Rapid transcriptional and metabolic adaptation of intestinal microbes to host immune activation

Import of Aspartate and Malate by DcuABC Drives H2/Fumarate Respiration to Promote Initial Salmonella Gut-Lumen Colonization in Mice

(2020) Bidong D. Nguyen et al.   Cell Host & Microbe

Dendritic cell–derived hepcidin sequesters iron from the microbiota to promote mucosal healing

(2020) Nicholas J. Bessman et al.   SCIENCE

Faecal bacterial and short-chain fatty acids signature in hypercholesterolemia

(2019) A. B. Granado-Serrano et al.   Scientific Reports

Oleate hydratase from Staphylococcusaureus protects against palmitoleic acid, the major antimicrobial fatty acid produced by mammalian skin

(2019) Chitra Subramanian et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

Exploring the emerging role of the microbiome in cancer immunotherapy

(2019) Jessica Fessler et al.   Journal for ImmunoTherapy of Cancer

Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn’s disease, produces an inflammatory polysaccharide

(2019) Matthew T. Henke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complex Bacterial Consortia Reprogram the Colitogenic Activity of Enterococcus faecalis in a Gnotobiotic Mouse Model of Chronic, Immune-Mediated Colitis

(2019) Isabella Lengfelder et al.   Frontiers in Immunology

Microbiota-derived lantibiotic restores resistance against vancomycin-resistant Enterococcus

(2019) Sohn G. Kim et al.   NATURE

Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women

(2018) Lesley Hoyles et al.   NATURE MEDICINE

Metabolic division of labor in microbial systems

(2018) Ryan Tsoi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

(2018) Melanie Schirmer et al.   Nature Microbiology

Inhibiting antibiotic-resistant Enterobacteriaceae by microbiota-mediated intracellular acidification

(2018) Matthew T. Sorbara et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Gut microbiome structure and metabolic activity in inflammatory bowel disease

(2018) Eric A. Franzosa et al.   Nature Microbiology

Commensal microbes provide first line defense againstListeria monocytogenesinfection

(2017) Simone Becattini et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling

(2016) Nicholas Edward Ilott et al.   ISME Journal

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

(2016) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health

(2016) Pamela Vernocchi et al.   Frontiers in Microbiology

Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium

(2016) Sandrine Brugiroux et al.   Nature Microbiology

The deleterious metabolic and genotoxic effects of the bacterial metabolite p-cresol on colonic epithelial cells

(2015) Mireille Andriamihaja et al.   FREE RADICAL BIOLOGY AND MEDICINE

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples

(2015) T. Korem et al.   SCIENCE

Surface-Associated Lipoproteins Link Enterococcus faecalis Virulence to Colitogenic Activity in IL-10-Deficient Mice Independent of Their Expression Levels

(2015) Soeren Ocvirk et al.   PLoS Pathogens

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

(2015) Thomas Brettin et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Role of the Microbiota in Immunity and Inflammation

(2014) Yasmine Belkaid et al.   CELL

Longitudinal study of murine microbiota activity and interactions with the host during acute inflammation and recovery

(2014) Clarissa Schwab et al.   ISME Journal

Metabonomics of human fecal extracts characterize ulcerative colitis, Crohn’s disease and healthy individuals

(2014) Jacob Tveiten Bjerrum et al.   Metabolomics

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

Rapid fucosylation of intestinal epithelium sustains host–commensal symbiosis in sickness

(2014) Joseph M. Pickard et al.   NATURE

Relating the metatranscriptome and metagenome of the human gut

(2014) E. A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unprecedented High-Resolution View of Bacterial Operon Architecture Revealed by RNA Sequencing

(2014) T. Conway et al.   mBio

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Analysis of Volatile Organic Compounds of Bacterial Origin in Chronic Gastrointestinal Diseases

(2013) Christopher Walton et al.   INFLAMMATORY BOWEL DISEASES

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

(2013) Yukihiro Furusawa et al.   NATURE

Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation

(2013) Nicholas Arpaia et al.   NATURE

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota

(2013) Koji Atarashi et al.   NATURE

RefSeq microbial genomes database: new representation and annotation strategy

(2013) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Computational analysis of bacterial RNA-Seq data

(2013) Ryan McClure et al.   NUCLEIC ACIDS RESEARCH

The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic Treg Cell Homeostasis

(2013) P. M. Smith et al.   SCIENCE

Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis

(2013) Jose U Scher et al.   eLife

Interleukin 23 Production by Intestinal CD103+CD11b+ Dendritic Cells in Response to Bacterial Flagellin Enhances Mucosal Innate Immune Defense

(2012) Melissa A. Kinnebrew et al.   IMMUNITY

Suppression of Clostridium difficile in the Gastrointestinal Tracts of Germfree Mice Inoculated with a Murine Isolate from the Family Lachnospiraceae

(2012) Angela E. Reeves et al.   INFECTION AND IMMUNITY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice

(2012) Trevor D. Lawley et al.   PLoS Pathogens

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health

(2011) Wendy R Russell et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

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

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

Chronic Intestinal Inflammation Induces Stress-Response Genes in Commensal Escherichia coli

(2011) Laura G. Patwa et al.   GASTROENTEROLOGY

Th17 Cells Express Interleukin-10 Receptor and Are Controlled by Foxp3− and Foxp3+ Regulatory CD4+ T Cells in an Interleukin-10-Dependent Manner

(2011) Samuel Huber et al.   IMMUNITY

Control of TH17 cells occurs in the small intestine

(2011) Enric Esplugues et al.   NATURE

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

Metabolomics Reveals Metabolic Biomarkers of Crohn's Disease

(2009) Janet Jansson et al.   PLoS One