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Select item 26600631.

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

Michael A. Mahowald, Federico E. Rey, Henning Seedorf, Peter J. Turnbaugh, Robert S. Fulton, Aye Wollam, Neha Shah, Chunyan Wang, Vincent Magrini, Richard K. Wilson, Brandi L. Cantarel, Pedro M. Coutinho, Bernard Henrissat, Lara W. Crock, Alison Russell, Nathan C. Verberkmoes, Robert L. Hettich, Jeffrey I. Gordon

Proc Natl Acad Sci U S A. 2009 Apr 7; 106(14): 5859–5864. Published online 2009 Mar 24. doi: 10.1073/pnas.0901529106

PMCID:: PMC2660063

Abstract Article PDF–604K

Select item 69891152.

A Master Regulator of Bacteroides thetaiotaomicron Gut Colonization Controls Carbohydrate Utilization and an Alternative Protein Synthesis Factor

Guy E. Townsend, II, Weiwei Han, Nathan D. Schwalm, III, Xinyu Hong, Natasha A. Bencivenga-Barry, Andrew L. Goodman, Eduardo A. Groisman

mBio. 2020 Jan-Feb; 11(1): e03221-19. Published online 2020 Jan 28. doi: 10.1128/mBio.03221-19

Correction in:: mBio. 2020 Mar-Apr; 11(2): e00301-20.

PMCID:: PMC6989115

Abstract Article PDF–1.5M

Select item 63957683.

An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria

Yulong Wei, Jordan R. Silke, Xuhua Xia

Sci Rep. 2019; 9: 3184. Published online 2019 Feb 28. doi: 10.1038/s41598-019-39369-x

PMCID:: PMC6395768

Abstract Article PDF–1.8M

Select item 62907874.

Bacteroides thetaiotaomicron Ameliorates Colon Inflammation in Preclinical Models of Crohn’s Disease

Margaret Delday, Imke Mulder, Elizabeth T Logan, George Grant

Inflamm Bowel Dis. 2019 Jan; 25(1): 85–96. Published online 2018 Sep 12. doi: 10.1093/ibd/izy281

PMCID:: PMC6290787

Abstract Article PDF–18M

Select item 60864855.

The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut

Whitman B. Schofield, Maria Zimmermann-Kogadeeva, Michael Zimmermann, Natasha A. Barry, Andrew L. Goodman

Cell Host Microbe. Author manuscript; available in PMC 2019 Jul 11.

Published in final edited form as: Cell Host Microbe. 2018 Jul 11; 24(1): 120–132.e6. Published online 2018 Jun 28. doi: 10.1016/j.chom.2018.06.002

PMCID:: PMC6086485

Abstract Article PDF–2.0M

Select item 60619676.

Transient osmotic perturbation causes long-term alteration to the gut microbiota

Carolina Tropini, Eli Lin Moss, Bryan Douglas Merrill, Katharine Michelle Ng, Steven Kyle Higginbottom, Ellen Pun Casavant, Carlos Gutierrez Gonzalez, Brayon Fremin, Donna Michelle Bouley, Joshua Eric Elias, Ami Siddharth Bhatt, Kerwyn Casey Huang, Justin Laine Sonnenburg

Cell. Author manuscript; available in PMC 2019 Jun 14.

Published in final edited form as: Cell. 2018 Jun 14; 173(7): 1742–1754.e17. doi: 10.1016/j.cell.2018.05.008

PMCID:: PMC6061967

Abstract Article PDF–1.8M

Select item 59436217.

Identifying Group-Specific Sequences for Microbial Communities Using Long k-mer Sequence Signatures

Ying Wang, Lei Fu, Jie Ren, Zhaoxia Yu, Ting Chen, Fengzhu Sun

Front Microbiol. 2018; 9: 872. Published online 2018 May 3. doi: 10.3389/fmicb.2018.00872

PMCID:: PMC5943621

Abstract Article PDF–4.0M

Select item 58723018.

Developing a Bacteroides System for Function-Based Screening of DNA from the Human Gut Microbiome

Kathy N. Lam, Eric C. Martens, Trevor C. Charles

mSystems. 2018 May-Jun; 3(3): e00195-17. Published online 2018 Mar 27. doi: 10.1128/mSystems.00195-17

PMCID:: PMC5872301

Abstract Article PDF–3.6M

Select item 53735899.

Selection of key sequence-based features for prediction of essential genes in 31 diverse bacterial species

Xiao Liu, Bao-Jin Wang, Luo Xu, Hong-Ling Tang, Guo-Qing Xu

PLoS One. 2017; 12(3): e0174638. Published online 2017 Mar 30. doi: 10.1371/journal.pone.0174638

PMCID:: PMC5373589

Abstract Article PDF–1.0M

Select item 528983510.

The Role of +4U as an Extended Translation Termination Signal in Bacteria

Yulong Wei, Xuhua Xia

Genetics. 2017 Feb; 205(2): 539–549. Published online 2016 Nov 29. doi: 10.1534/genetics.116.193961

PMCID:: PMC5289835

Abstract Article PDF–1.5M

Select item 508852411.

Computational workflow for the fine-grained analysis of metagenomic samples

Esteban Pérez-Wohlfeil, Jose A. Arjona-Medina, Oscar Torreno, Eugenia Ulzurrun, Oswaldo Trelles

BMC Genomics. 2016; 17(Suppl 8): 802. Published online 2016 Oct 25. doi: 10.1186/s12864-016-3063-x

PMCID:: PMC5088524

Abstract Article PDF–2.9M

Select item 464233012.

Essentiality drives the orientation bias of bacterial genes in a continuous manner

Wen-Xin Zheng, Cheng-Si Luo, Yan-Yan Deng, Feng-Biao Guo

Sci Rep. 2015; 5: 16431. Published online 2015 Nov 12. doi: 10.1038/srep16431

PMCID:: PMC4642330

Abstract Article PDF–736K

Select item 455886113.

Rare Events of Intragenus and Intraspecies Horizontal Transfer of the 16S rRNA Gene

Ren-Mao Tian, Lin Cai, Wei-Peng Zhang, Hui-Luo Cao, Pei-Yuan Qian

Genome Biol Evol. 2015 Aug; 7(8): 2310–2320. Published online 2015 Jul 27. doi: 10.1093/gbe/evv143

PMCID:: PMC4558861

Abstract Article PDF–776K

Select item 453649014.

Evolutionary conservation analysis between the essential and nonessential genes in bacterial genomes

Hao Luo, Feng Gao, Yan Lin

Sci Rep. 2015; 5: 13210. Published online 2015 Aug 14. doi: 10.1038/srep13210

PMCID:: PMC4536490

Abstract Article PDF–895K

Select item 451973415.

Comparative analysis of essential genes in prokaryotic genomic islands

Xi Zhang, Chong Peng, Ge Zhang, Feng Gao

Sci Rep. 2015; 5: 12561. Published online 2015 Jul 30. doi: 10.1038/srep12561

PMCID:: PMC4519734

Abstract Article PDF–974K

Select item 446631716.

Statistical Analysis of Hurst Exponents of Essential/Nonessential Genes in 33 Bacterial Genomes

Xiao Liu, Baojin Wang, Luo Xu

PLoS One. 2015; 10(6): e0129716. Published online 2015 Jun 12. doi: 10.1371/journal.pone.0129716

PMCID:: PMC4466317

Abstract Article PDF–578K

Select item 443228317.

Characterizing the Interactions between a Naturally Primed Immunoglobulin A and Its Conserved Bacteroides thetaiotaomicron Species-specific Epitope in Gnotobiotic Mice

Daniel A. Peterson, Joseph D. Planer, Janaki L. Guruge, Lai Xue, Whitt Downey-Virgin, Andrew L. Goodman, Henning Seedorf, Jeffrey I. Gordon

J Biol Chem. 2015 May 15; 290(20): 12630–12649. Published online 2015 Mar 20. doi: 10.1074/jbc.M114.633800

PMCID:: PMC4432283

Abstract Article PDF–4.7M

Select item 438092418.

Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics

Stephanie J Yaung, Luxue Deng, Ning Li, Jonathan L Braff, George M Church, Lynn Bry, Harris H Wang, Georg K Gerber

Mol Syst Biol. 2015 Mar; 11(3): 788. Published online 2015 Mar 11. doi: 10.15252/msb.20145866

PMCID:: PMC4380924

Abstract Article PDF–2.2M

Select item 437274519.

The Bacteroides thetaiotaomicron Protein Bacteroides Host Factor A Participates in Integration of the Integrative Conjugative Element CTnDOT into the Chromosome

Kenneth Ringwald, Jeffrey Gardner

J Bacteriol. 2015 Apr; 197(8): 1339–1349. Prepublished online 2015 Feb 2. Published online 2015 Mar 24. doi: 10.1128/JB.02198-14

PMCID:: PMC4372745

Abstract Article PDF–2.4M

Select item 414897820.

Genome sequence and description of Bacteroides timonensis sp. nov.

Dhamodharan Ramasamy, Jean-Christophe Lagier, Morgane Rossi-Tamisier, Anne Pfleiderer, Caroline Michelle, Carine Couderc, Didier Raoult, Pierre-Edouard Fournier

Stand Genomic Sci. 2014 Jun 15; 9(3): 1181–1197. Published online 2014 Mar 15. doi: 10.4056/sigs.5389564