_saxton_et al._2018, title={Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)}, volume={10}, url={https://doi.org/10.1101/437616}, DOI={10.1101/437616}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Assié, Adrien and Leisch, Nikolaus and Meier, Dimitri V. and Gruber-Vodicka, Harald and Tegetmeyer, Halina E. and Meyerdirks, Anke and Kleiner, Manuel and Hinzke, Tjorven and Joye, Samantha and Saxton, Matthew and et al.}, year={2018}, month={Oct} }
 @article{kleiner_dong_hinzke_wippler_thorson_mayer_strous_2018, title={Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities}, volume={115}, ISSN={["0027-8424"]}, url={http://europepmc.org/abstract/med/29844191}, DOI={10.1073/pnas.1722325115}, abstractNote={Significance}, number={24}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Kleiner, Manuel and Dong, Xiaoli and Hinzke, Tjorven and Wippler, Juliane and Thorson, Erin and Mayer, Bernhard and Strous, Marc}, year={2018}, month={Jun}, pages={E5576–E5584} }
 @article{duerkop_kleiner_paez-espino_zhu_bushnell_hassell_winter_kyrpides_hooper_2018, title={Murine colitis reveals a disease-associated bacteriophage community}, volume={3}, ISSN={["2058-5276"]}, url={https://doi.org/10.1038/s41564-018-0210-y}, DOI={10.1038/s41564-018-0210-y}, abstractNote={The dysregulation of intestinal microbial communities is associated with inflammatory bowel diseases (IBD). Studies aimed at understanding the contribution of the microbiota to inflammatory diseases have primarily focused on bacteria, yet the intestine harbours a viral component dominated by prokaryotic viruses known as bacteriophages (phages). Phage numbers are elevated at the intestinal mucosal surface and phages increase in abundance during IBD, suggesting that phages play an unidentified role in IBD. We used a sequence-independent approach for the selection of viral contigs and then applied quantitative metagenomics to study intestinal phages in a mouse model of colitis. We discovered that during colitis the intestinal phage population is altered and transitions from an ordered state to a stochastic dysbiosis. We identified phages specific to pathobiotic hosts associated with intestinal disease, whose abundances are altered during colitis. Additionally, phage populations in healthy and diseased mice overlapped with phages from healthy humans and humans with IBD. Our findings indicate that intestinal phage communities are altered during inflammatory disease, establishing a platform for investigating phage involvement in IBD.}, number={9}, journal={NATURE MICROBIOLOGY}, author={Duerkop, Breck A. and Kleiner, Manuel and Paez-Espino, David and Zhu, Wenhan and Bushnell, Brian and Hassell, Brian and Winter, Sebastian E. and Kyrpides, Nikos C. and Hooper, Lora V}, year={2018}, month={Sep}, pages={1023–1031} }
 @article{fida_voordouw_ataeian_kleiner_okpala_mand_voordouw_2018, title={Synergy of Sodium Nitroprusside and Nitrate in Inhibiting the Activity of Sulfate Reducing Bacteria in Oil-Containing Bioreactors}, volume={9}, ISSN={["1664-302X"]}, url={http://europepmc.org/abstract/med/29867883}, DOI={10.3389/fmicb.2018.00981}, abstractNote={Sodium nitroprusside (SNP) disrupts microbial biofilms through the release of nitric oxide (NO). The actions of SNP on bacteria have been mostly limited to the genera Pseudomonas, Clostridium, and Bacillus. There are no reports of its biocidal action on sulfate-reducing bacteria (SRB), which couple the reduction of sulfate to sulfide with the oxidation of organic electron donors. Here, we report the inhibition and kill of SRB by low SNP concentrations [0.05 mM (15 ppm)] depending on biomass concentration. Chemical reaction of SNP with sulfide did not compromise its efficacy. SNP was more effective than five biocides commonly used to control SRB. Souring, the SRB activity in oil reservoirs, is often controlled by injection of nitrate. Control of SRB-mediated souring in oil-containing bioreactors was inhibited by 4 mM (340 ppm) of sodium nitrate, but required only 0.05 mM (15 ppm) of SNP. Interestingly, nitrate and SNP were found to be highly synergistic with 0.003 mM (1 ppm) of SNP and 1 mM (85 ppm) of sodium nitrate being sufficient in inhibiting souring. Hence, using SNP as an additive may greatly increase the efficacy of nitrate injection in oil reservoirs.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Fida, Tekle T. and Voordouw, Johanna and Ataeian, Maryam and Kleiner, Manuel and Okpala, Gloria and Mand, Jaspreet and Voordouw, Gerrit}, year={2018}, month={May} }
 @article{kleiner_thorson_sharp_dong_liu_li_strous_2017, title={Assessing species biomass contributions in microbial communities via metaproteomics}, volume={8}, ISSN={["2041-1723"]}, url={https://www.nature.com/articles/s41467-017-01544-x}, DOI={10.1038/s41467-017-01544-x}, abstractNote={Abstract}, journal={NATURE COMMUNICATIONS}, publisher={Cold Spring Harbor Laboratory}, author={Kleiner, Manuel and Thorson, Erin and Sharp, Christine E. and Dong, Xiaoli and Liu, Dan and Li, Carmen and Strous, Marc}, year={2017}, month={Nov} }
 @article{kleiner_thorson_sharp_dong_liu_li_strous_2017, title={Assessing species biomass contributions in microbial communities via metaproteomics}, volume={4}, url={https://doi.org/10.1101/130575}, DOI={10.1101/130575}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Kleiner, Manuel and Thorson, Erin and Sharp, Christine E. and Dong, Xiaoli and Liu, Dan and Li, Carmen and Strous, Marc}, year={2017}, month={Apr} }
 @article{dong_kleiner_sharp_thorson_li_liu_strous_2017, title={Fast and Simple Analysis of MiSeq Amplicon Sequencing Data with MetaAmp}, volume={8}, DOI={10.3389/fmicb.2017.01461}, abstractNote={Microbial community profiling by barcoded 16S rRNA gene amplicon sequencing currently has many applications in microbial ecology. The low costs of the parallel sequencing of multiplexed samples, combined with the relative ease of data processing and interpretation (compared to shotgun metagenomes) have made this an entry-level approach. Here we present the MetaAmp pipeline for processing of SSU rRNA gene and other non-coding or protein-coding amplicon sequencing data by investigators that are inexperienced with bioinformatics procedures. It accepts single-end or paired-end sequences in fasta or fastq format from various sequencing platforms. It includes read quality control, and merging of forward and reverse reads of paired-end reads. It makes use of UPARSE, Mothur, and the SILVA database for clustering, removal of chimeric reads, taxonomic classification and generation of diversity metrics. The pipeline has been validated with a mock community of known composition. MetaAmp provides a convenient web interface as well as command line interface. It is freely available at: http://ebg.ucalgary.ca/metaamp. Since its launch two years ago, MetaAmp has been used >2,800 times, by many users worldwide.}, journal={Frontiers in Microbiology}, publisher={Frontiers Media SA}, author={Dong, Xiaoli and Kleiner, Manuel and Sharp, Christine E. and Thorson, Erin and Li, Carmen and Liu, Dan and Strous, Marc}, year={2017}, month={Aug} }
 @article{dong_kleiner_sharp_thorson_li_liu_strous_2017, title={Fast and simple analysis of MiSeq amplicon sequencing data with MetaAmp}, volume={4}, DOI={10.1101/131631}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Dong, Xiaoli and Kleiner, Manuel and Sharp, Christine E. and Thorson, Erin and Li, Carmen and Liu, Dan and Strous, Marc}, year={2017}, month={Apr} }
 @article{genome sequence of the sulfur-oxidizing bathymodiolus thermophilus gill endosymbiont._2017, url={http://europepmc.org/abstract/med/28878861}, DOI={10.1186/s40793-017-0266-y}, abstractNote={Abstract}, journal={Standards in Genomic Sciences}, year={2017} }
 @article{ponnudurai_kleiner_sayavedra_petersen_moche_otto_becher_takeuchi_satoh_dubilier_et al._2017, title={Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis}, volume={11}, url={https://doi.org/10.1038/ismej.2016.124}, DOI={10.1038/ismej.2016.124}, abstractNote={Abstract}, number={2}, journal={The ISME Journal}, publisher={Springer Science and Business Media LLC}, author={Ponnudurai, Ruby and Kleiner, Manuel and Sayavedra, Lizbeth and Petersen, Jillian M and Moche, Martin and Otto, Andreas and Becher, Dörte and Takeuchi, Takeshi and Satoh, Noriyuki and Dubilier, Nicole and et al.}, year={2017}, month={Feb}, pages={463–477} }
 @misc{metaproteomics of phototrophic biomats from two soda lakes in the canadian rocky mountains_2017, url={http://www.ebi.ac.uk/pride/archive/projects/PXD006343}, year={2017} }
 @article{kleiner_2017, title={Normalization of metatranscriptomic and metaproteomic data for differential gene expression analyses: The importance of accounting for organism abundance}, volume={5}, url={https://doi.org/10.7287/peerj.preprints.2846v1}, DOI={10.7287/peerj.preprints.2846v1}, abstractNote={Metatranscriptomics and metaproteomics make it possible to measure gene expression in microbial communities. So far these approaches were mostly used to get a general overview of the dominant metabolism and physiologies of community members. Recently, environmental microbiologists have started using metatranscriptomics and metaproteomics to look at gene expression differences between different environments or conditions. This has been mostly done by using makeshift adaptations of pure culture focused differential transcriptomics and proteomics approaches. However, since meta-omics data has many more variables attached to it as compared to pure culture derived data, such makeshift adaptations are problematic at best. One particular challenge is posed by the data normalization strategies used to account for technical and biological variables in meta-omic data. Here I discuss the most common normalization strategy for transcriptomic and proteomic data and why it is not valid by itself for meta-omic data. I provide logical proof that variation in species abundances between samples is an additional variable that must be accounted for during normalization of meta-omic data. Finally, I show how the existing normalization methods for transcriptomic and proteomic data can be augmented to be applicable to meta-omic data.}, journal={PeerJ Preprints}, publisher={PeerJ}, author={Kleiner, M.}, year={2017}, pages={e2846v1} }
 @article{kleiner_2017, title={Normalization of metatranscriptomic and metaproteomic data for differential gene expression analyses: The importance of accounting for organism abundance}, volume={3}, url={https://doi.org/10.7287/peerj.preprints.2846}, DOI={10.7287/peerj.preprints.2846}, abstractNote={Metatranscriptomics and metaproteomics make it possible to measure gene expression in microbial communities. So far these approaches were mostly used to get a general overview of the dominant metabolism and physiologies of community members. Recently, environmental microbiologists have started using metatranscriptomics and metaproteomics to look at gene expression differences between different environments or conditions. This has been mostly done by using makeshift adaptations of pure culture focused differential transcriptomics and proteomics approaches. However, since meta-omics data has many more variables attached to it as compared to pure culture derived data, such makeshift adaptations are problematic at best. One particular challenge is posed by the data normalization strategies used to account for technical and biological variables in meta-omic data. Here I discuss the most common normalization strategy for transcriptomic and proteomic data and why it is not valid by itself for meta-omic data. I provide logical proof that variation in species abundances between samples is an additional variable that must be accounted for during normalization of meta-omic data. Finally, I show how the existing normalization methods for transcriptomic and proteomic data can be augmented to be applicable to meta-omic data.}, publisher={PeerJ}, author={Kleiner, Manuel}, year={2017}, month={Mar} }
 @misc{quantification of mock microbial communities with metagenomes, 16s rrna gene amplicons and metaproteomics_2017, url={http://www.ebi.ac.uk/pride/archive/projects/PXD006118}, year={2017} }
 @misc{re-analysis of an ultra-deep and quantitative saliva proteome_2017, url={http://www.ebi.ac.uk/pride/archive/projects/PXD006366}, year={2017} }
 @article{rubin-blum_antony_borowski_sayavedra_pape_sahling_bohrmann_kleiner_redmond_valentine_et al._2017, title={Short-chain alkanes fuel mussels and sponge Cycloclasticus symbionts from deep-sea gas and oil seeps}, volume={2}, url={https://doi.org/10.1038/nmicrobiol.2017.93}, DOI={10.1038/nmicrobiol.2017.93}, abstractNote={Cycloclasticus bacteria are ubiquitous in oil-rich regions of the ocean and are known for their ability to degrade polycyclic aromatic hydrocarbons (PAHs). In this study, we describe Cycloclasticus that have established a symbiosis with Bathymodiolus heckerae mussels and poecilosclerid sponges from asphalt-rich, deep-sea oil seeps at Campeche Knolls in the southern Gulf of Mexico. Genomic and transcriptomic analyses revealed that, in contrast to all previously known Cycloclasticus, the symbiotic Cycloclasticus appears to lack the genes needed for PAH degradation. Instead, these symbionts use propane and other short-chain alkanes such as ethane and butane as carbon and energy sources, thus expanding the limited range of substrates known to power chemosynthetic symbioses. Analyses of short-chain alkanes in the environment of the Campeche Knolls symbioses revealed that these are present at high concentrations (in the μM to mM range). Comparative genomic analyses revealed high similarities between the genes used by the symbiotic Cycloclasticus to degrade short-chain alkanes and those of free-living Cycloclasticus that bloomed during the Deepwater Horizon oil spill. Our results indicate that the metabolic versatility of bacteria within the Cycloclasticus clade is higher than previously assumed, and highlight the expanded role of these keystone species in the degradation of marine hydrocarbons. Cycloclasticus bacterial symbionts of mussels and sponges that live in deep-sea gas and oil seeps are capable of using short-chain alkanes as their primary energy source, providing further insight into chemosynthetic symbioses.}, journal={Nature Microbiology}, publisher={Springer Nature}, author={Rubin-Blum, Maxim and Antony, Chakkiath Paul and Borowski, Christian and Sayavedra, Lizbeth and Pape, Thomas and Sahling, Heiko and Bohrmann, Gerhard and Kleiner, Manuel and Redmond, Molly C. and Valentine, David L. and et al.}, year={2017}, pages={17093} }
 @misc{bathymodiolus azoricus host-symbiont proteomics_2016, url={http://www.ebi.ac.uk/pride/archive/projects/PXD004061}, year={2016} }
 @article{petersen_kemper_gruber-vodicka_cardini_geest_kleiner_bulgheresi_mußmann_herbold_seah_et al._2016, title={Chemosynthetic sulphur-oxidizing symbionts of marine invertebrate animals are capable of nitrogen fixation}, volume={2}, url={https://doi.org/10.1038/nmicrobiol.2016.195}, DOI={10.1038/nmicrobiol.2016.195}, abstractNote={Abstract}, journal={Nature Microbiology}, publisher={Springer Nature}, author={Petersen, Jillian M. and Kemper, Anna and Gruber-Vodicka, Harald and Cardini, Ulisse and Geest, Matthijs and Kleiner, Manuel and Bulgheresi, Silvia and Mußmann, Marc and Herbold, Craig and Seah, Brandon K.B. and et al.}, year={2016}, pages={16195} }
 @article{zimmermann_wentrup_sadowski_blazejak_gruber-vodicka_kleiner_ott_cronholm_de_erséus_et al._2016, title={Closely coupled evolutionary history of ecto- and endosymbionts from two distantly-related animal phyla}, volume={25}, url={http://europepmc.org/abstract/med/26826340}, DOI={10.1111/mec.13554}, abstractNote={Abstract}, number={13}, journal={Molecular Ecology}, author={Zimmermann, J and Wentrup, C and Sadowski, M and Blazejak, A and Gruber-Vodicka, H and Kleiner, M and Ott, J and Cronholm, B and De, Wit P and Erséus, C and et al.}, year={2016}, pages={3203–3223} }
 @misc{differential proteomics of lenisia limosa (breviatea) and its epibiotic arcobacter symbiont_2016, url={http://www.ebi.ac.uk/pride/archive/projects/PXD003275}, year={2016} }
 @article{hamann_gruber-vodicka_kleiner_tegetmeyer_riedel_littmann_chen_milucka_viehweger_becker_et al._2016, title={Environmental Breviatea harbor mutualistic Arcobacter epibionts}, volume={534}, url={http://europepmc.org/abstract/med/27279223}, DOI={10.1038/nature18297}, abstractNote={Breviatea form a lineage of free living, unicellular protists, distantly related to animals and fungi. This lineage emerged almost one billion years ago, when the oceanic oxygen content was low, and extant Breviatea have evolved or retained an anaerobic lifestyle. Here we report the cultivation of Lenisia limosa, gen. et sp. nov., a newly discovered breviate colonized by relatives of animal-associated Arcobacter. Physiological experiments show that the association of L. limosa with Arcobacter is driven by the transfer of hydrogen and is mutualistic, providing benefits to both partners. With whole-genome sequencing and differential proteomics, we show that an experimentally observed fitness gain of L. limosa could be explained by the activity of a so far unknown type of NAD(P)H-accepting hydrogenase, which is expressed in the presence, but not in the absence, of Arcobacter. Differential proteomics further reveal that the presence of Lenisia stimulates expression of known 'virulence' factors by Arcobacter. These proteins typically enable colonization of animal cells during infection, but may in the present case act for mutual benefit. Finally, re-investigation of two currently available transcriptomic data sets of other Breviatea reveals the presence and activity of related hydrogen-consuming Arcobacter, indicating that mutualistic interaction between these two groups of microbes might be pervasive. Our results support the notion that molecular mechanisms involved in virulence can also support mutualism, as shown here for Arcobacter and Breviatea.}, number={7606}, journal={Nature}, author={Hamann, E. and Gruber-Vodicka, H. and Kleiner, M. and Tegetmeyer, H.E. and Riedel, D. and Littmann, S. and Chen, J. and Milucka, J. and Viehweger, B. and Becker, K.W. and et al.}, year={2016}, pages={254–258} }
 @article{schimak_kleiner_wetzel_liebeke_dubilier_fuchs_2016, title={MiL-FISH: Multi-labelled oligonucleotides for fluorescence in situ hybridisation improve visualization of bacterial cells}, volume={82}, url={http://europepmc.org/abstract/med/26475101}, DOI={10.1128/AEM.02776-15}, abstractNote={ABSTRACT}, number={1}, journal={Applied and Environmental Microbiology}, author={Schimak, M.P. and Kleiner, M. and Wetzel, S. and Liebeke, M. and Dubilier, N. and Fuchs, B.}, year={2016}, pages={62–70} }
 @misc{proteomics of candidatus thiodiazotropha endoloripes, the chemosynthetic symbiont of the lucinid clam loripes lucinalis from the bay of fetovaia_2016, url={http://www.ebi.ac.uk/pride/archive/projects/PXD004536}, year={2016} }
 @misc{proteomics of cycloclasticus endosymbiont of deep-sea mussel bathymodiolus heckerae from campeche knolls, southern gulf of mexico_2016, url={http://www.ebi.ac.uk/pride/archive/projects/PXD005351}, year={2016} }
 @article{yu_kleiner_velicer_2016, title={Spontaneous Reversions of an Evolutionary Trait Loss Reveal Regulators of a Small RNA That Controls Multicellular Development in Myxobacteria}, volume={198}, DOI={10.1128/jb.00389-16}, abstractNote={ABSTRACT}, number={23}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Yu, Yuen-Tsu N. and Kleiner, Manuel and Velicer, Gregory J.}, editor={Mullineaux, C. W.Editor}, year={2016}, month={Sep}, pages={3142–3151} }
 @article{wippler_kleiner_lott_gruhl_abraham_giannone_young_hettich_dubilier_2016, title={Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis}, volume={17}, DOI={10.1186/s12864-016-3293-y}, abstractNote={The gutless marine worm Olavius algarvensis has a completely reduced digestive and excretory system, and lives in an obligate nutritional symbiosis with bacterial symbionts. While considerable knowledge has been gained of the symbionts, the host has remained largely unstudied. Here, we generated transcriptomes and proteomes of O. algarvensis to better understand how this annelid worm gains nutrition from its symbionts, how it adapted physiologically to a symbiotic lifestyle, and how its innate immune system recognizes and responds to its symbiotic microbiota.Key adaptations to the symbiosis include (i) the expression of gut-specific digestive enzymes despite the absence of a gut, most likely for the digestion of symbionts in the host's epidermal cells; (ii) a modified hemoglobin that may bind hydrogen sulfide produced by two of the worm's symbionts; and (iii) the expression of a very abundant protein for oxygen storage, hemerythrin, that could provide oxygen to the symbionts and the host under anoxic conditions. Additionally, we identified a large repertoire of proteins involved in interactions between the worm's innate immune system and its symbiotic microbiota, such as peptidoglycan recognition proteins, lectins, fibrinogen-related proteins, Toll and scavenger receptors, and antimicrobial proteins.We show how this worm, over the course of evolutionary time, has modified widely-used proteins and changed their expression patterns in adaptation to its symbiotic lifestyle and describe expressed components of the innate immune system in a marine oligochaete. Our results provide further support for the recent realization that animals have evolved within the context of their associations with microbes and that their adaptive responses to symbiotic microbiota have led to biological innovations.}, number={1}, journal={BMC Genomics}, publisher={Springer Nature}, author={Wippler, Juliane and Kleiner, Manuel and Lott, Christian and Gruhl, Alexander and Abraham, Paul E. and Giannone, Richard J. and Young, Jacque C. and Hettich, Robert L. and Dubilier, Nicole}, year={2016}, month={Nov} }
 @misc{transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm olavius algarvensis_2016, url={https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=77bbe652de0b4439b9a9e89016f99c93}, year={2016} }
 @article{sayavedra_kleiner_ponnudurai_wetzel_pelletier_barbe_satoh_shoguchi_fink_breusing_et al._2015, title={Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels}, volume={4}, url={http://europepmc.org/abstract/med/26371554}, DOI={10.7554/eLife.07966}, abstractNote={Bathymodiolus mussels live in symbiosis with intracellular sulfur-oxidizing (SOX) bacteria that provide them with nutrition. We sequenced the SOX symbiont genomes from two Bathymodiolus species. Comparison of these symbiont genomes with those of their closest relatives revealed that the symbionts have undergone genome rearrangements, and up to 35% of their genes may have been acquired by horizontal gene transfer. Many of the genes specific to the symbionts were homologs of virulence genes. We discovered an abundant and diverse array of genes similar to insecticidal toxins of nematode and aphid symbionts, and toxins of pathogens such as Yersinia and Vibrio. Transcriptomics and proteomics revealed that the SOX symbionts express the toxin-related genes (TRGs) in their hosts. We hypothesize that the symbionts use these TRGs in beneficial interactions with their host, including protection against parasites. This would explain why a mutualistic symbiont would contain such a remarkable ‘arsenal’ of TRGs.}, journal={eLife}, author={Sayavedra, L. and Kleiner, M. and Ponnudurai, R. and Wetzel, S. and Pelletier, E. and Barbe, V. and Satoh, N. and Shoguchi, E. and Fink, D. and Breusing, C. and et al.}, year={2015}, pages={e07966} }
 @article{kleiner_hooper_duerkop_2015, title={Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes}, volume={16}, url={http://europepmc.org/abstract/med/25608871}, DOI={10.1186/s12864-014-1207-4}, abstractNote={Viruses are a significant component of the intestinal microbiota in mammals. In recent years, advances in sequencing technologies and data analysis techniques have enabled detailed metagenomic studies investigating intestinal viromes (collections of bacteriophage and eukaryotic viral nucleic acids) and their potential contributions to the ecology of the microbiota. An important component of virome studies is the isolation and purification of virus-like particles (VLPs) from intestinal contents or feces. Several methods have been applied to isolate VLPs from intestinal samples, yet to our knowledge, the efficiency and reproducibility between methods have not been explored. A rigorous evaluation of methods for VLP purification is critical as many studies begin to move from descriptive analyses of virus diversity to studies striving to quantitatively compare viral abundances across many samples. Therefore, reproducible VLP purification methods which allow for high sample throughput are needed. Here we compared and evaluated four methods for VLP purification using artificial intestinal microbiota samples of known bacterial and viral composition.We compared the following four methods of VLP purification from fecal samples: (i) filtration + DNase, (ii) dithiothreitol treatment + filtration + DNase, (iii) filtration + DNase + PEG precipitation and (iv) filtration + DNase + CsCl density gradient centrifugation. Three of the four tested methods worked well for VLP purification. We observed several differences between methods related to the removal efficiency of bacterial and host DNAs and biases against specific phages. In particular the CsCl density gradient centrifugation method, which is frequently used for VLP purification, was most efficient in removing host derived DNA, but also showed strong discrimination against specific phages and showed a lower reproducibility of quantitative results.Based on our data we recommend the use of methods (i) or (ii) for large scale studies when quantitative comparison of viral abundances across samples is required. The CsCl density gradient centrifugation method, while being excellently suited to achieve highly purified samples, in our opinion, should be used with caution when performing quantitative studies.}, number={7}, journal={BMC Genomics}, author={Kleiner, M. and Hooper, L.V. and Duerkop, B.A.}, year={2015}, pages={7} }
 @article{kleiner_wentrup_holler_lavik_harder_lott_littmann_kuypers_dubilier_2015, title={Use of carbon monoxide and hydrogen by a bacteria-animal symbiosis from seagrass sediments}, volume={17}, url={http://europepmc.org/abstract/med/26013766}, DOI={10.1111/1462-2920.12912}, abstractNote={Summary}, number={12}, journal={Environmental Microbiology}, author={Kleiner, M. and Wentrup, C. and Holler, T. and Lavik, G. and Harder, J. and Lott, C. and Littmann, S. and Kuypers, M.M.M. and Dubilier, N.}, year={2015}, pages={5023–5035} }
 @article{winkel_pjevac_kleiner_littmann_meyerdierks_amann_mußmann_2014, title={Identification and activity of acetate-assimilating bacteria in diffuse fluids venting from deep-sea hydrothermal systems}, volume={90}, url={http://europepmc.org/abstract/med/25244359}, DOI={10.1111/1574-6941.12429}, abstractNote={Diffuse hydrothermal fluids often contain organic compounds such as hydrocarbons, lipids, and organic acids. Microorganisms consuming these compounds at hydrothermal sites are so far only known from cultivation-dependent studies. To identify potential heterotrophs without prior cultivation, we combined microbial community analysis with short-term incubations using (13)C-labeled acetate at two distinct hydrothermal systems. We followed cell growth and assimilation of (13)C into single cells by nanoSIMS combined with fluorescence in situ hybridization (FISH). In 55 °C-fluids from the Menez Gwen hydrothermal system/Mid-Atlantic Ridge, a novel epsilonproteobacterial group accounted for nearly all assimilation of acetate, representing the first aerobic acetate-consuming member of the Nautiliales. In contrast, Gammaproteobacteria dominated the (13) C-acetate assimilation in incubations of 37 °C-fluids from the back-arc hydrothermal system in the Manus Basin/Papua New Guinea. Here, 16S rRNA gene sequences were mostly related to mesophilic Marinobacter, reflecting the high content of seawater in these fluids. The rapid growth of microorganisms upon acetate addition suggests that acetate consumers in diffuse fluids are copiotrophic opportunists, which quickly exploit their energy sources, whenever available under the spatially and temporally highly fluctuating conditions. Our data provide first insights into the heterotrophic microbial community, catalyzing an under-investigated part of microbial carbon cycling at hydrothermal vents.}, number={3}, journal={FEMS Microbiology Ecology}, author={Winkel, M. and Pjevac, P. and Kleiner, M. and Littmann, S. and Meyerdierks, A. and Amann, R. and Mußmann, M.}, year={2014}, pages={731–746} }
 @article{kleiner_young_shah_verberkmoes_dubilier_2013, title={Metaproteomics Reveals Abundant Transposase Expression in Mutualistic Endosymbionts}, volume={4}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000321187400018&KeyUID=WOS:000321187400018}, DOI={10.1128/mBio.00223-13}, abstractNote={ABSTRACT}, number={3}, journal={Mbio}, author={Kleiner, Manuel and Young, Jacque C. and Shah, Manesh and VerBerkmoes, Nathan C. and Dubilier, Nicole}, year={2013} }
 @article{kleiner_petersen_dubilier_2012, title={Convergent and divergent evolution of metabolism in sulfur-oxidizing symbionts and the role of horizontal gene transfer}, volume={15}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000311181000012&KeyUID=WOS:000311181000012}, DOI={10.1016/j.mlb.2012.09.003}, number={5}, journal={Current Opinion in Microbiology}, author={Kleiner, Manuel and Petersen, Jillian M. and Dubilier, Nicole}, year={2012}, pages={621–631} }
 @article{kleiner_petersen_dubilier_2012, title={Convergent and divergent evolution of metabolism in sulfur-oxidizing symbionts and the role of horizontal gene transfer}, volume={15}, ISSN={1369-5274}, url={http://dx.doi.org/10.1016/j.mib.2012.09.003}, DOI={10.1016/j.mib.2012.09.003}, abstractNote={Symbioses between marine invertebrates and autotrophic sulfur-oxidizing bacteria have evolved from multiple lineages within the Gammaproteobacteria in a striking example of convergent evolution. These GammaSOX symbionts all perform the same basic function: they provide their hosts with nutrition through the fixation of CO2 into biomass using reduced sulfur compounds as an energy source. However, our review of recent –omics based studies and genome mining for this study revealed that the GammaSOX symbionts diverge in many other metabolic capabilities and functions, and we show how these divergences could reflect adaptations to different hosts and habitat conditions. Our phylogenetic analyses of key metabolic genes in GammaSOX symbionts revealed that these differed markedly from 16S rRNA phylogenies. We hypothesize that horizontal gene transfer (HGT) would explain many of these incongruencies, and conclude that HGT may have played a significant role in shaping the metabolic evolution of GammaSOX symbionts.}, number={5}, journal={Current Opinion in Microbiology}, publisher={Elsevier BV}, author={Kleiner, Manuel and Petersen, Jillian M and Dubilier, Nicole}, year={2012}, month={Oct}, pages={621–631} }
 @article{kleiner_wentrup_lott_teeling_wetzel_young_chang_shah_verberkmoes_zarzycki_et al._2012, title={Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use}, volume={109}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000304090600007&KeyUID=WOS:000304090600007}, DOI={10.1073/pnas.1121198109}, abstractNote={
            Low nutrient and energy availability has led to the evolution of numerous strategies for overcoming these limitations, of which symbiotic associations represent a key mechanism. Particularly striking are the associations between chemosynthetic bacteria and marine animals that thrive in nutrient-poor environments such as the deep sea because the symbionts allow their hosts to grow on inorganic energy and carbon sources such as sulfide and CO
            2
            . Remarkably little is known about the physiological strategies that enable chemosynthetic symbioses to colonize oligotrophic environments. In this study, we used metaproteomics and metabolomics to investigate the intricate network of metabolic interactions in the chemosynthetic association between
            Olavius algarvensis
            , a gutless marine worm, and its bacterial symbionts. We propose previously undescribed pathways for coping with energy and nutrient limitation, some of which may be widespread in both free-living and symbiotic bacteria. These pathways include (
            i
            ) a pathway for symbiont assimilation of the host waste products acetate, propionate, succinate and malate; (
            ii
            ) the potential use of carbon monoxide as an energy source, a substrate previously not known to play a role in marine invertebrate symbioses; (
            iii
            ) the potential use of hydrogen as an energy source; (
            iv
            ) the strong expression of high-affinity uptake transporters; and (
            v
            ) as yet undescribed energy-efficient steps in CO
            2
            fixation and sulfate reduction. The high expression of proteins involved in pathways for energy and carbon uptake and conservation in the
            O
            .
            algarvensis
            symbiosis indicates that the oligotrophic nature of its environment exerted a strong selective pressure in shaping these associations.
          }, number={19}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Kleiner, Manuel and Wentrup, Cecilia and Lott, Christian and Teeling, Hanno and Wetzel, Silke and Young, Jacque and Chang, Yun-Juan and Shah, Manesh and VerBerkmoes, Nathan C. and Zarzycki, Jan and et al.}, year={2012}, pages={E1173–E1182} }
 @article{markert_gardebrecht_felbeck_sievert_klose_becher_albrecht_thurmer_daniel_kleiner_et al._2011, title={Status quo in physiological proteomics of the uncultured Riftia pachyptila endosymbiont}, volume={11}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000293269100015&KeyUID=WOS:000293269100015}, DOI={10.1002/pmic.201100059}, abstractNote={Abstract}, number={15}, journal={Proteomics}, author={Markert, S. and Gardebrecht, A. and Felbeck, H. and Sievert, S. M. and Klose, J. and Becher, D. and Albrecht, D. and Thurmer, A. and Daniel, R. and Kleiner, M. and et al.}, year={2011}, pages={3106–3117} }
 @article{kleiner_woyke_ruehland_dubilier_2011, title={The Olavius algarvensis Metagenome Revisited: Lessons Learned from the Analysis of the Low-Diversity Microbial Consortium of a Gutless Marine Worm}, DOI={10.1002/9781118010549.ch32}, abstractNote={This chapter contains sections titled: Introduction Method Discussion: Challenges of Analyzing Co-Occurring Symbionts in Very Small Hosts Major Findings of the Study in Brief The Metagenome Revisited Conclusions Internet Resources for the O. Algarvensis Metagenome References}, journal={Handbook of Molecular Microbial Ecology II}, publisher={Wiley-Blackwell}, author={Kleiner, Manuel and Woyke, Tanja and Ruehland, Caroline and Dubilier, Nicole}, year={2011}, month={Nov}, pages={319–333} }