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inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains

(2021) Matthew R. Olm et al.   NATURE BIOTECHNOLOGY

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The effect of a microbial ecosystem therapeutic (MET-2) on recurrent Clostridioides difficile infection: a phase 1, open-label, single-group trial

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Limited intestinal inflammation despite diarrhea, fecal viral RNA and SARS-CoV-2-specific IgA in patients with acute COVID-19

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Fecal Microbiota Transplantation Influences Procarcinogenic Escherichia coli in Recipient Recurrent Clostridioides difficile Patients

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Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes

(2021) Varun Aggarwala et al.   Nature Microbiology

SER-109, an Investigational Microbiome Drug to Reduce Recurrence after Clostridioides difficile infection: Lessons Learned from a Phase 2 Trial

(2020) Barbara H McGovern et al.   CLINICAL INFECTIOUS DISEASES

Fecal Microbiota Transplantation (FMT) with Colonoscopy Is Superior to Enema and Nasogastric Tube While Comparable to Capsule for the Treatment of Recurrent Clostridioides difficile Infection: A Systematic Review and Meta-Analysis

(2020) Daryl Ramai et al.   DIGESTIVE DISEASES AND SCIENCES

Intestinal bile acids directly modulate the structure and function ofC. difficileTcdB toxin

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A Phase 1b safety study of SER-287, a spore-based microbiome therapeutic, for active mild to moderate ulcerative colitis

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Visualizing the effects of predictor variables in black box supervised learning models

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Effect of Fecal Microbiota Transplantation on 8-Week Remission in Patients With Ulcerative Colitis

(2019) Samuel P. Costello et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

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(2019) Eduardo J Contijoch et al.   eLife

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

A defined commensal consortium elicits CD8 T cells and anti-cancer immunity

(2019) Takeshi Tanoue et al.   NATURE

Efficacy of Fecal Microbiota Transplantation in Irritable Bowel Syndrome

(2019) Dabo Xu et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

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Alzheimer’s Disease Microbiome Is Associated with Dysregulation of the Anti-Inflammatory P-Glycoprotein Pathway

(2019) John P. Haran et al.   mBio

Butyrate Protects Mice from Clostridium difficile-Induced Colitis through an HIF-1-Dependent Mechanism

(2019) José Luís Fachi et al.   Cell Reports

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease

(2019) Almut Heinken et al.   Microbiome

Effects of Fecal Microbiota Transplantation With Oral Capsules in Obese Patients

(2019) Jessica R. Allegretti et al.   Clinical Gastroenterology and Hepatology

Drug-Resistant E. coli Bacteremia Transmitted by Fecal Microbiota Transplant

(2019) Zachariah DeFilipp et al.   NEW ENGLAND JOURNAL OF MEDICINE

Fecal Microbiota Transplantation for Dysbiosis — Predictable Risks

(2019) Martin J. Blaser   NEW ENGLAND JOURNAL OF MEDICINE

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(2019) Jenessa A. Winston et al.   Gut Microbes

Restoration of short chain fatty acid and bile acid metabolism following fecal microbiota transplantation in patients with recurrent Clostridium difficile infection

(2018) Anna M. Seekatz et al.   ANAEROBE

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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

Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation

(2018) Christopher S. Smillie et al.   Cell Host & Microbe

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

(2018) Pamela Ferretti et al.   Cell Host & Microbe

Clinical Practice Guidelines for Clostridium difficile Infection in Adults and Children: 2017 Update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA)

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Microbial metabolites, short-chain fatty acids, restrain tissue bacterial load, chronic inflammation, and associated cancer in the colon of mice

(2018) Myunghoo Kim et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Interactions Between Diet and the Intestinal Microbiota Alter Intestinal Permeability and Colitis Severity in Mice

(2018) Sean R. Llewellyn et al.   GASTROENTEROLOGY

Selective maternal seeding and environment shape the human gut microbiome

(2018) Katri Korpela et al.   GENOME RESEARCH

Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes

(2018) Liping Zhao et al.   SCIENCE

Translocation of a gut pathobiont drives autoimmunity in mice and humans

(2018) S. Manfredo Vieira et al.   SCIENCE

Bile-Salt-Hydrolases from the Probiotic Strain Lactobacillus johnsonii La1 Mediate Anti-giardial Activity in Vitro and in Vivo

(2018) Thibault Allain et al.   Frontiers in Microbiology

Mechanistic Insights in the Success of Fecal Microbiota Transplants for the Treatment of Clostridium difficile Infections

(2018) Amoe Baktash et al.   Frontiers in Microbiology

Dietary Fiber Treatment Corrects the Composition of Gut Microbiota, Promotes SCFA Production, and Suppresses Colon Carcinogenesis

(2018) Faraz Bishehsari et al.   Genes

Metabolism of Oxo-Bile Acids and Characterization of Recombinant 12α-Hydroxysteroid Dehydrogenases from Bile Acid 7α-Dehydroxylating Human Gut Bacteria

(2018) Heidi Doden et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Development of a synthetic live bacterial therapeutic for the human metabolic disease phenylketonuria

(2018) Vincent M Isabella et al.   NATURE BIOTECHNOLOGY

Predicting recurrence of Clostridium difficile infection following encapsulated fecal microbiota transplantation

(2018) Christopher Staley et al.   Microbiome

Inhibitory Effect of Ursodeoxycholic Acid on Clostridium difficile Germination Is Insufficient to Prevent Colitis: A Study in Hamsters and Humans

(2018) Lola-Jade Palmieri et al.   Frontiers in Microbiology

Recovery of gut microbiota of healthy adults following antibiotic exposure

(2018) Albert Palleja et al.   Nature Microbiology

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Microbial shifts and signatures of long-term remission in ulcerative colitis after faecal microbiota transplantation

(2017) Susana Fuentes et al.   ISME Journal

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(2017) Dina Kao et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Microbiome-driven allergic lung inflammation is ameliorated by short-chain fatty acids

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antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification

(2017) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Microbiota-Derived Short-Chain Fatty Acids Modulate Expression of Campylobacter jejuni Determinants Required for Commensalism and Virulence

(2017) Paul M. Luethy et al.   mBio

Gut Microbiota as a Target for Preventive and Therapeutic Intervention against Food Allergy

(2017) Rosita Aitoro et al.   Nutrients

A two-part mixed-effects model for analyzing longitudinal microbiome compositional data

(2016) Eric Z. Chen et al.   BIOINFORMATICS

Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves

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(2016) Ilan Youngster et al.   BMC Medicine

Toward Accurate and Quantitative Comparative Metagenomics

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Ursodeoxycholic Acid Inhibits Clostridium difficile Spore Germination and Vegetative Growth, and Prevents the Recurrence of Ileal Pouchitis Associated With the Infection

(2016) Alexa R. Weingarden et al.   JOURNAL OF CLINICAL GASTROENTEROLOGY

Complete Microbiota Engraftment Is Not Essential for Recovery from Recurrent Clostridium difficile Infection following Fecal Microbiota Transplantation

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Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome

(2016) Marc A. Sze et al.   mBio

Dietary Fiber and Bacterial SCFA Enhance Oral Tolerance and Protect against Food Allergy through Diverse Cellular Pathways

(2016) Jian Tan et al.   Cell Reports

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(2016) Anna Maria Seekatz et al.   Genome Medicine

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(2016) Wiep Klaas Smits et al.   Nature Reviews Disease Primers

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

Faecal microbiota transplant for recurrentClostridium difficileinfection using long-term frozen stool is effective: clinical efficacy and bacterial viability data

(2015) S. P. Costello et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Th17 Cell Induction by Adhesion of Microbes to Intestinal Epithelial Cells

(2015) Koji Atarashi et al.   CELL

Survival of Microencapsulated Probiotic Bacteria after Processing and during Storage: A Review

(2015) Dianawati Dianawati et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

Fecal Microbiota Transplantation Induces Remission in Patients With Active Ulcerative Colitis in a Randomized Controlled Trial

(2015) Paul Moayyedi et al.   GASTROENTEROLOGY

A biosynthetic pathway for a prominent class of microbiota-derived bile acids

(2015) A Sloan Devlin et al.   Nature Chemical Biology

NCBI BLAST+ integrated into Galaxy

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Fecal Microbiota Transplant for Treatment of Clostridium difficile Infection in Immunocompromised Patients

(2014) Colleen R Kelly et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Role of the Microbiota in Immunity and Inflammation

(2014) Yasmine Belkaid et al.   CELL

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection

(2014) Casey M. Theriot et al.   Nature Communications

A Gnotobiotic Mouse Model Demonstrates That Dietary Fiber Protects against Colorectal Tumorigenesis in a Microbiota- and Butyrate-Dependent Manner

(2014) D. R. Donohoe et al.   Cancer Discovery

Intestinal Dysbiosis and Depletion of Butyrogenic Bacteria in Clostridium difficile Infection and Nosocomial Diarrhea

(2013) V. C. Antharam et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

(2013) Yukihiro Furusawa et al.   NATURE

Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota

(2013) Koji Atarashi et al.   NATURE

Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile

(2013) Els van Nood et al.   NEW ENGLAND JOURNAL OF MEDICINE

Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut

(2013) A. Reyes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut

(2013) Elaine O Petrof et al.   Microbiome

Fecal microbiome transplantation for recurrent Clostridium difficile infection: Report on a case series

(2012) Timothy A. Rubin et al.   ANAEROBE

Evaluation of an Oral Suspension of VP20621, Spores of Nontoxigenic Clostridium difficile Strain M3, in Healthy Subjects

(2012) Stephen A. Villano et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

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Treating Clostridium difficile Infection With Fecal Microbiota Transplantation

(2011) Johan S. Bakken et al.   Clinical Gastroenterology and Hepatology

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(2011) Marjolein P. M. Hensgens et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Predicting a Human Gut Microbiota's Response to Diet in Gnotobiotic Mice

(2011) J. J. Faith et al.   SCIENCE

Permutation importance: a corrected feature importance measure

(2010) André Altmann et al.   BIOINFORMATICS

Comparative Metagenomic Study of Alterations to the Intestinal Microbiota and Risk of NosocomialClostridum difficile–Associated Disease

(2010) Amee R. Manges et al.   JOURNAL OF INFECTIOUS DISEASES

Isolation and characterization of a bile acid inducible 7α-dehydroxylating operon in Clostridium hylemonae TN271

(2009) Jason M. Ridlon et al.   ANAEROBE

Biopython: freely available Python tools for computational molecular biology and bioinformatics

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Bile Salts and Glycine as Cogerminants for Clostridium difficile Spores

(2008) J. A. Sorg et al.   JOURNAL OF BACTERIOLOGY