Long-term impact of fecal transplantation in healthy volunteers

A Novel Sparse Compositional Technique Reveals Microbial Perturbations

(2019) Cameron Martino et al.   mSystems

Microbial abundance, activity and population genomic profiling with mOTUs2

(2019) Alessio Milanese et al.   Nature Communications

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

The dirty aspects of fecal microbiota transplantation: a review of its adverse effects and complications

(2019) Francis E Dailey et al.   CURRENT OPINION IN PHARMACOLOGY

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

Longitudinal microbiome analysis of single donor fecal microbiota transplantation in patients with recurrent Clostridium difficile infection and/or ulcerative colitis

(2018) Michael Mintz et al.   PLoS One

World Health Organization (WHO) guidelines on use of medically important antimicrobials in food-producing animals

(2018) Awa Aidara-Kane et al.   Antimicrobial Resistance and Infection Control

Predicting recurrence of Clostridium difficile infection following encapsulated fecal microbiota transplantation

(2018) Christopher Staley et al.   Microbiome

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

(2018) Gherman V. Uritskiy et al.   Microbiome

European consensus conference on faecal microbiota transplantation in clinical practice

(2017) Giovanni Cammarota et al.   GUT

Homeostatic Immunity and the Microbiota

(2017) Yasmine Belkaid et al.   IMMUNITY

Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients

(2017) V. Gopalakrishnan et al.   SCIENCE

Clinical and immunologic effects of faecal microbiota transplantation in a patient with collagenous colitis

(2017) Sezin Günaltay et al.   WORLD JOURNAL OF GASTROENTEROLOGY

Fecal Microbiota Transplantation, Commensal Escherichia coli and Lactobacillus johnsonii Strains Differentially Restore Intestinal and Systemic Adaptive Immune Cell Populations Following Broad-spectrum Antibiotic Treatment

(2017) Ira Ekmekciu et al.   Frontiers in Microbiology

Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study

(2017) Dae-Wook Kang et al.   Microbiome

metaSNV: A tool for metagenomic strain level analysis

(2017) Paul Igor Costea et al.   PLoS One

Fecal microbiota transplantation for patients with steroid-resistant acute graft-versus-host disease of the gut

(2016) K. Kakihana et al.   BLOOD

Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease

(2016) Timothy R. Sampson et al.   CELL

OrthoANI: An improved algorithm and software for calculating average nucleotide identity

(2016) Imchang Lee et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Transferring the blues: Depression-associated gut microbiota induces neurobehavioural changes in the rat

(2016) John R. Kelly et al.   JOURNAL OF PSYCHIATRIC RESEARCH

Effects of Fecal Microbial Transplantation on Microbiome and Immunity in Simian Immunodeficiency Virus-Infected Macaques

(2016) Tiffany Hensley-McBain et al.   JOURNAL OF VIROLOGY

Pretreatment with antibiotics may enhance the efficacy of fecal microbiota transplantation in ulcerative colitis: a meta-analysis

(2016) A H Keshteli et al.   Mucosal Immunology

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Durable coexistence of donor and recipient strains after fecal microbiota transplantation

(2016) Simone S. Li et al.   SCIENCE

Resurrecting the intestinal microbiota to combat antibiotic-resistant pathogens

(2016) Eric G. Pamer   SCIENCE

Fecal Transplants: What Is Being Transferred?

(2016) Diana P. Bojanova et al.   PLOS BIOLOGY

Fecal microbiota transplantation for the intestinal decolonization of extensively antimicrobial-resistant opportunistic pathogens: a review

(2016) Amee R. Manges et al.   Infectious Diseases

Systematic Review: Adverse Events of Fecal Microbiota Transplantation

(2016) Sinan Wang et al.   PLoS One

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

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

(2015) Noortje G. Rossen et al.   GASTROENTEROLOGY

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

(2015) Doris Vandeputte et al.   GUT

Fecal Microbial Transplant Effect on Clinical Outcomes and Fecal Microbiome in Active Crohnʼs Disease

(2015) David L. Suskind et al.   INFLAMMATORY BOWEL DISEASES

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection

(2015) Alexa Weingarden et al.   Microbiome

Fecal Microbiota Transplantation in the Treatment of Clostridium difficile Infections

(2014) Matthew Austin et al.   AMERICAN JOURNAL OF MEDICINE

Gut Microbiota Elicits a Protective Immune Response against Malaria Transmission

(2014) Bahtiyar Yilmaz et al.   CELL

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Immunosuppression after Sepsis: Systemic Inflammation and Sepsis Induce a Loss of Naïve T-Cells but No Enduring Cell-Autonomous Defects in T-Cell Function

(2014) Robby Markwart et al.   PLoS One

Recovery of the Gut Microbiome following Fecal Microbiota Transplantation

(2014) A. M. Seekatz et al.   mBio

The Microbiome and Inflammatory Bowel Disease: Is There a Therapeutic Role for Fecal Microbiota Transplantation?

(2012) Christopher J Damman et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead 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

Toward an Understanding of Changes in Diversity Associated with Fecal Microbiome Transplantation Based on 16S rRNA Gene Deep Sequencing

(2012) D. Shahinas et al.   mBio

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

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

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities

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