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

Antimicrobial peptide resistance mediates resilience of prominent gut commensals during inflammation

(2015) T. W. Cullen et al.   SCIENCE

Glycan complexity dictates microbial resource allocation in the large intestine

(2015) Artur Rogowski et al.   Nature Communications

Transcriptome analysis of Enterococcus faecalis toward its adaption to surviving in the mouse intestinal tract

(2014) Angela G. Lindenstrauß et al.   ARCHIVES OF MICROBIOLOGY

Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks

(2013) Dmitry A Ravcheev et al.   BMC GENOMICS

RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria

(2013) Pavel S Novichkov et al.   BMC GENOMICS

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

The Transporter Classification Database

(2013) Milton H. Saier et al.   NUCLEIC ACIDS RESEARCH

Metabolic niche of a prominent sulfate-reducing human gut bacterium

(2013) F. E. Rey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut

(2013) A. Reyes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota

(2013) P. C. Kashyap et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome

(2013) Nathan P. McNulty et al.   PLOS BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Dual diaminopimelate biosynthesis pathways in Bacteroides fragilis and Clostridium thermocellum

(2011) André O. Hudson et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries

(2011) Andrew L Goodman et al.   Nature Protocols

Predicting a Human Gut Microbiota's Response to Diet in Gnotobiotic Mice

(2011) J. J. Faith et al.   SCIENCE

Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts

(2011) Eric C. Martens et al.   PLOS BIOLOGY

Sap Transporter Mediated Import and Subsequent Degradation of Antimicrobial Peptides in Haemophilus

(2011) Catherine L. Shelton et al.   PLoS Pathogens

Xylan degradation, a metabolic property shared by rumen and human colonic Bacteroidetes

(2010) Dylan Dodd et al.   MOLECULAR MICROBIOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

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

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Coordinate Regulation of Glycan Degradation and Polysaccharide Capsule Biosynthesis by a Prominent Human Gut Symbiont

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

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

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