Diet-induced remission in chronic enteropathy is associated with altered microbial community structure and synthesis of secondary bile acids

Taxonomic profiling and populational patterns of bacterial bile salt hydrolase (BSH) genes based on worldwide human gut microbiome

(2019) Ziwei Song et al.   Microbiome

Evolving role of diet in the pathogenesis and treatment of inflammatory bowel diseases

(2018) Arie Levine et al.   GUT

Metagenomic insights into the roles of Proteobacteria in the gastrointestinal microbiomes of healthy dogs and cats

(2018) Christina D. Moon et al.   MicrobiologyOpen

Similarity of the dog and human gut microbiomes in gene content and response to diet

(2018) Luis Pedro Coelho et al.   Microbiome

Genome-wide association studies of inflammatory bowel disease in German shepherd dogs

(2018) Atiyeh Peiravan et al.   PLoS One

Effect of probiotic treatment on the clinical course, intestinal microbiome, and toxigenic Clostridium perfringens in dogs with acute hemorrhagic diarrhea

(2018) Anna-Lena Ziese et al.   PLoS One

Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort

(2018) Thomas Gurry et al.   Scientific Reports

FXR-Dependent Modulation of the Human Small Intestinal Microbiome by the Bile Acid Derivative Obeticholic Acid

(2018) Elliot S. Friedman et al.   GASTROENTEROLOGY

Effect of an extruded animal protein-free diet on fecal microbiota of dogs with food-responsive enteropathy

(2018) Francesca Bresciani et al.   JOURNAL OF VETERINARY INTERNAL MEDICINE

Comparison of intestinal expression of the apical sodium-dependent bile acid transporter between dogs with and without chronic inflammatory enteropathy

(2018) Paula R. Giaretta et al.   JOURNAL OF VETERINARY INTERNAL MEDICINE

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Differences in Outcomes Over Time With Exclusive Enteral Nutrition Compared With Steroids in Children With Mild to Moderate Crohn’s Disease: Results From the GROWTH CD Study

(2017) Noa Cohen-Dolev et al.   Journal of Crohns & Colitis

MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments

(2017) Francislon S Oliveira 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

Bile acid sensitivity and in vivo virulence of clinical Clostridium difficile isolates

(2016) Brittany B. Lewis et al.   ANAEROBE

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

(2016) Mahesh S. Desai et al.   CELL

Bile Acids Control Inflammation and Metabolic Disorder through Inhibition of NLRP3 Inflammasome

(2016) Chuansheng Guo et al.   IMMUNITY

Early Changes in Microbial Community Structure Are Associated with Sustained Remission After Nutritional Treatment of Pediatric Crohnʼs Disease

(2016) Katherine A. Dunn et al.   INFLAMMATORY BOWEL DISEASES

Exclusive enteral nutrition in active pediatric Crohn disease: Effects on intestinal microbiota and immune regulation

(2016) Tobias Schwerd et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

(2016) Hilary P. Browne et al.   NATURE

Role of antibiotics for treatment of inflammatory bowel disease

(2016) Orna Nitzan   WORLD JOURNAL OF GASTROENTEROLOGY

Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks

(2016) Yoshiki Vázquez-Baeza 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

Extensive Modulation of the Fecal Metagenome in Children With Crohn’s Disease During Exclusive Enteral Nutrition

(2015) Christopher Quince et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

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

Diet in the Pathogenesis and Treatment of Inflammatory Bowel Diseases

(2015) Dale Lee et al.   GASTROENTEROLOGY

Comparative Effectiveness of Nutritional and Biological Therapy in North American Children with Active Crohnʼs Disease

(2015) Dale Lee et al.   INFLAMMATORY BOWEL DISEASES

Vertically transmitted faecal IgA levels determine extra-chromosomal phenotypic variation

(2015) Clara Moon et al.   NATURE

Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome

(2015) Benoit Chassaing et al.   NATURE

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Lithocholic acid and derivatives: Antibacterial activity

(2015) Patrícia G.G. do Nascimento et al.   STEROIDS

Subsistence strategies in traditional societies distinguish gut microbiomes

(2015) Alexandra J. Obregon-Tito et al.   Nature Communications

Effect of Exclusive Enteral Nutrition on the Microbiota of Children With Newly Diagnosed Crohn’s Disease

(2015) Nadeem O Kaakoush et al.   Clinical and Translational Gastroenterology

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

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

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

(2014) Gary D Wu et al.   GUT

Partial Enteral Nutrition with a Crohnʼs Disease Exclusion Diet Is Effective for Induction of Remission in Children and Young Adults with Crohnʼs Disease

(2014) Rotem Sigall-Boneh et al.   INFLAMMATORY BOWEL DISEASES

Decline in Presumptively Protective Gut Bacterial Species and Metabolites Are Paradoxically Associated with Disease Improvement in Pediatric Crohn’s Disease During Enteral Nutrition

(2014) Konstantinos Gerasimidis et al.   INFLAMMATORY BOWEL DISEASES

Consensus guidelines of ECCO/ESPGHAN on the medical management of pediatric Crohn's disease

(2014) F.M. Ruemmele et al.   Journal of Crohns & Colitis

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

Prevalence of Clostridium perfringens , Clostridium perfringens enterotoxin and dysbiosis in fecal samples of dogs with diarrhea

(2014) Yasushi Minamoto et al.   VETERINARY MICROBIOLOGY

An Altered Gut Microbiome Profile in a Child Affected by Crohn's Disease Normalized After Nutritional Therapy

(2013) Valeria D'Argenio et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome

(2013) Dan Knights et al.   GUT

NOD2-mediated dysbiosis predisposes mice to transmissible colitis and colorectal cancer

(2013) Aurélie Couturier-Maillard et al.   JOURNAL OF CLINICAL INVESTIGATION

Enterotoxigenic Clostridium perfringens infection and pediatric patients with inflammatory bowel disease

(2013) Aleksandra Banaszkiewicz et al.   Journal of Crohns & Colitis

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

16S rRNA Gene Pyrosequencing Reveals Bacterial Dysbiosis in the Duodenum of Dogs with Idiopathic Inflammatory Bowel Disease

(2012) Jan S. Suchodolski et al.   PLoS One

Dietary Intake and Risk of Developing Inflammatory Bowel Disease: A Systematic Review of the Literature

(2011) Jason K Hou et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Antibiotic Therapy in Inflammatory Bowel Disease: A Systematic Review and Meta-Analysis

(2011) Khurram J Khan et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Bile Acid Is a Host Factor That Regulates the Composition of the Cecal Microbiota in Rats

(2011) K.B.M. Saiful Islam et al.   GASTROENTEROLOGY

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

Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

(2011) B. D. Muegge et al.   SCIENCE

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

A Randomized, Open-Label, Positively-Controlled Field Trial of a Hydrolyzed Protein Diet in Dogs with Chronic Small Bowel Enteropathy

(2010) P.J.J. Mandigers et al.   JOURNAL OF VETERINARY INTERNAL MEDICINE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Inflammatory bowel disease in the dog: Differences and similarities with humans

(2010) Matteo Cerquetella   WORLD JOURNAL OF GASTROENTEROLOGY

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The Bile Acid Receptor FXR Is a Modulator of Intestinal Innate Immunity

(2009) P. Vavassori et al.   JOURNAL OF IMMUNOLOGY

Effect of bile salts on the DNA and membrane integrity of enteric bacteria

(2009) M. E. Merritt et al.   JOURNAL OF MEDICAL MICROBIOLOGY