Spatially distinct physiology of Bacteroides fragilis within the proximal colon of gnotobiotic mice

Capturing sequence diversity in metagenomes with comprehensive and scalable probe design

(2019) Hayden C. Metsky et al.   NATURE BIOTECHNOLOGY

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

(2018) Whitman B. Schofield et al.   Cell Host & Microbe

Gut microbiota utilize immunoglobulin A for mucosal colonization

(2018) G. P. Donaldson et al.   SCIENCE

Salmonella persisters undermine host immune defenses during antibiotic treatment

(2018) Daphne A. C. Stapels et al.   SCIENCE

Tissue dual RNA-seq allows fast discovery of infection-specific functions and riboregulators shaping host–pathogen transcriptomes

(2017) Aaron M. Nuss et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice

(2017) Jessica L. Mark Welch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Host-inherent variability influences the transcriptional response of Staphylococcus aureus during in vivo infection

(2017) Robert Thänert et al.   Nature Communications

Resolving host–pathogen interactions by dual RNA-seq

(2017) Alexander J. Westermann et al.   PLoS Pathogens

A Laboratory Methodology for Dual RNA-Sequencing of Bacteria and their Host Cells In Vitro

(2017) James W. Marsh et al.   Frontiers in Microbiology

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

(2016) Matthias Scholz et al.   NATURE METHODS

Expansion of the Gene Ontology knowledgebase and resources

(2016)   NUCLEIC ACIDS RESEARCH

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease

(2016) H. Chu et al.   SCIENCE

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

(2016) Moran Yassour et al.   Science Translational Medicine

The Epigenomic Landscape of Prokaryotes

(2016) Matthew J. Blow et al.   PLoS Genetics

Quantitative Imaging of Gut Microbiota Spatial Organization

(2015) Kristen A. Earle et al.   Cell Host & Microbe

Biogeography of the Intestinal Mucosal and Lumenal Microbiome in the Rhesus Macaque

(2015) Koji Yasuda et al.   Cell Host & Microbe

The co-transcriptome of uropathogenicEscherichia coli-infected mouse macrophages reveals new insights into host-pathogen interactions

(2015) Charalampos Harris Mavromatis et al.   CELLULAR MICROBIOLOGY

Simultaneous generation of many RNA-seq libraries in a single reaction

(2015) Alexander A Shishkin et al.   NATURE METHODS

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

Gut biogeography of the bacterial microbiota

(2015) Gregory P. Donaldson et al.   NATURE REVIEWS MICROBIOLOGY

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Individual intestinal symbionts induce a distinct population of ROR + regulatory T cells

(2015) E. Sefik et al.   SCIENCE

Symbiotic Human Gut Bacteria with Variable Metabolic Priorities for Host Mucosal Glycans

(2015) N. A. Pudlo et al.   mBio

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

The composition of the gut microbiota shapes the colon mucus barrier

(2014) H. E. Jakobsson et al.   EMBO REPORTS

Correlation Between Intraluminal Oxygen Gradient and Radial Partitioning of Intestinal Microbiota

(2014) Lindsey Albenberg et al.   GASTROENTEROLOGY

Efficient utilization of complex N-linked glycans is a selective advantage for Bacteroides fragilis in extraintestinal infections

(2014) Y. Cao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Laser microdissection coupled with RNA-seq analysis of porcine enterocytes infected with an obligate intracellular pathogen (Lawsonia intracellularis)

(2013) Fabio A Vannucci et al.   BMC GENOMICS

Bacterial colonization factors control specificity and stability of the gut microbiota

(2013) S. Melanie Lee et al.   NATURE

Simultaneous Transcriptional Profiling of Bacteria and Their Host Cells

(2013) Michael S. Humphrys et al.   PLoS One

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

Emergence of Epidemic Multidrug-Resistant Enterococcus faecium from Animal and Commensal Strains

(2013) F. Lebreton et al.   mBio

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Defining bacterial species in the genomic era: insights from the genus Acinetobacter

(2012) Jacqueline Z-M Chan et al.   BMC MICROBIOLOGY

Detailed O-glycomics of the Muc2 mucin from colon of wild-type, core 1- and core 3-transferase-deficient mice highlights differences compared with human MUC2

(2012) Kristina A Thomsson et al.   GLYCOBIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A Crypt-Specific Core Microbiota Resides in the Mouse Colon

(2012) T. Pedron et al.   mBio

The human commensal Bacteroides fragilis binds intestinal mucin

(2011) Julie Y. Huang et al.   ANAEROBE

Sulfatases and a RadicalS-Adenosyl-l-methionine (AdoMet) Enzyme Are Key for Mucosal Foraging and Fitness of the Prominent Human Gut Symbiont,Bacteroides thetaiotaomicron

(2011) Alhosna Benjdia et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Toll-Like Receptor 2 Pathway Establishes Colonization by a Commensal of the Human Microbiota

(2011) J. L. Round et al.   SCIENCE

Hybrid selection for sequencing pathogen genomes from clinical samples

(2011) Alexandre Melnikov et al.   GENOME BIOLOGY

Bacterial Colonization of Colonic Crypt Mucous Gel and Disease Activity in Ulcerative Colitis

(2010) Fiachra Rowan et al.   ANNALS OF SURGERY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Regional Mucosa-Associated Microbiota Determine Physiological Expression of TLR2 and TLR4 in Murine Colon

(2010) Yunwei Wang et al.   PLoS One

Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota

(2010) J. L. Round et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

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

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

A microbial symbiosis factor prevents intestinal inflammatory disease

(2008) Sarkis K. Mazmanian et al.   NATURE

Role of glycan synthesis in colonization of the mammalian gut by the bacterial symbiont Bacteroides fragilis

(2008) M. J. Coyne et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of surface architecture by symbiotic bacteria mediates host colonization

(2008) C. H. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovering Sequence Motifs with Arbitrary Insertions and Deletions

(2008) Martin C. Frith et al.   PLoS Computational Biology