Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals

Sealer: a scalable gap-closing application for finishing draft genomes

(2015) Daniel Paulino et al.   BMC BIOINFORMATICS

An Integrative View of Microbiome-Host Interactions in Inflammatory Bowel Diseases

(2015) Marta Wlodarska et al.   Cell Host & Microbe

Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella

(2015) Petia Kovatcheva-Datchary et al.   Cell Metabolism

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Innate and Adaptive Humoral Responses Coat Distinct Commensal Bacteria with Immunoglobulin A

(2015) Jeffrey J. Bunker et al.   IMMUNITY

Engineering the gut microbiota to treat hyperammonemia

(2015) Ting-Chin David Shen et al.   JOURNAL OF CLINICAL INVESTIGATION

The microbiome of the urinary tract—a role beyond infection

(2015) Samantha A. Whiteside et al.   Nature Reviews Urology

Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides

(2015) M. Wu et al.   SCIENCE

Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut

(2015) Christian Milani et al.   Scientific Reports

Inter-individual differences in the gene content of human gut bacterial species

(2015) Ana Zhu et al.   GENOME BIOLOGY

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes

(2015) Stefanía Magnúsdóttir et al.   Frontiers in Genetics

Effects of Season and Host Physiological State on the Diversity, Density, and Activity of the Arctic Ground Squirrel Cecal Microbiota

(2014) Timothy J. Stevenson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease

(2014) Noah W. Palm et al.   CELL

An Expanded Genomic Representation of the Phylum Cyanobacteria

(2014) Rochelle M. Soo et al.   Genome Biology and Evolution

Description of Mariniphaga anaerophila gen. nov., sp. nov., a facultatively aerobic marine bacterium isolated from tidal flat sediment, reclassification of the Draconibacteriaceae as a later heterotypic synonym of the Prolixibacteraceae and description of the family Marinifilaceae fam. nov.

(2014) T. Iino et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

(2014) Molly K Gibson et al.   ISME Journal

Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission

(2014) Michelle G Rooks et al.   ISME Journal

Porphyromonas gingivalisand related bacteria: from colonial pigmentation to the type IX secretion system and gliding motility

(2014) K. Nakayama   JOURNAL OF PERIODONTAL RESEARCH

A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes

(2014) Johan Larsbrink et al.   NATURE

Exercise Prevents Weight Gain and Alters the Gut Microbiota in a Mouse Model of High Fat Diet-Induced Obesity

(2014) Christian C. Evans et al.   PLoS One

Gut microbiome of the Hadza hunter-gatherers

(2014) Stephanie L. Schnorr et al.   Nature Communications

Microbial Urease in Health and Disease

(2014) Diego Mora et al.   PLoS Pathogens

Coprobacter fastidiosus gen. nov., sp. nov., a novel member of the family Porphyromonadaceae isolated from infant faeces

(2013) A. N. Shkoporov et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Shallow breathing: bacterial life at low O2

(2013) Rachel L. Morris et al.   NATURE REVIEWS MICROBIOLOGY

IMG 4 version of the integrated microbial genomes comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing

(2013) D. Berry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The effect of environmental conditions on expression of Bacteroides fragilis and Bacteroides thetaiotaomicron C10 protease genes

(2012) Roibeard F Thornton et al.   BMC MICROBIOLOGY

PG0026 Is the C-terminal Signal Peptidase of a Novel Secretion System ofPorphyromonas gingivalis

(2012) Michelle D. Glew et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

The human microbiome: at the interface of health and disease

(2012) Ilseung Cho et al.   NATURE REVIEWS GENETICS

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Complex Carbohydrate Utilization by the Healthy Human Microbiome

(2012) Brandi L. Cantarel et al.   PLoS One

The cytochrome bd respiratory oxygen reductases

(2011) Vitaliy B. Borisov et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

The cysteine proteinase SpeB fromStreptococcus pyogenes– a potent modifier of immunologically important host and bacterial proteins

(2011) Daniel C Nelson et al.   BIOLOGICAL CHEMISTRY

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Eating For Two: How Metabolism Establishes Interspecies Interactions in the Gut

(2011) Michael A. Fischbach et al.   Cell Host & Microbe

Metabolic adaptation to a high-fat diet is associated with a change in the gut microbiota

(2011) Matteo Serino et al.   GUT

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

The Evolution of Respiratory Chain Complex I from a Smaller Last Common Ancestor Consisting of 11 Protein Subunits

(2011) Vamsi K. Moparthi et al.   JOURNAL OF MOLECULAR EVOLUTION

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Unravelling the effects of the environment and host genotype on the gut microbiome

(2011) Aymé Spor et al.   NATURE REVIEWS MICROBIOLOGY

The microbiome-gut-brain axis: from bowel to behavior

(2011) J. F. Cryan et al.   NEUROGASTROENTEROLOGY AND MOTILITY

Oxalate-Degrading Activity in Bifidobacterium animalis subsp. lactis: Impact of Acidic Conditions on the Transcriptional Levels of the Oxalyl Coenzyme A (CoA) Decarboxylase and Formyl-CoA Transferase Genes

(2010) S. Turroni et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   BIOINFORMATICS

The dissemination of C10 cysteine protease genes in Bacteroides fragilis by mobile genetic elements

(2010) Roibeard F Thornton et al.   BMC MICROBIOLOGY

Specificity of Polysaccharide Use in Intestinal Bacteroides Species Determines Diet-Induced Microbiota Alterations

(2010) Erica D. Sonnenburg et al.   CELL

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

(2009) P. D. Karp et al.   BRIEFINGS IN BIOINFORMATICS

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat

(2009) Andrew L. Goodman et al.   Cell Host & Microbe

Complex Glycan Catabolism by the Human Gut Microbiota: The Bacteroidetes Sus-like Paradigm

(2009) Eric C. Martens et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Interpain A, a Cysteine Proteinase from Prevotella intermedia, Inhibits Complement by Degrading Complement Factor C3

(2009) Michal Potempa et al.   PLoS Pathogens

Bioinformatic Comparison of Bacterial Secretomes

(2009) Catharine Song et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Mucosal Glycan Foraging Enhances Fitness and Transmission of a Saccharolytic Human Gut Bacterial Symbiont

(2008) Eric C. Martens et al.   Cell Host & Microbe

The metalloprotease PrtV from Vibrio cholerae

(2008) Karolis Vaitkevicius et al.   FEBS Journal

Antibiotic-Induced Perturbations of the Intestinal Microbiota Alter Host Susceptibility to Enteric Infection

(2008) I. Sekirov et al.   INFECTION AND IMMUNITY

Surface components ofPorphyromonas gingivalis

(2008) F. Yoshimura et al.   JOURNAL OF PERIODONTAL RESEARCH