Role of dietary fiber in the recovery of the human gut microbiome and its metabolome

Establishing or Exaggerating Causality for the Gut Microbiome: Lessons from Human Microbiota-Associated Rodents

(2020) Jens Walter et al.   CELL

Dynamics of Human Gut Microbiota and Short-Chain Fatty Acids in Response to Dietary Interventions with Three Fermentable Fibers

(2019) Nielson T. Baxter et al.   mBio

A Forward Chemical Genetic Screen Reveals Gut Microbiota Metabolites That Modulate Host Physiology

(2019) Haiwei Chen et al.   CELL

Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans

(2019) Abigail J. Johnson et al.   Cell Host & Microbe

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

Mapping Interactions of Microbial Metabolites with Human G-Protein-Coupled Receptors

(2019) Dominic A. Colosimo et al.   Cell Host & Microbe

Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs

(2019) Katharine Michelle Ng et al.   Cell Host & Microbe

Fiber-Mediated Nourishment of Gut Microbiota Protects against Diet-Induced Obesity by Restoring IL-22-Mediated Colonic Health

(2018) Jun Zou et al.   Cell Host & Microbe

Precision editing of the gut microbiota ameliorates colitis

(2018) Wenhan Zhu et al.   NATURE

Microbially Produced Imidazole Propionate Impairs Insulin Signaling through mTORC1

(2018) Ara Koh et al.   CELL

Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches

(2017) R. Balfour Sartor et al.   GASTROENTEROLOGY

Targeting of microbe-derived metabolites to improve human health: The next frontier for drug discovery

(2017) J. Mark Brown et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Commensal bacteria make GPCR ligands that mimic human signalling molecules

(2017) Louis J. Cohen et al.   NATURE

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

(2017) Dylan Dodd et al.   NATURE

HMDB 4.0: the human metabolome database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania

(2017) Samuel A. Smits et al.   SCIENCE

A role for bacterial urease in gut dysbiosis and Crohn’s disease

(2017) Josephine Ni et al.   Science Translational Medicine

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility

(2016) Mahesh S. Desai et al.   CELL

Formation of propionate and butyrate by the human colonic microbiota

(2016) Petra Louis et al.   ENVIRONMENTAL MICROBIOLOGY

Diet-induced extinctions in the gut microbiota compound over generations

(2016) Erica D. Sonnenburg et al.   NATURE

Microbial metabolism of dietary components to bioactive metabolites: opportunities for new therapeutic interventions

(2016) Linda S. Zhang et al.   Genome Medicine

Extreme Dysbiosis of the Microbiome in Critical Illness

(2016) Daniel McDonald et al.   mSphere

Personalized Nutrition by Prediction of Glycemic Responses

(2015) David Zeevi et al.   CELL

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease

(2015) James D. Lewis 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

Remaining Mysteries of Molecular Biology: The Role of Polyamines in the Cell

(2015) Leonor Miller-Fleming et al.   JOURNAL OF MOLECULAR BIOLOGY

Small molecules from the human microbiota

(2015) M. S. Donia et al.   SCIENCE

Bile Acid-Activated Receptors, Intestinal Microbiota, and the Treatment of Metabolic Disorders

(2015) Stefano Fiorucci et al.   TRENDS IN MOLECULAR MEDICINE

Fat, fibre and cancer risk in African Americans and rural Africans

(2015) Stephen J. D. O’Keefe et al.   Nature Communications

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production

(2014) Gary D Wu et al.   GUT

Symbiotic Bacterial Metabolites Regulate Gastrointestinal Barrier Function via the Xenobiotic Sensor PXR and Toll-like Receptor 4

(2014) Madhukumar Venkatesh et al.   IMMUNITY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data

(2014) M. Vital et al.   mBio

Host lifestyle affects human microbiota on daily timescales

(2014) Lawrence A David et al.   GENOME BIOLOGY

Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders

(2013) Elaine Y. Hsiao et al.   CELL

Geographical variability and environmental risk factors in inflammatory bowel disease

(2013) Siew C Ng et al.   GUT

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

(2013) Yukihiro Furusawa et al.   NATURE

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

The abundance and variety of carbohydrate-active enzymes in the human gut microbiota

(2013) Abdessamad El Kaoutari et al.   NATURE REVIEWS MICROBIOLOGY

Utilisation of Mucin Glycans by the Human Gut Symbiont Ruminococcus gnavus Is Strain-Dependent

(2013) Emmanuelle H. Crost et al.   PLoS One

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Complex Carbohydrate Utilization by the Healthy Human Microbiome

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

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

(2011) Y. Zhao et al.   BIOINFORMATICS

Role of the microbiota in inflammatory bowel diseases

(2011) Nabeetha A. Nagalingam et al.   INFLAMMATORY BOWEL DISEASES

Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease

(2011) Zeneng Wang et al.   NATURE

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

(2011) A. L. Goodman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Mucolytic Bacteria With Increased Prevalence in IBD Mucosa Augment In Vitro Utilization of Mucin by Other Bacteria

(2010) Chin Wen Png et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

(2010) Gary D Wu et al.   BMC MICROBIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis

(2009) D A Hill et al.   Mucosal Immunology