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

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

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

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

(2021) Dina Kao et al.   Lancet Gastroenterology & Hepatology

Fecal IgA Levels Are Determined by Strain-Level Differences in Bacteroides ovatus and Are Modifiable by Gut Microbiota Manipulation

(2020) Chao Yang et al.   Cell Host & Microbe

Diversity within species: interpreting strains in microbiomes

(2020) Thea Van Rossum et al.   NATURE REVIEWS MICROBIOLOGY

Fecal Microbiota Transplant is Highly Effective in Real-World Practice: Initial Results from the FMT National Registry

(2020) Colleen R. Kelly et al.   GASTROENTEROLOGY

Defined microbiota transplant restores Th17/RORγt+regulatory T cell balance in mice colonized with inflammatory bowel disease microbiotas

(2020) Graham J. Britton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt+ Regulatory T Cells and Exacerbate Colitis in Mice

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A human gut bacterial genome and culture collection for improved metagenomic analyses

(2019) Samuel C. Forster et al.   NATURE BIOTECHNOLOGY

Microbial Engraftment and Efficacy of Fecal Microbiota Transplant for Clostridium Difficile in Patients With and Without Inflammatory Bowel Disease

(2019) Robert P Hirten et al.   INFLAMMATORY BOWEL DISEASES

Adaptive Strategies of the Candidate Probiotic E. coli Nissle in the Mammalian Gut

(2019) Nathan Crook et al.   Cell Host & Microbe

Adaptive Evolution within Gut Microbiomes of Healthy People

(2019) Shijie Zhao et al.   Cell Host & Microbe

A Reverse Ecology Approach Based on a Biological Definition of Microbial Populations

(2019) Philip Arevalo et al.   CELL

The evolution of the use of faecal microbiota transplantation and emerging therapeutic indications

(2019) Jessica R Allegretti et al.   LANCET

A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research

(2019) M. Poyet et al.   NATURE MEDICINE

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

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

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

Commensal Koch's postulates: establishing causation in human microbiota research

(2018) B Anne Neville et al.   CURRENT OPINION IN MICROBIOLOGY

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Clinical Application and Potential of Fecal Microbiota Transplantation

(2018) R.E. Ooijevaar et al.   Annual Review of Medicine

Effect of Oral Capsule– vs Colonoscopy-Delivered Fecal Microbiota Transplantation on Recurrent Clostridium difficile Infection

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

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

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

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

Strain competition restricts colonization of an enteric pathogen and prevents colitis

(2016) Aaron L Hecht et al.   EMBO REPORTS

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

(2016) Hilary P. Browne et al.   NATURE

Durable coexistence of donor and recipient strains after fecal microbiota transplantation

(2016) Simone S. Li et al.   SCIENCE

Adapting Koch's postulates

(2016) A. L. Byrd et al.   SCIENCE

Unique Features of Ethnic Mongolian Gut Microbiome revealed by metagenomic analysis

(2016) Wenjun Liu et al.   Scientific Reports

Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling

(2016) Jennifer T. Lau et al.   Genome Medicine

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

(2015) Paul Moayyedi et al.   GASTROENTEROLOGY

ConStrains identifies microbial strains in metagenomic datasets

(2015) Chengwei Luo et al.   NATURE BIOTECHNOLOGY

Identifying strains that contribute to complex diseases through the study of microbial inheritance

(2015) Jeremiah J. Faith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Mining the Human Gut Microbiota for Effector Strains that Shape the Immune System

(2014) Philip P. Ahern et al.   IMMUNITY

Oral, Capsulized, Frozen Fecal Microbiota Transplantation for RelapsingClostridium difficileInfection

(2014) Ilan Youngster et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

Recovery of the Gut Microbiome following Fecal Microbiota Transplantation

(2014) A. M. Seekatz et al.   mBio

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile

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

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Human gut microbiota community structures in urban and rural populations in Russia

(2013) Alexander V. Tyakht et al.   Nature Communications

Microbial culturomics: paradigm shift in the human gut microbiome study

(2012) J.-C. Lagier et al.   CLINICAL MICROBIOLOGY AND INFECTION

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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(2012) Ben Langmead et al.   NATURE METHODS

Bacterial competition: surviving and thriving in the microbial jungle

(2009) Michael E. Hibbing et al.   NATURE REVIEWS MICROBIOLOGY