Self-reinoculation with fecal flora changes microbiota density and composition leading to an altered bile-acid profile in the mouse small intestine

Gut microbiota density influences host physiology and is shaped by host and microbial factors

(2019) Eduardo J Contijoch et al.   eLife

Spatial and Temporal Analysis of the Stomach and Small-Intestinal Microbiota in Fasted Healthy Humans

(2019) Anna M. Seekatz et al.   mSphere

Bile salt hydrolases: Gatekeepers of bile acid metabolism and host-microbiome crosstalk in the gastrointestinal tract

(2019) Matthew H. Foley et al.   PLoS Pathogens

Systematic review with meta-analysis: the prevalence of small intestinal bacterial overgrowth in inflammatory bowel disease

(2019) Ayesha Shah et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Composition of the mucosa-associated microbiota along the entire gastrointestinal tract of human individuals

(2019) FER Vuik et al.   United European Gastroenterology Journal

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders

(2019) George B. Saffouri et al.   Nature Communications

Genetic determinants of gut microbiota composition and bile acid profiles in mice

(2019) Julia H. Kemis et al.   PLoS Genetics

Small Intestine Microbiota Regulate Host Digestive and Absorptive Adaptive Responses to Dietary Lipids

(2018) Kristina Martinez-Guryn et al.   Cell Host & Microbe

Role of bile acids in the gut-liver axis

(2018) Kai Markus Schneider et al.   JOURNAL OF HEPATOLOGY

Microbiome-mediated bile acid modification: Role in intestinal drug absorption and metabolism

(2018) Elaine F. Enright et al.   PHARMACOLOGICAL RESEARCH

A selective gut bacterial bile salt hydrolase alters host metabolism

(2018) Lina Yao et al.   eLife

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features

(2018) Niv Zmora et al.   CELL

Bile salt hydrolases: Structure and function, substrate preference, and inhibitor development

(2018) Zixing Dong et al.   PROTEIN SCIENCE

The influence of caging, bedding, and diet on the composition of the microbiota in different regions of the mouse gut

(2018) Aaron C. Ericsson et al.   Scientific Reports

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

(2018) Nicole M. Davis et al.   Microbiome

Microbiota and reproducibility of rodent models

(2017) Craig L Franklin et al.   LAB ANIMAL

Gut microbiome interactions with drug metabolism, efficacy, and toxicity

(2017) Ian D. Wilson et al.   Translational Research

Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus

(2017) Cristina Llorente et al.   Nature Communications

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Balance Trees Reveal Microbial Niche Differentiation

(2017) James T. Morton et al.   mSystems

Ciprofloxacin blocked enterohepatic circulation of diclofenac and alleviated NSAID-induced enteropathy in rats partly by inhibiting intestinal β-glucuronidase activity

(2016) Ze-yu Zhong et al.   ACTA PHARMACOLOGICA SINICA

It's all relative: analyzing microbiome data as compositions

(2016) Gregory B. Gloor et al.   ANNALS OF EPIDEMIOLOGY

Small intestinal bacterial overgrowth is associated with irritable bowel syndrome and is independent of proton pump inhibitor usage

(2016) Evangelos J. Giamarellos-Bourboulis et al.   BMC GASTROENTEROLOGY

Quantitation of next generation sequencing library preparation protocol efficiencies using droplet digital PCR assays - a systematic comparison of DNA library preparation kits for Illumina sequencing

(2016) Louise Aigrain et al.   BMC GENOMICS

Human Microbiota-Associated Mice: A Model with Challenges

(2016) Marie-Claire Arrieta et al.   Cell Host & Microbe

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

(2016) Annika Wahlström et al.   Cell Metabolism

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing

(2016) Jongoh Shin et al.   Scientific Reports

Bacterial bile salt hydrolase: an intestinal microbiome target for enhanced animal health

(2016) Wenjing Geng et al.   ANIMAL HEALTH RESEARCH REVIEWS

Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome

(2016) Antoine M. Snijders et al.   Nature Microbiology

Antibiotic-Induced Alterations of the Gut Microbiota Alter Secondary Bile Acid Production and Allow for Clostridium difficile Spore Germination and Outgrowth in the Large Intestine

(2016) Casey M. Theriot et al.   mSphere

Spatial Heterogeneity of Gut Microbial Composition along the Gastrointestinal Tract in Natural Populations of House Mice

(2016) Taichi A. Suzuki et al.   PLoS One

Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes

(2016) Shoko Iwai et al.   PLoS One

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.

(2015) Kathrin P. Aßhauer et al.   BIOINFORMATICS

Regulators of Gut Motility Revealed by a Gnotobiotic Model of Diet-Microbiome Interactions Related to Travel

(2015) Neelendu Dey et al.   CELL

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

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

The small intestine microbiota, nutritional modulation and relevance for health

(2015) Sahar El Aidy et al.   CURRENT OPINION IN BIOTECHNOLOGY

How informative is the mouse for human gut microbiota research?

(2015) T. L. A. Nguyen et al.   Disease Models & Mechanisms

Intestinal microbiota contributes to individual susceptibility to alcoholic liver disease

(2015) M Llopis et al.   GUT

A catalog of the mouse gut metagenome

(2015) Liang Xiao et al.   NATURE BIOTECHNOLOGY

Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping

(2015) Jennifer B Treweek et al.   Nature Protocols

Macronutrient intakes in obese subjects with or without small intestinal bacterial overgrowth: an alimentary survey

(2015) Enzo Ierardi et al.   SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

Pediatric small intestine bacterial overgrowth in low-income countries

(2015) Jeffrey R. Donowitz et al.   TRENDS IN MOLECULAR MEDICINE

Diet and specific microbial exposure trigger features of environmental enteropathy in a novel murine model

(2015) Eric M. Brown et al.   Nature Communications

Proportionality: A Valid Alternative to Correlation for Relative Data

(2015) David Lovell et al.   PLoS Computational Biology

Bidirectional interactions between indomethacin and the murine intestinal microbiota

(2015) Xue Liang et al.   eLife

The human gut sterolbiome: bile acid-microbiome endocrine aspects and therapeutics

(2015) Jason M. Ridlon et al.   Acta Pharmaceutica Sinica B

Hydrogen sulphide protects against NSAID-enteropathy through modulation of bile and the microbiota

(2014) Rory W Blackler et al.   BRITISH JOURNAL OF PHARMACOLOGY

Anti-Infective Activities of Lactobacillus Strains in the Human Intestinal Microbiota: from Probiotics to Gastrointestinal Anti-Infectious Biotherapeutic Agents

(2014) V. Lievin-Le Moal et al.   CLINICAL MICROBIOLOGY REVIEWS

Which is more important for classifying microbial communities: who’s there or what they can do?

(2014) Zhenjiang Xu et al.   ISME Journal

Regulation of host weight gain and lipid metabolism by bacterial bile acid modification in the gut

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

Role of small intestinal bacterial overgrowth in severe small intestinal damage in chronic non-steroidal anti-inflammatory drug users

(2014) Motoko Muraki et al.   SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY

Surface area of the digestive tract – revisited

(2014) Herbert F Helander et al.   SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY

Cholesterol-lowering effect of Lactobacillus plantarum NCU116 in a hyperlipidaemic rat model

(2014) Chuan Li et al.   Journal of Functional Foods

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

Cholesterol lowering with bile salt hydrolase-active probiotic bacteria, mechanism of action, clinical evidence, and future direction for heart health applications

(2013) Mitchell L Jones et al.   EXPERT OPINION ON BIOLOGICAL THERAPY

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Bacterial Community Mapping of the Mouse Gastrointestinal Tract

(2013) Shenghua Gu et al.   PLoS One

Upper gastrointestinal microbiota and digestive diseases

(2013) Zi-Kai Wang   WORLD JOURNAL OF GASTROENTEROLOGY

Bacterial β-glucuronidase inhibition protects mice against enteropathy induced by indomethacin, ketoprofen or diclofenac: mode of action and pharmacokinetics

(2013) Kyle S. Saitta et al.   XENOBIOTICA

Gut Immune Maturation Depends on Colonization with a Host-Specific Microbiota

(2012) Hachung Chung et al.   CELL

Enterobacteria-mediated deconjugation of taurocholic acid enhances ileal farnesoid X receptor signaling

(2012) Hideaki Kuribayashi et al.   EUROPEAN JOURNAL OF PHARMACOLOGY

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Predominant Effect of Host Genetics on Levels of Lactobacillus johnsonii Bacteria in the Mouse Gut

(2011) Keren Buhnik-Rosenblau et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Activation of the farnesoid-X receptor protects against gastrointestinal injury caused by non-steroidal anti-inflammatory drugs in mice

(2011) Stefano Fiorucci et al.   BRITISH JOURNAL OF PHARMACOLOGY

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Proton Pump Inhibitors Exacerbate NSAID-Induced Small Intestinal Injury by Inducing Dysbiosis

(2011) John L. Wallace et al.   GASTROENTEROLOGY

NUTRITIONAL IMPLICATIONS OF COPROPHAGY

(2010) Richard H. Barnes   NUTRITION REVIEWS

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

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

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

Hypocholesterolemic effects of Lactobacillus plantarum KCTC3928 by increased bile acid excretion in C57BL/6 mice

(2009) Jungae Jeun et al.   NUTRITION

NSAID-induced intestinal damage: are luminal bacteria the therapeutic target?

(2008) C Scarpignato   GUT

Improved annotation of conjugated bile acid hydrolase superfamily members in Gram-positive bacteria

(2008) J. M. Lambert et al.   MICROBIOLOGY-SGM

Systemic multicompartmental effects of the gut microbiome on mouse metabolic phenotypes

(2008) Sandrine P Claus et al.   Molecular Systems Biology

Resuscitation and quantification of stressed Escherichia coli K12 NCTC8797 in water samples

(2007) R. Özkanca et al.   MICROBIOLOGICAL RESEARCH