Quantitative sequencing clarifies the role of disruptor taxa, oral microbiota, and strict anaerobes in the human small-intestine microbiome

ACG Clinical Guideline

(2020) Mark Pimentel et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Small Intestinal Bacterial Overgrowth in Irritable Bowel Syndrome

(2020) Ayesha Shah et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Mapping the Segmental Microbiomes in the Human Small Bowel in Comparison with Stool: A REIMAGINE Study

(2020) Gabriela G. S. Leite et al.   DIGESTIVE DISEASES AND SCIENCES

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

(2020) Said R. Bogatyrev et al.   Microbiome

A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities

(2020) Jacob T. Barlow et al.   Nature Communications

AGA Clinical Practice Update on Small Intestinal Bacterial Overgrowth: Expert Review

(2020) Eamonn MM. Quigley et al.   GASTROENTEROLOGY

Duodenal Microbiota in Stunted Undernourished Children with Enteropathy

(2020) Robert Y. Chen et al.   NEW ENGLAND JOURNAL OF MEDICINE

The duodenal microbiome is altered in small intestinal bacterial overgrowth

(2020) Gabriela Leite et al.   PLoS One

Metabolic multistability and hysteresis in a model aerobe-anaerobe microbiome community

(2020) Tahmineh Khazaei et al.   Science Advances

Commensal Enterobacteriaceae Protect against Salmonella Colonization through Oxygen Competition

(2019) Yael Litvak et al.   Cell Host & Microbe

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

(2019) Eduardo J Contijoch et al.   eLife

Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass

(2019) Vincent Caruso et al.   mSystems

Intestinal Epithelial Cells and the Microbiome Undergo Swift Reprogramming at the Inception of Colonic Citrobacter rodentium Infection

(2019) Eve G. D. Hopkins et al.   mBio

Extensive transmission of microbes along the gastrointestinal tract

(2019) Thomas SB Schmidt et al.   eLife

Establishing microbial composition measurement standards with reference frames

(2019) James T. Morton et al.   Nature Communications

Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders

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

Optimizing microbiome sequencing for small intestinal aspirates: validation of novel techniques through the REIMAGINE study

(2019) Gabriela Guimaraes Sousa Leite et al.   BMC MICROBIOLOGY

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria

(2018) Christine M. Dejea et al.   SCIENCE

Early Salmonella Typhimurium infection in pigs disrupts Microbiome composition and functionality principally at the ileum mucosa

(2018) Héctor Argüello et al.   Scientific Reports

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

Meta-analysis: proton pump inhibitors moderately increase the risk of small intestinal bacterial overgrowth

(2017) Tingting Su et al.   JOURNAL OF GASTROENTEROLOGY

Obesity increases the risk of small intestinal bacterial overgrowth (SIBO)

(2017) B. C. Roland et al.   NEUROGASTROENTEROLOGY AND MOTILITY

Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation

(2017) Koji Atarashi et al.   SCIENCE

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

HACEK endocarditis: a review

(2016) Sima L. Sharara et al.   Expert Review of Anti-Infective Therapy

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples

(2016) Angela Glassing et al.   Gut Pathogens

Dysbiosis of small intestinal microbiota in liver cirrhosis and its association with etiology

(2016) Yanfei Chen et al.   Scientific Reports

Coaggregation and biofilm growth of Granulicatella spp. with Fusobacterium nucleatum and Aggregatibacter actinomycetemcomitans

(2015) Maribasappa Karched et al.   BMC MICROBIOLOGY

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

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

How informative is the mouse for human gut microbiota research?

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

Small Intestinal Transit Time Is Delayed in Small Intestinal Bacterial Overgrowth

(2015) Bani Chander Roland et al.   JOURNAL OF CLINICAL GASTROENTEROLOGY

Investigation of the effects of pH and bile on the growth of oral Campylobacter concisus strains isolated from patients with inflammatory bowel disease and controls

(2015) R. Ma et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Antigen sampling by intestinal M cells is the principal pathway initiating mucosal IgA production to commensal enteric bacteria

(2015) D Rios et al.   Mucosal Immunology

Gut biogeography of the bacterial microbiota

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

Regulation of Intestinal Immune System by Dendritic Cells

(2015) Hyun-Jeong Ko et al.   Immune Network

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

(2014) Dirk Gevers et al.   Cell Host & Microbe

Antibiotic Treatment of Constipation-Predominant Irritable Bowel Syndrome

(2014) Mark Pimentel et al.   DIGESTIVE DISEASES AND SCIENCES

Segmented filamentous bacteria in human ileostomy samples after high-fiber intake

(2013) Hans Jonsson   FEMS MICROBIOLOGY LETTERS

Dysbiosis in inflammatory bowel diseases: the oxygen hypothesis

(2013) Lionel Rigottier-Gois   ISME Journal

The gastrointestinal mucus system in health and disease

(2013) Malin E. V. Johansson et al.   Nature Reviews Gastroenterology & Hepatology

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

(2012) Jian Ye et al.   BMC BIOINFORMATICS

The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates

(2012) Erwin G Zoetendal et al.   ISME Journal

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Detection of Bacterial 16S rRNA and Identification of Four Clinically Important Bacteria by Real-Time PCR

(2012) Robert J. Clifford et al.   PLoS One

Bacterial Interactions in Dental Biofilm Development

(2009) K. Hojo et al.   JOURNAL OF DENTAL RESEARCH

Human gut microbiome adopts an alternative state following small bowel transplantation

(2009) A. L. Hartman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA