Directed remodeling of the mouse gut microbiome inhibits the development of atherosclerosis

Probiotics and prebiotics in intestinal health and disease: from biology to the clinic

(2019) Mary Ellen Sanders et al.   Nature Reviews Gastroenterology & Hepatology

The Human Gut Microbiome: From Association to Modulation

(2018) Thomas S.B. Schmidt et al.   CELL

An exclusive metabolic niche enables strain engraftment in the gut microbiota

(2018) Elizabeth Stanley Shepherd et al.   NATURE

Microbial modulation of cardiovascular disease

(2018) J. Mark Brown et al.   NATURE REVIEWS MICROBIOLOGY

Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism

(2018) Amir Zarrinpar et al.   Nature Communications

Extensive impact of non-antibiotic drugs on human gut bacteria

(2018) Lisa Maier et al.   NATURE

Precision editing of the gut microbiota ameliorates colitis

(2018) Wenhan Zhu et al.   NATURE

Mouse Microbiota Models: Comparing Germ-Free Mice and Antibiotics Treatment as Tools for Modifying Gut Bacteria

(2018) Elizabeth A. Kennedy et al.   Frontiers in Physiology

A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites

(2017) Dylan Dodd et al.   NATURE

Bile acid–microbiota crosstalk in gastrointestinal inflammation and carcinogenesis

(2017) Wei Jia et al.   Nature Reviews Gastroenterology & Hepatology

Antiinflammatory Therapy with Canakinumab for Atherosclerotic Disease

(2017) Paul M Ridker et al.   NEW ENGLAND JOURNAL OF MEDICINE

Stable engraftment of human microbiota into mice with a single oral gavage following antibiotic conditioning

(2017) Christopher Staley et al.   Microbiome

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites

(2016) Ara Koh et al.   CELL

The Central Nervous System and the Gut Microbiome

(2016) Gil Sharon et al.   CELL

Intestinal Crosstalk between Bile Acids and Microbiota and Its Impact on Host Metabolism

(2016) Annika Wahlström et al.   Cell Metabolism

Human gut microbes impact host serum metabolome and insulin sensitivity

(2016) Helle Krogh Pedersen et al.   NATURE

Acetate mediates a microbiome–brain–β-cell axis to promote metabolic syndrome

(2016) Rachel J. Perry et al.   NATURE

Diet-induced extinctions in the gut microbiota compound over generations

(2016) Erica D. Sonnenburg et al.   NATURE

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Intestinal Short Chain Fatty Acids and their Link with Diet and Human Health

(2016) David Ríos-Covián et al.   Frontiers in Microbiology

Non-lethal Inhibition of Gut Microbial Trimethylamine Production for the Treatment of Atherosclerosis

(2015) Zeneng Wang et al.   CELL

Diet Dominates Host Genotype in Shaping the Murine Gut Microbiota

(2015) Rachel N. Carmody et al.   Cell Host & Microbe

Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF

(2015) Sarah J. Hainer et al.   GENES & DEVELOPMENT

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

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

(2015) E. Sefik et al.   SCIENCE

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

(2014) S. Anders et al.   BIOINFORMATICS

Microbial Modulation of Insulin Sensitivity

(2014) Muhammad Tanweer Khan et al.   Cell Metabolism

The alarmin IL-33 promotes regulatory T-cell function in the intestine

(2014) Chris Schiering et al.   NATURE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Oxysterols are agonist ligands of ROR t and drive Th17 cell differentiation

(2014) P. Soroosh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders

(2013) Elaine Y. Hsiao et al.   CELL

Pleiotropic Roles of Bile Acids in Metabolism

(2013) Thomas Q. de Aguiar Vallim et al.   Cell Metabolism

Gut Microbiota Regulates Bile Acid Metabolism by Reducing the Levels of Tauro-beta-muricholic Acid, a Naturally Occurring FXR Antagonist

(2013) Sama I. Sayin et al.   Cell Metabolism

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

(2013) Yukihiro Furusawa et al.   NATURE

Fatty acid–induced mitochondrial uncoupling elicits inflammasome-independent IL-1α and sterile vascular inflammation in atherosclerosis

(2013) Stefan Freigang et al.   NATURE IMMUNOLOGY

The gut microbiota and obesity: from correlation to causality

(2013) Liping Zhao   NATURE REVIEWS MICROBIOLOGY

Microbiome remodelling leads to inhibition of intestinal farnesoid X receptor signalling and decreased obesity

(2013) Fei Li et al.   Nature Communications

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

The human microbiome: at the interface of health and disease

(2012) Ilseung Cho et al.   NATURE REVIEWS GENETICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Human nutrition, the gut microbiome and the immune system

(2011) Andrew L. Kau et al.   NATURE

Effects of gut microbiota on obesity and atherosclerosis via modulation of inflammation and lipid metabolism

(2010) R. Caesar et al.   JOURNAL OF INTERNAL MEDICINE

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

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

(2009) P. J. Turnbaugh et al.   Science Translational Medicine

CD4+Foxp3+ regulatory T cells in the control of autoimmunity: in vivo veritas

(2008) Ciriaco A Piccirillo et al.   CURRENT OPINION IN IMMUNOLOGY

A microbial symbiosis factor prevents intestinal inflammatory disease

(2008) Sarkis K. Mazmanian et al.   NATURE

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH