Identification of Clostridioides difficile-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community Assembly

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

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

Inhibiting Growth of Clostridioides difficile by Restoring Valerate, Produced by the Intestinal Microbiota

(2018) Julie A.K. McDonald et al.   GASTROENTEROLOGY

Culturing the human microbiota and culturomics

(2018) Jean-Christophe Lagier et al.   NATURE REVIEWS MICROBIOLOGY

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Subspecies in the global human gut microbiome

(2017) Paul I Costea et al.   Molecular Systems Biology

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Enterotypes in the landscape of gut microbial community composition

(2017) Paul I. Costea et al.   Nature Microbiology

Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle

(2017) Milton Thomas et al.   Scientific Reports

A Novel Microbiome Therapeutic Increases Gut Microbial Diversity and Prevents RecurrentClostridium difficileInfection

(2016) Sahil Khanna et al.   JOURNAL OF INFECTIOUS DISEASES

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2016) Hilary P. Browne et al.   NATURE

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes

(2016) Daniel R. Mende et al.   NUCLEIC ACIDS RESEARCH

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

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

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

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer

(2016) Aaron Weimann et al.   mSystems

Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study

(2016) Christian Milani et al.   Scientific Reports

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

MetaQUAST: evaluation of metagenome assemblies

(2015) Alla Mikheenko et al.   BIOINFORMATICS

Development of Fecal Microbiota Transplantation Suitable for Mainstream Medicine

(2015) Alexander Khoruts et al.   Clinical Gastroenterology and Hepatology

Cultivation of stable, reproducible microbial communities from different fecal donors using minibioreactor arrays (MBRAs)

(2015) Jennifer M. Auchtung et al.   Microbiome

Weight Gain After Fecal Microbiota Transplantation

(2015) N. Alang et al.   Open Forum Infectious Diseases

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Do it yourself guide to genome assembly

(2014) B. Wajid et al.   Briefings in Functional Genomics

From Stool Transplants to Next-Generation Microbiota Therapeutics

(2014) Elaine O. Petrof et al.   GASTROENTEROLOGY

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Links between diet, gut microbiota composition and gut metabolism

(2014) Harry J. Flint et al.   PROCEEDINGS OF THE NUTRITION SOCIETY

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

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

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

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

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Probiotic Bacteria Reduce Salmonella Typhimurium Intestinal Colonization by Competing for Iron

(2013) Elisa Deriu et al.   Cell Host & Microbe

Bacteriotherapy for the treatment of intestinal dysbiosis caused by Clostridium difficile infection

(2013) Blessing O Adamu et al.   CURRENT OPINION IN MICROBIOLOGY

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Accurate and universal delineation of prokaryotic species

(2013) Daniel R Mende et al.   NATURE METHODS

Nutritional Basis for Colonization Resistance by Human Commensal Escherichia coli Strains HS and Nissle 1917 against E. coli O157:H7 in the Mouse Intestine

(2013) Rosalie Maltby et al.   PLoS One

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

(2013) Elaine O Petrof et al.   Microbiome

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

(2012) Limin Fu et al.   BIOINFORMATICS

Microbial culturomics: paradigm shift in the human gut microbiome study

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The human microbiome: ecosystem resilience and health

(2012) David A Relman   NUTRITION REVIEWS

Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice

(2012) Trevor D. Lawley et al.   PLoS Pathogens

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Treating Clostridium difficile Infection With Fecal Microbiota Transplantation

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

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

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

Changes in the Composition of the Human Fecal Microbiome After Bacteriotherapy for Recurrent Clostridium Difficile-associated Diarrhea

(2010) Alexander Khoruts et al.   JOURNAL OF CLINICAL GASTROENTEROLOGY

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Comparison of Carbon Nutrition for Pathogenic and Commensal Escherichia coli Strains in the Mouse Intestine

(2008) A. J. Fabich et al.   INFECTION AND IMMUNITY