Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions

Feng, Jun; Qian, Yili; Zhou, Zhichao; Ertmer, Sarah; Vivas, Eugenio I.; Lan, Freeman; Hamilton, Joshua J.; Rey, Federico E.; Anantharaman, Karthik; Venturelli, Ophelia S.

doi:10.1016/j.chom.2021.12.006

Title: Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions

Journal Article · 05 January 2022 · Cell Host & Microbe

DOI: https://doi.org/10.1016/j.chom.2021.12.006 · OSTI ID:1976962

^[1];

^[2]; Zhou, Zhichao ^[2]; Ertmer, Sarah ^[2]; Vivas, Eugenio I. ^[2];

^[2]; Hamilton, Joshua J. ^[2]; Rey, Federico E. ^[2]; Anantharaman, Karthik ^[2];

^[2]

University of Wisconsin, Madison, WI (United States); OSTI
University of Wisconsin, Madison, WI (United States)

Polysaccharide utilization loci (PULs) are co-regulated bacterial genes that sense nutrients and enable glycan digestion. Human gut microbiome members, notably Bacteroides, contain numerous PULs that enable glycan utilization and shape ecological dynamics. To investigate the role of PULs on fitness and inter-species interactions, we develop a CRISPR-based genome editing tool to study 23 PULs in Bacteroides uniformis (BU). BU PULs show distinct glycan-degrading functions and transcriptional coordination that enables the population to adapt upon loss of other PULs. Exploiting a BU mutant barcoding strategy, we demonstrate that in vitro fitness and BU colonization in the murine gut are enhanced by deletion of specific PULs and modulated by glycan availability. PULs mediate glycan-dependent interactions with butyrate producers that depend on the degradation mechanism and glycan utilization ability of the butyrate producer. Thus, PULs determine community dynamics and butyrate production and provide a selective advantage or disadvantage depending on the nutritional landscape.

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Research Organization:: University of Wisconsin, Madison, WI (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Institutes of Health (NIH); National Institute of Biomedical Imaging and Bioengineering; Multi University Research Initiative (MURI)

Grant/Contract Number:: FC02-07ER64494

OSTI ID:: 1976962

Journal Information:: Cell Host & Microbe, Journal Name: Cell Host & Microbe Journal Issue: 2 Vol. 30; ISSN 1931-3128

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (93)

A β-mannan utilization locus in Bacteroides ovatus involves a GH36 α-galactosidase active on galactomannans Reddy, Sumitha K.; Bågenholm, Viktoria; Pudlo, Nicholas A. FEBS Letters, Vol. 590, Issue 14 https://doi.org/10.1002/1873-3468.12250	journal	June 2016
Laboratory Maintenance and Cultivation of Bacteroides Species Bacic, Melissa K.; Smith, C. Jeffrey Current Protocols in Microbiology, Vol. 9, Issue 1 https://doi.org/10.1002/9780471729259.mc13c01s9	journal	May 2008
Specificity of Polysaccharide Use in Intestinal Bacteroides Species Determines Diet-Induced Microbiota Alterations Sonnenburg, Erica D.; Zheng, Hongjun; Joglekar, Payal Cell, Vol. 141, Issue 7 https://doi.org/10.1016/j.cell.2010.05.005	journal	June 2010
Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System Zetsche, Bernd; Gootenberg, Jonathan S.; Abudayyeh, Omar O. Cell, Vol. 163, Issue 3, p. 759-771 https://doi.org/10.1016/j.cell.2015.09.038	journal	October 2015
From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites Koh, Ara; De Vadder, Filipe; Kovatcheva-Datchary, Petia Cell, Vol. 165, Issue 6 https://doi.org/10.1016/j.cell.2016.05.041	journal	June 2016
A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility Desai, Mahesh S.; Seekatz, Anna M.; Koropatkin, Nicole M. Cell, Vol. 167, Issue 5 https://doi.org/10.1016/j.cell.2016.10.043	journal	November 2016
Tunable Expression Tools Enable Single-Cell Strain Distinction in the Gut Microbiome Whitaker, Weston R.; Shepherd, Elizabeth Stanley; Sonnenburg, Justin L. Cell, Vol. 169, Issue 3 https://doi.org/10.1016/j.cell.2017.03.041	journal	April 2017
Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut Lim, Bentley; Zimmermann, Michael; Barry, Natasha A. Cell, Vol. 169, Issue 3 https://doi.org/10.1016/j.cell.2017.03.045	journal	April 2017
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle Pasolli, Edoardo; Asnicar, Francesco; Manara, Serena Cell, Vol. 176, Issue 3 https://doi.org/10.1016/j.cell.2019.01.001	journal	January 2019
Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota Mimee, Mark; Tucker, Alex C.; Voigt, Christopher A. Cell Systems, Vol. 1, Issue 1 https://doi.org/10.1016/j.cels.2015.06.001	journal	July 2015
Mucosal Glycan Foraging Enhances Fitness and Transmission of a Saccharolytic Human Gut Bacterial Symbiont Martens, Eric C.; Chiang, Herbert C.; Gordon, Jeffrey I. Cell Host & Microbe, Vol. 4, Issue 5 https://doi.org/10.1016/j.chom.2008.09.007	journal	November 2008
Eating For Two: How Metabolism Establishes Interspecies Interactions in the Gut Fischbach, Michael A.; Sonnenburg, Justin L. Cell Host & Microbe, Vol. 10, Issue 4 https://doi.org/10.1016/j.chom.2011.10.002	journal	October 2011
Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota Devlin, A. Sloan; Marcobal, Angela; Dodd, Dylan Cell Host & Microbe, Vol. 20, Issue 6 https://doi.org/10.1016/j.chom.2016.10.021	journal	December 2016
The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease Makki, Kassem; Deehan, Edward C.; Walter, Jens Cell Host & Microbe, Vol. 23, Issue 6 https://doi.org/10.1016/j.chom.2018.05.012	journal	June 2018
Adaptive Evolution within Gut Microbiomes of Healthy People Zhao, Shijie; Lieberman, Tami D.; Poyet, Mathilde Cell Host & Microbe, Vol. 25, Issue 5 https://doi.org/10.1016/j.chom.2019.03.007	journal	May 2019
Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates Fehlner-Peach, Hannah; Magnabosco, Cara; Raghavan, Varsha Cell Host & Microbe, Vol. 26, Issue 5 https://doi.org/10.1016/j.chom.2019.10.013	journal	November 2019
An Ecological Network of Polysaccharide Utilization among Human Intestinal Symbionts Rakoff-Nahoum, Seth; Coyne, Michael J.; Comstock, Laurie E. Current Biology, Vol. 24, Issue 1 https://doi.org/10.1016/j.cub.2013.10.077	journal	January 2014
Development of a novel plasmid vector pTIO-1 adapted for electrotransformation of Porphyromonas gingivalis Tagawa, Junpei; Inoue, Tetsuyoshi; Naito, Mariko Journal of Microbiological Methods, Vol. 105 https://doi.org/10.1016/j.mimet.2014.07.032	journal	October 2014
Starch Catabolism by a Prominent Human Gut Symbiont Is Directed by the Recognition of Amylose Helices Koropatkin, Nicole M.; Martens, Eric C.; Gordon, Jeffrey I. Structure, Vol. 16, Issue 7 https://doi.org/10.1016/j.str.2008.03.017	journal	July 2008
A human gut microbial gene catalogue established by metagenomic sequencing Qin, Junjie; Li, Ruiqiang; Raes, Jeroen Nature, Vol. 464, Issue 7285 https://doi.org/10.1038/nature08821	journal	March 2010
A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes Larsbrink, Johan; Rogers, Theresa E.; Hemsworth, Glyn R. Nature, Vol. 506, Issue 7489 https://doi.org/10.1038/nature12907	journal	January 2014
Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism Cuskin, Fiona; Lowe, Elisabeth C.; Temple, Max J. Nature, Vol. 517, Issue 7533 https://doi.org/10.1038/nature13995	journal	January 2015
The evolution of cooperation within the gut microbiota Rakoff-Nahoum, Seth; Foster, Kevin R.; Comstock, Laurie E. Nature, Vol. 533, Issue 7602 https://doi.org/10.1038/nature17626	journal	April 2016
Complex pectin metabolism by gut bacteria reveals novel catalytic functions Ndeh, Didier; Rogowski, Artur; Cartmell, Alan Nature, Vol. 544, Issue 7648 https://doi.org/10.1038/nature21725	journal	March 2017
Glycan complexity dictates microbial resource allocation in the large intestine Rogowski, Artur; Briggs, Jonathon A.; Mortimer, Jennifer C. Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms8481	journal	June 2015
Fast and sensitive protein alignment using DIAMOND Buchfink, Benjamin; Xie, Chao; Huson, Daniel H. Nature Methods, Vol. 12, Issue 1 https://doi.org/10.1038/nmeth.3176	journal	November 2014
An insider's perspective: Bacteroides as a window into the microbiome Wexler, Aaron G.; Goodman, Andrew L. Nature Microbiology, Vol. 2, Issue 5 https://doi.org/10.1038/nmicrobiol.2017.26	journal	April 2017
The Phyre2 web portal for protein modeling, prediction and analysis Kelley, Lawrence A.; Mezulis, Stefans; Yates, Christopher M. Nature Protocols, Vol. 10, Issue 6 https://doi.org/10.1038/nprot.2015.053	journal	May 2015
How glycan metabolism shapes the human gut microbiota Koropatkin, Nicole M.; Cameron, Elizabeth A.; Martens, Eric C. Nature Reviews Microbiology, Vol. 10, Issue 5 https://doi.org/10.1038/nrmicro2746	journal	April 2012
The abundance and variety of carbohydrate-active enzymes in the human gut microbiota Kaoutari, Abdessamad El; Armougom, Fabrice; Gordon, Jeffrey I. Nature Reviews Microbiology, Vol. 11, Issue 7 https://doi.org/10.1038/nrmicro3050	journal	June 2013
Molecular basis of an agarose metabolic pathway acquired by a human intestinal symbiont Pluvinage, Benjamin; Grondin, Julie M.; Amundsen, Carolyn Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-03366-x	journal	March 2018
Bacteroidetes use thousands of enzyme combinations to break down glycans Lapébie, Pascal; Lombard, Vincent; Drula, Elodie Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-10068-5	journal	May 2019
Metabolism of multiple glycosaminoglycans by Bacteroides thetaiotaomicron is orchestrated by a versatile core genetic locus Ndeh, Didier; Baslé, Arnaud; Strahl, Henrik Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-14509-4	journal	January 2020
Design of synthetic human gut microbiome assembly and butyrate production Clark, Ryan L.; Connors, Bryce M.; Stevenson, David M. Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-22938-y	journal	May 2021
Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides Luis, Ana S.; Briggs, Jonathon; Zhang, Xiaoyang Nature Microbiology, Vol. 3, Issue 2 https://doi.org/10.1038/s41564-017-0079-1	journal	December 2017
A surface endogalactanase in Bacteroides thetaiotaomicron confers keystone status for arabinogalactan degradation Cartmell, Alan; Muñoz-Muñoz, Jose; Briggs, Jonathon A. Nature Microbiology, Vol. 3, Issue 11 https://doi.org/10.1038/s41564-018-0258-8	journal	October 2018
Complex N-glycan breakdown by gut Bacteroides involves an extensive enzymatic apparatus encoded by multiple co-regulated genetic loci Briliūtė, Justina; Urbanowicz, Paulina A.; Luis, Ana S. Nature Microbiology, Vol. 4, Issue 9 https://doi.org/10.1038/s41564-019-0466-x	journal	June 2019
Gut microbiota in human metabolic health and disease Fan, Yong; Pedersen, Oluf Nature Reviews Microbiology, Vol. 19, Issue 1 https://doi.org/10.1038/s41579-020-0433-9	journal	September 2020
A new genomic blueprint of the human gut microbiota Almeida, Alexandre; Mitchell, Alex L.; Boland, Miguel Nature, Vol. 568, Issue 7753 https://doi.org/10.1038/s41586-019-0965-1	journal	February 2019
SignalP 5.0 improves signal peptide predictions using deep neural networks Almagro Armenteros, José Juan; Tsirigos, Konstantinos D.; Sønderby, Casper Kaae Nature Biotechnology, Vol. 37, Issue 4 https://doi.org/10.1038/s41587-019-0036-z	journal	February 2019
A unified catalog of 204,938 reference genomes from the human gut microbiome Almeida, Alexandre; Nayfach, Stephen; Boland, Miguel Nature Biotechnology, Vol. 39, Issue 1 https://doi.org/10.1038/s41587-020-0603-3	journal	July 2020
A mitochondrial-like aconitase in the bacterium Bacteroides fragilis : Implications for the evolution of the mitochondrial Krebs cycle Baughn, Anthony D.; Malamy, Michael H. Proceedings of the National Academy of Sciences, Vol. 99, Issue 7 https://doi.org/10.1073/pnas.052710199	journal	March 2002
Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla Mahowald, M. A.; Rey, F. E.; Seedorf, H. Proceedings of the National Academy of Sciences, Vol. 106, Issue 14 https://doi.org/10.1073/pnas.0901529106	journal	March 2009
Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice Goodman, A. L.; Kallstrom, G.; Faith, J. J. Proceedings of the National Academy of Sciences, Vol. 108, Issue 15 https://doi.org/10.1073/pnas.1102938108	journal	March 2011
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products Datsenko, K. A.; Wanner, B. L. Proceedings of the National Academy of Sciences, Vol. 97, Issue 12, p. 6640-6645 https://doi.org/10.1073/pnas.120163297	journal	May 2000
Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut Reyes, A.; Wu, M.; McNulty, N. P. Proceedings of the National Academy of Sciences, Vol. 110, Issue 50 https://doi.org/10.1073/pnas.1319470110	journal	November 2013
Coordinate Regulation of Glycan Degradation and Polysaccharide Capsule Biosynthesis by a Prominent Human Gut Symbiont Martens, Eric C.; Roth, Robyn; Heuser, John E. Journal of Biological Chemistry, Vol. 284, Issue 27 https://doi.org/10.1074/jbc.M109.008094	journal	July 2009
Dissecting the in Vivo Metabolic Potential of Two Human Gut Acetogens Rey, Federico E.; Faith, Jeremiah J.; Bain, James Journal of Biological Chemistry, Vol. 285, Issue 29 https://doi.org/10.1074/jbc.M110.117713	journal	May 2010
Galactomannan Catabolism Conferred by a Polysaccharide Utilization Locus of Bacteroides ovatus : ENZYME SYNERGY AND CRYSTAL STRUCTURE OF A β-MANNANASE Bågenholm, Viktoria; Reddy, Sumitha K.; Bouraoui, Hanene Journal of Biological Chemistry, Vol. 292, Issue 1 https://doi.org/10.1074/jbc.M116.746438	journal	November 2016
Complex Glycan Catabolism by the Human Gut Microbiota: The Bacteroidetes Sus-like Paradigm Martens, Eric C.; Koropatkin, Nicole M.; Smith, Thomas J. Journal of Biological Chemistry, Vol. 284, Issue 37 https://doi.org/10.1074/jbc.R109.022848	journal	June 2009
Contribution of acetate to butyrate formation by human faecal bacteria Duncan, Sylvia H.; Holtrop, Grietje; Lobley, Gerald E. British Journal of Nutrition, Vol. 91, Issue 6 https://doi.org/10.1079/BJN20041150	journal	June 2004
PSLpred: prediction of subcellular localization of bacterial proteins Bhasin, M.; Garg, A.; Raghava, G. P. S. Bioinformatics, Vol. 21, Issue 10 https://doi.org/10.1093/bioinformatics/bti309	journal	February 2005
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes Yu, Nancy Y.; Wagner, James R.; Laird, Matthew R. Bioinformatics, Vol. 26, Issue 13 https://doi.org/10.1093/bioinformatics/btq249	journal	May 2010
PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang, J.; Kobert, K.; Flouri, T. Bioinformatics, Vol. 30, Issue 5 https://doi.org/10.1093/bioinformatics/btt593	journal	October 2013
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features Liao, Y.; Smyth, G. K.; Shi, W. Bioinformatics, Vol. 30, Issue 7 https://doi.org/10.1093/bioinformatics/btt656	journal	November 2013
Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences Zhu, Anqi; Ibrahim, Joseph G.; Love, Michael I. Bioinformatics, Vol. 35, Issue 12 https://doi.org/10.1093/bioinformatics/bty895	journal	November 2018
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database Chaumeil, Pierre-Alain; Mussig, Aaron J.; Hugenholtz, Philip Bioinformatics https://doi.org/10.1093/bioinformatics/btz848	journal	November 2019
PULDB: the expanded database of Polysaccharide Utilization Loci Terrapon, Nicolas; Lombard, Vincent; Drula, Élodie Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1022	journal	October 2017
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation Zhang, Han; Yohe, Tanner; Huang, Le Nucleic Acids Research, Vol. 46, Issue W1 https://doi.org/10.1093/nar/gky418	journal	May 2018
Structural dissection of a complex Bacteroides ovatus gene locus conferring xyloglucan metabolism in the human gut Hemsworth, Glyn R.; Thompson, Andrew J.; Stepper, Judith Open Biology, Vol. 6, Issue 7 https://doi.org/10.1098/rsob.160142	journal	July 2016
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T. Genome Research, Vol. 25, Issue 7 https://doi.org/10.1101/gr.186072.114	journal	May 2015
Glycan Foraging in Vivo by an Intestine-Adapted Bacterial Symbiont Sonnenburg, J. L. Science, Vol. 307, Issue 5717 https://doi.org/10.1126/science.1109051	journal	March 2005
Adaptation of Syntenic Xyloglucan Utilization Loci of Human Gut Bacteroidetes to Polysaccharide Side Chain Diversity Déjean, Guillaume; Tauzin, Alexandra S.; Bennett, Stuart W. Applied and Environmental Microbiology, Vol. 85, Issue 20 https://doi.org/10.1128/AEM.01491-19	journal	August 2019
Reduced Dietary Intake of Carbohydrates by Obese Subjects Results in Decreased Concentrations of Butyrate and Butyrate-Producing Bacteria in Feces Duncan, S. H.; Belenguer, A.; Holtrop, G. Applied and Environmental Microbiology, Vol. 73, Issue 4 https://doi.org/10.1128/AEM.02340-06	journal	December 2006
Characterization of the Primary Starch Utilization Operon in the Obligate Anaerobe Bacteroides fragilis : Regulation by Carbon Source and Oxygen Spence, Cheryl; Wells, W. Greg; Smith, C. Jeffrey Journal of Bacteriology, Vol. 188, Issue 13 https://doi.org/10.1128/JB.00125-06	journal	July 2006
Physiological Characterization of SusG, an Outer Membrane Protein Essential for Starch Utilization byBacteroides thetaiotaomicron Shipman, Joseph A.; Cho, Kyu Hong; Siegel, Hilary A. Journal of Bacteriology, Vol. 181, Issue 23 https://doi.org/10.1128/JB.181.23.7206-7211.1999	journal	December 1999
Characterization of a Bacteroides Mobilizable Transposon, NBU2, Which Carries a Functional Lincomycin Resistance Gene Wang, Jun; Shoemaker, Nadja B.; Wang, Gui-Rong Journal of Bacteriology, Vol. 182, Issue 12 https://doi.org/10.1128/JB.182.12.3559-3571.2000	journal	June 2000
Characterization of Four Outer Membrane Proteins Involved in Binding Starch to the Cell Surface ofBacteroides thetaiotaomicron Shipman, Joseph A.; Berleman, James E.; Salyers, Abigail A. Journal of Bacteriology, Vol. 182, Issue 19 https://doi.org/10.1128/JB.182.19.5365-5372.2000	journal	October 2000
Location and characterization of genes involved in binding of starch to the surface of Bacteroides thetaiotaomicron. Tancula, E.; Feldhaus, M. J.; Bedzyk, L. A. Journal of Bacteriology, Vol. 174, Issue 17 https://doi.org/10.1128/jb.174.17.5609-5616.1992	journal	September 1992
Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides Déjean, Guillaume; Tamura, Kazune; Cabrera, Adriana mBio, Vol. 11, Issue 2 https://doi.org/10.1128/mBio.00095-20	journal	April 2020
Reciprocal Prioritization to Dietary Glycans by Gut Bacteria in a Competitive Environment Promotes Stable Coexistence Tuncil, Yunus E.; Xiao, Yao; Porter, Nathan T. mBio, Vol. 8, Issue 5 https://doi.org/10.1128/mBio.01068-17	journal	October 2017
Multiple Signals Govern Utilization of a Polysaccharide in the Gut Bacterium Bacteroides thetaiotaomicron Schwalm, Nathan D.; Townsend, Guy E.; Groisman, Eduardo A. mBio, Vol. 7, Issue 5 https://doi.org/10.1128/mBio.01342-16	journal	October 2016
Streamlined Genetic Manipulation of Diverse Bacteroides and Parabacteroides Isolates from the Human Gut Microbiota García-Bayona, Leonor; Comstock, Laurie E. mBio, Vol. 10, Issue 4 https://doi.org/10.1128/mBio.01762-19	journal	August 2019
Molecular Dissection of Xyloglucan Recognition in a Prominent Human Gut Symbiont Tauzin, Alexandra S.; Kwiatkowski, Kurt J.; Orlovsky, Nicole I. mBio, Vol. 7, Issue 2 https://doi.org/10.1128/mBio.02134-15	journal	April 2016
Intestinal IgA Regulates Expression of a Fructan Polysaccharide Utilization Locus in Colonizing Gut Commensal Bacteroides thetaiotaomicron Joglekar, Payal; Ding, Hua; Canales-Herrerias, Pablo mBio, Vol. 10, Issue 6 https://doi.org/10.1128/mBio.02324-19	journal	November 2019
The Critical Roles of Polysaccharides in Gut Microbial Ecology and Physiology Porter, Nathan T.; Martens, Eric C. Annual Review of Microbiology, Vol. 71, Issue 1 https://doi.org/10.1146/annurev-micro-102215-095316	journal	September 2017
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes Vandesompele, Jo; De Preter, Katleen; Pattyn, Filip Genome Biology, Vol. 3, Issue 7 https://doi.org/10.1186/gb-2002-3-7-research0034	journal	June 2002
Xylan degradation by the human gut Bacteroides xylanisolvens XB1AT involves two distinct gene clusters that are linked at the transcriptional level Despres, Jordane; Forano, Evelyne; Lepercq, Pascale BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2680-8	journal	May 2016
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Love, Michael I.; Huber, Wolfgang; Anders, Simon Genome Biology, Vol. 15, Issue 12 https://doi.org/10.1186/s13059-014-0550-8	journal	December 2014
The healthy human microbiome Lloyd-Price, Jason; Abu-Ali, Galeb; Huttenhower, Curtis Genome Medicine, Vol. 8, Issue 1 https://doi.org/10.1186/s13073-016-0307-y	journal	April 2016
Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts Martens, Eric C.; Lowe, Elisabeth C.; Chiang, Herbert PLoS Biology, Vol. 9, Issue 12 https://doi.org/10.1371/journal.pbio.1001221	journal	December 2011
Population Diversification in a Yeast Metabolic Program Promotes Anticipation of Environmental Shifts Venturelli, Ophelia S.; Zuleta, Ignacio; Murray, Richard M. PLOS Biology, Vol. 13, Issue 1 https://doi.org/10.1371/journal.pbio.1002042	journal	January 2015
Complex Carbohydrate Utilization by the Healthy Human Microbiome Cantarel, Brandi L.; Lombard, Vincent; Henrissat, Bernard PLoS ONE, Vol. 7, Issue 6 https://doi.org/10.1371/journal.pone.0028742	journal	June 2012
CELLO2GO: A Web Server for Protein subCELlular LOcalization Prediction with Functional Gene Ontology Annotation Yu, Chin-Sheng; Cheng, Chih-Wen; Su, Wen-Chi PLoS ONE, Vol. 9, Issue 6 https://doi.org/10.1371/journal.pone.0099368	journal	June 2014
Deciphering microbial interactions in synthetic human gut microbiome communities Venturelli, Ophelia S.; Carr, Alex V.; Fisher, Garth Molecular Systems Biology, Vol. 14, Issue 6 https://doi.org/10.15252/msb.20178157	journal	June 2018
An Adaptive Metropolis Algorithm Haario, Heikki; Saksman, Eero; Tamminen, Johanna Bernoulli, Vol. 7, Issue 2 https://doi.org/10.2307/3318737	journal	April 2001
The Glycolytic Versatility of Bacteroides uniformis CECT 7771 and Its Genome Response to Oligo and Polysaccharides Benítez-Páez, Alfonso; Gómez del Pulgar, Eva M.; Sanz, Yolanda Frontiers in Cellular and Infection Microbiology, Vol. 7 https://doi.org/10.3389/fcimb.2017.00383	journal	August 2017
Bacteroides thetaiotaomicron Starch Utilization Promotes Quercetin Degradation and Butyrate Production by Eubacterium ramulus Rodriguez-Castaño, Gina Paola; Dorris, Matthew R.; Liu, Xingbo Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01145	journal	May 2019
Metabolism of Glycosphingolipids and Their Role in the Pathophysiology of Lysosomal Storage Disorders Ryckman, Alex E.; Brockhausen, Inka; Walia, Jagdeep S. International Journal of Molecular Sciences, Vol. 21, Issue 18 https://doi.org/10.3390/ijms21186881	journal	September 2020
Degradation of Marine Algae-Derived Carbohydrates by Bacteroidetes Isolated from Human Gut Microbiota Li, Miaomiao; Shang, Qingsen; Li, Guangsheng Marine Drugs, Vol. 15, Issue 4 https://doi.org/10.3390/md15040092	journal	March 2017
Bacteroides thetaiotaomicron Fosters the Growth of Butyrate-Producing Anaerostipes caccae in the Presence of Lactose and Total Human Milk Carbohydrates Chia, Loo Wee; Mank, Marko; Blijenberg, Bernadet Microorganisms, Vol. 8, Issue 10 https://doi.org/10.3390/microorganisms8101513	journal	October 2020
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Title: Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions

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