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

Metagenomic engineering of the mammalian gut microbiome in situ

(2019) Carlotta Ronda et al.   NATURE METHODS

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses

(2019) Yuanqiang Zou et al.   NATURE BIOTECHNOLOGY

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

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

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

(2019) Takeshi Tanoue et al.   NATURE

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

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies

(2018) Melanie Tramontano et al.   Nature Microbiology

Extensive impact of non-antibiotic drugs on human gut bacteria

(2018) Lisa Maier et al.   NATURE

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Fecal microbiota transplant from a rational stool donor improves hepatic encephalopathy: A randomized clinical trial

(2017) Benjamin H. Mullish et al.   HEPATOLOGY

Dimethylguanidino valeric acid is a marker of liver fat and predicts diabetes

(2017) John F. O’Sullivan et al.   JOURNAL OF CLINICAL INVESTIGATION

Gut microbiome interactions with drug metabolism, efficacy, and toxicity

(2017) Ian D. Wilson et al.   Translational Research

RiboDB Database: A Comprehensive Resource for Prokaryotic Systematics

(2016) Frédéric Jauffrit et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2016) Hilary P. Browne et al.   NATURE

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

Helicobacter pylori Diversity and Gastric Cancer Risk

(2016) Timothy L. Cover   mBio

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

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

Culture of previously uncultured members of the human gut microbiota by culturomics

(2016) Jean-Christophe Lagier et al.   Nature Microbiology

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering

(2015) Tal Galili   BIOINFORMATICS

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species

(2015) Sharon Greenblum et al.   CELL

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

(2015) Paul Moayyedi 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

Akkermansia muciniphilaand improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology

(2015) Maria Carlota Dao et al.   GUT

Engineering the gut microbiota to treat hyperammonemia

(2015) Ting-Chin David Shen et al.   JOURNAL OF CLINICAL INVESTIGATION

Microbial cocktails join fecal transplants in IBD treatment trials

(2015) Mark Ratner   NATURE BIOTECHNOLOGY

Akkermansia muciniphila inversely correlates with the onset of inflammation, altered adipose tissue metabolism and metabolic disorders during obesity in mice

(2015) Marc Schneeberger et al.   Scientific Reports

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria

(2014) Elizabeth A. Rettedal et al.   Nature Communications

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

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

Faecalibacterium prausnitzii and human intestinal health

(2013) S Miquel et al.   CURRENT OPINION IN MICROBIOLOGY

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

Stool Microbiome and Metabolome Differences between Colorectal Cancer Patients and Healthy Adults

(2013) Tiffany L. Weir et al.   PLoS One

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Predicting and Manipulating Cardiac Drug Inactivation by the Human Gut Bacterium Eggerthella lenta

(2013) H. J. Haiser et al.   SCIENCE

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

(2012) Limin Fu et al.   BIOINFORMATICS

GapFiller: a de novo assembly approach to fill the gap within paired reads

(2012) Francesca Nadalin et al.   BMC BIOINFORMATICS

Genomic determinants of sporulation inBacilliandClostridia: towards the minimal set of sporulation-specific genes

(2012) Michael Y. Galperin et al.   ENVIRONMENTAL MICROBIOLOGY

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

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

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

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The “Most Wanted” Taxa from the Human Microbiome for Whole Genome Sequencing

(2012) Anthony A. Fodor et al.   PLoS One

Intestinal Inflammation Targets Cancer-Inducing Activity of the Microbiota

(2012) J. C. Arthur et al.   SCIENCE

Therapeutic Modulation of Microbiota-Host Metabolic Interactions

(2012) E. Holmes et al.   Science Translational Medicine

Cultured Representatives of Two Major Phylogroups of Human Colonic Faecalibacterium prausnitzii Can Utilize Pectin, Uronic Acids, and Host-Derived Substrates for Growth

(2011) Mireia Lopez-Siles et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Relevance of protein fermentation to gut health

(2011) Karen Windey et al.   MOLECULAR NUTRITION & FOOD RESEARCH

Emerging molecular insights into the interaction between probiotics and the host intestinal mucosa

(2011) Peter A. Bron et al.   NATURE REVIEWS MICROBIOLOGY

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

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

Glycoprofiling Bifidobacterial Consumption of Galacto-Oligosaccharides by Mass Spectrometry Reveals Strain-Specific, Preferential Consumption of Glycans

(2009) M. Barboza et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Metabolomics Reveals Metabolic Biomarkers of Crohn's Disease

(2009) Janet Jansson et al.   PLoS One

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