Design, construction, and in vivo augmentation of a complex gut microbiome

Genetic manipulation of gut microbes enables single-gene interrogation in a complex microbiome

(2022) Wen-Bing Jin et al.   CELL

Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota

(2022) Andrés Aranda-Díaz et al.   Cell Host & Microbe

Dissecting the contribution of host genetics and the microbiome in complex behaviors

(2021) Shelly A. Buffington et al.   CELL

Rationally designed bacterial consortia to treat chronic immune-mediated colitis and restore intestinal homeostasis

(2021) Daniel van der Lelie et al.   Nature Communications

Bacterial metabolism of bile acids promotes generation of peripheral regulatory T cells

(2020) Clarissa Campbell et al.   NATURE

A complete domain-to-species taxonomy for Bacteria and Archaea

(2020) Donovan H. Parks et al.   NATURE BIOTECHNOLOGY

A metabolic pathway for bile acid dehydroxylation by the gut microbiome

(2020) Masanori Funabashi et al.   NATURE

Vitamin Biosynthesis by Human Gut Butyrate-Producing Bacteria and Cross-Feeding in Synthetic Microbial Communities

(2020) Eva C. Soto-Martin et al.   mBio

Commensal Enterobacteriaceae Protect against Salmonella Colonization through Oxygen Competition

(2019) Yael Litvak et al.   Cell Host & Microbe

Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection

(2019) Eric M. Velazquez et al.   Nature Microbiology

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

(2019) Nandita R. Garud et al.   PLOS BIOLOGY

Novel insights from uncultivated genomes of the global human gut microbiome

(2019) Stephen Nayfach et al.   NATURE

The ancestral and industrialized gut microbiota and implications for human health

(2019) Erica D. Sonnenburg et al.   NATURE REVIEWS MICROBIOLOGY

Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice

(2019) Gil Sharon et al.   CELL

Gut Microbiota Alteration is Characterized by a Proteobacteria and Fusobacteria Bloom in Kwashiorkor and a Bacteroidetes Paucity in Marasmus

(2019) Thi-Phuong-Thao Pham et al.   Scientific Reports

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Interspecies Competition Impacts Targeted Manipulation of Human Gut Bacteria by Fiber-Derived Glycans

(2019) Michael L. Patnode et al.   CELL

Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs

(2019) Katharine Michelle Ng et al.   Cell Host & Microbe

Depletion of microbiome-derived molecules in the host using Clostridium genetics

(2019) Chun-Jun Guo et al.   SCIENCE

To engraft or not to engraft: an ecological framework for gut microbiome modulation with live microbes

(2018) Jens Walter et al.   CURRENT OPINION IN BIOTECHNOLOGY

Deciphering microbial interactions in synthetic human gut microbiome communities

(2018) Ophelia S Venturelli et al.   Molecular Systems Biology

The commensal microbiome is associated with anti–PD-1 efficacy in metastatic melanoma patients

(2018) Vyara Matson et al.   SCIENCE

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Depicting the composition of gut microbiota in a population with varied ethnic origins but shared geography

(2018) Mélanie Deschasaux et al.   NATURE MEDICINE

Regional variation limits applications of healthy gut microbiome reference ranges and disease models

(2018) Yan He et al.   NATURE MEDICINE

Emergent simplicity in microbial community assembly

(2018) Joshua E. Goldford et al.   SCIENCE

Adherent-invasiveEscherichia coliin inflammatory bowel disease

(2017) Carolina Palmela et al.   GUT

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites

(2017) Dylan Dodd et al.   NATURE

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

(2017) V. Gopalakrishnan et al.   SCIENCE

Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors

(2017) Bertrand Routy et al.   SCIENCE

The effects of micronutrient deficiencies on bacterial species from the human gut microbiota

(2017) Matthew C. Hibberd et al.   Science Translational Medicine

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

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

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

(2016) Stephen Nayfach et al.   GENOME RESEARCH

Challenges in microbial ecology: building predictive understanding of community function and dynamics

(2016) Stefanie Widder et al.   ISME Journal

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

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

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

The Altered Schaedler Flora: Continued Applications of a Defined Murine Microbial Community

(2015) Meghan Wymore Brand et al.   ILAR JOURNAL

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Identifying personal microbiomes using metagenomic codes

(2015) Eric A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides

(2015) M. Wu et al.   SCIENCE

The Devil Lies in the Details: How Variations in Polysaccharide Fine-Structure Impact the Physiology and Evolution of Gut Microbes

(2014) Eric C. Martens et al.   JOURNAL OF MOLECULAR BIOLOGY

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

The Prevalence of Species and Strains in the Human Microbiome: A Resource for Experimental Efforts

(2014) Laurens Kraal et al.   PLoS One

Identifying Gut Microbe-Host Phenotype Relationships Using Combinatorial Communities in Gnotobiotic Mice

(2014) J. J. Faith et al.   Science Translational Medicine

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

(2013) V. K. Ridaura et al.   SCIENCE

Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome

(2013) Nathan P. McNulty et al.   PLOS BIOLOGY

Intestinal colonization resistance

(2012) Trevor D. Lawley et al.   IMMUNOLOGY

Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon

(2012) Xiaolei Ze 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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Grinder: a versatile amplicon and shotgun sequence simulator

(2012) Florent E. Angly et al.   NUCLEIC ACIDS RESEARCH

Bacteroides in the Infant Gut Consume Milk Oligosaccharides via Mucus-Utilization Pathways

(2011) Angela Marcobal et al.   Cell Host & Microbe

Social interaction in synthetic and natural microbial communities

(2011) J. B. Xavier   Molecular Systems Biology

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

Predicting a Human Gut Microbiota's Response to Diet in Gnotobiotic Mice

(2011) J. J. Faith et al.   SCIENCE

The Impact of a Consortium of Fermented Milk Strains on the Gut Microbiome of Gnotobiotic Mice and Monozygotic Twins

(2011) N. P. McNulty et al.   Science Translational Medicine

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen 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

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat

(2009) Andrew L. Goodman et al.   Cell Host & Microbe