Dynamic Colonization of Microbes and Their Functions after Fecal Microbiota Transplantation for Inflammatory Bowel Disease

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

Transmission of human-associated microbiota along family and social networks

(2019) Ilana L. Brito et al.   Nature Microbiology

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

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

An exclusive metabolic niche enables strain engraftment in the gut microbiota

(2018) Elizabeth Stanley Shepherd et al.   NATURE

Gut microbiota utilize immunoglobulin A for mucosal colonization

(2018) G. P. Donaldson et al.   SCIENCE

Orthogonal Dietary Niche Enables Reversible Engraftment of a Gut Bacterial Commensal

(2018) Sean M. Kearney et al.   Cell Reports

Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients With Clostridium difficile Infection

(2017) Stephan J. Ott et al.   GASTROENTEROLOGY

Faecal Microbiota Transplantation for Inflammatory Bowel Disease: A Systematic Review and Meta-analysis

(2017) Sudarshan Paramsothy et al.   Journal of Crohns & Colitis

Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial

(2017) Sudarshan Paramsothy et al.   LANCET

Natural polyreactive IgA antibodies coat the intestinal microbiota

(2017) Jeffrey J. Bunker et al.   SCIENCE

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses

(2017) Claire Duvallet et al.   Nature Communications

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

(2017) Andrew Brantley Hall et al.   Genome Medicine

Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides

(2017) Dmitry A. Ravcheev et al.   Frontiers in Genetics

Dynamics of the human gut microbiome in inflammatory bowel disease

(2017) Jonas Halfvarson et al.   Nature Microbiology

Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data

(2017) Marius Vital et al.   mSystems

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

Effect of Fecal Microbiota Transplantation on Recurrence in Multiply Recurrent Clostridium difficile Infection

(2016) Colleen R. Kelly et al.   ANNALS OF INTERNAL MEDICINE

Host Selection of Microbiota via Differential Adhesion

(2016) Kirstie McLoughlin et al.   Cell Host & Microbe

Fecal Microbial Transplants Reduce Antibiotic-resistant Genes in Patients With RecurrentClostridium difficileInfection

(2016) Braden Millan et al.   CLINICAL INFECTIOUS DISEASES

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

Durable coexistence of donor and recipient strains after fecal microbiota transplantation

(2016) Simone S. Li et al.   SCIENCE

The maternal microbiota drives early postnatal innate immune development

(2016) M. Gomez de Aguero et al.   SCIENCE

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

(2016) Christopher Staley et al.   mBio

Clearance of Vancomycin-ResistantEnterococcusConcomitant With Administration of a Microbiota-Based Drug Targeted at RecurrentClostridium difficileInfection

(2016) Erik R. Dubberke et al.   Open Forum Infectious Diseases

Systematic Review: Adverse Events of Fecal Microbiota Transplantation

(2016) Sinan Wang et al.   PLoS One

Fecal microbiota transplantation restores dysbiosis in patients with methicillin resistant Staphylococcus aureus enterocolitis

(2015) Yao Wei et al.   BMC INFECTIOUS DISEASES

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

(2015) Paul Moayyedi et al.   GASTROENTEROLOGY

Findings From a Randomized Controlled Trial of Fecal Transplantation for Patients With Ulcerative Colitis

(2015) Noortje G. Rossen et al.   GASTROENTEROLOGY

Update on Fecal Microbiota Transplantation 2015: Indications, Methodologies, Mechanisms, and Outlook

(2015) Colleen R. Kelly et al.   GASTROENTEROLOGY

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on

(2015) Lihong Chen et al.   NUCLEIC ACIDS RESEARCH

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

(2015) James Kaminski et al.   PLoS Computational Biology

Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease

(2014) Noah W. Palm et al.   CELL

The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition

(2014) Pamela V. Chang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fecal Microbiota Transplantation for Clostridium difficile Infection: Systematic Review and Meta-Analysis

(2013) Zain Kassam et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

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

(2013) Yukihiro Furusawa et al.   NATURE

Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation

(2013) Nicholas Arpaia et al.   NATURE

Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile

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

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response

(2012) Scott Schwartz et al.   GENOME BIOLOGY

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

The Microbiome and Butyrate Regulate Energy Metabolism and Autophagy in the Mammalian Colon

(2011) Dallas R. Donohoe et al.   Cell Metabolism

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

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

(2010) Heng Li et al.   BIOINFORMATICS

Specificity of Polysaccharide Use in Intestinal Bacteroides Species Determines Diet-Induced Microbiota Alterations

(2010) Erica D. Sonnenburg et al.   CELL

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

Longitudinal study of quality of life and psychological functioning for active, fluctuating, and inactive disease patterns in inflammatory bowel disease

(2008) Lisa M. Lix et al.   INFLAMMATORY BOWEL DISEASES

Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

(2008) H. Sokol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY