Within-host evolution of the gut microbiome

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

Diet leaves a genetic signature in a keystone member of the gut microbiota

(2022) Tanja Dapa et al.   Cell Host & Microbe

Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions

(2022) Jun Feng et al.   Cell Host & Microbe

Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults

(2022) Benjamin A. Siranosian et al.   Nature Communications

Diverse events have transferred genes for edible seaweed digestion from marine to human gut bacteria

(2022) Nicholas A. Pudlo et al.   Cell Host & Microbe

Rapid evolution and strain turnover in the infant gut microbiome

(2022) Daisy W. Chen et al.   GENOME RESEARCH

High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome

(2022) Wenshan Zheng et al.   SCIENCE

Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution

(2022) Martijn F. Schenk et al.   Nature Ecology & Evolution

Within-host evolution of a gut pathobiont facilitates liver translocation

(2022) Yi Yang et al.   NATURE

Emergent evolutionary forces in spatial models of luminal growth and their application to the human gut microbiota

(2022) Olivia M. Ghosh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2022) Alice G. Cheng et al.   CELL

Codiversification of gut microbiota with humans

(2022) Taichi A. Suzuki et al.   SCIENCE

Two modes of evolution shape bacterial strain diversity in the mammalian gut for thousands of generations

(2022) N. Frazão et al.   Nature Communications

Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice

(2021) Bahtiyar Yilmaz et al.   Cell Host & Microbe

Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments

(2021) Hualan Liu et al.   Cell Reports

Elevated rates of horizontal gene transfer in the industrialized human microbiome

(2021) Mathieu Groussin et al.   CELL

Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species spread and geographical clustering

(2021) Leonor García-Bayona et al.   PLoS Genetics

Dispersal strategies shape persistence and evolution of human gut bacteria

(2021) Falk Hildebrand et al.   Cell Host & Microbe

Quantifying rapid bacterial evolution and transmission within the mouse intestine

(2021) Kimberly S. Vasquez et al.   Cell Host & Microbe

Molecular signatures of resource competition: Clonal interference favors ecological diversification and can lead to incipient speciation

(2021) Massimo Amicone et al.   EVOLUTION

Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment

(2021) Morteza Roodgar et al.   GENOME RESEARCH

A metabolomics pipeline for the mechanistic interrogation of the gut microbiome

(2021) Shuo Han et al.   NATURE

The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping

(2021) Benjamin S. Beresford-Jones et al.   Cell Host & Microbe

The population genetics of collateral resistance and sensitivity

(2021) Sarah M Ardell et al.   eLife

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

Complete, closed bacterial genomes from microbiomes using nanopore sequencing

(2020) Eli L. Moss et al.   NATURE BIOTECHNOLOGY

Bacterial adaptation is constrained in complex communities

(2020) Thomas Scheuerl et al.   Nature Communications

Specific Eco-evolutionary Contexts in the Mouse Gut Reveal Escherichia coli Metabolic Versatility

(2020) João Barroso-Batista et al.   CURRENT BIOLOGY

The Landscape of Adaptive Evolution of a Gut Commensal Bacteria in Aging Mice

(2020) Hugo C. Barreto et al.   CURRENT BIOLOGY

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale

(2020) Soumaya Zlitni et al.   Genome Medicine

Co-evolution and Co-speciation of Host-Gut Bacteria Systems

(2020) Mathieu Groussin et al.   Cell Host & Microbe

A unified catalog of 204,938 reference genomes from the human gut microbiome

(2020) Alexandre Almeida et al.   NATURE BIOTECHNOLOGY

Phages and their potential to modulate the microbiome and immunity

(2020) Sara Federici et al.   Cellular & Molecular Immunology

Does diversity beget diversity in microbiomes?

(2020) Naïma Madi et al.   eLife

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

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

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

Rethinking gut microbiome residency and the Enterobacteriaceae in healthy human adults

(2019) Jonathan N. V. Martinson et al.   ISME Journal

Discovery and inhibition of an interspecies gut bacterial pathway for Levodopa metabolism

(2019) Vayu Maini Rekdal et al.   SCIENCE

Long‐term evolution of the natural isolate of Escherichia coli 536 in the mouse gut colonized after maternal transmission reveals convergence in the constitutive expression of the lactose operon

(2019) Mohamed Ghalayini et al.   MOLECULAR ECOLOGY

Microbiota-derived lantibiotic restores resistance against vancomycin-resistant Enterococcus

(2019) Sohn G. Kim et al.   NATURE

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

(2019) M. Poyet et al.   NATURE MEDICINE

Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut

(2019) Nelson Frazão et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic manipulation of wild human gut Bacteroides

(2019) Natasha A. Bencivenga-Barry et al.   JOURNAL OF BACTERIOLOGY

Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation

(2019) Eitan Yaffe et al.   Nature Microbiology

Selective maternal seeding and environment shape the human gut microbiome

(2018) Katri Korpela et al.   GENOME RESEARCH

An exclusive metabolic niche enables strain engraftment in the gut microbiota

(2018) Elizabeth Stanley Shepherd et al.   NATURE

Adaptation of commensal proliferatingEscherichia colito the intestinal tract of young children with cystic fibrosis

(2018) Susana Matamouros et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gut microbiota utilize immunoglobulin A for mucosal colonization

(2018) G. P. Donaldson et al.   SCIENCE

Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria

(2018) Inês S. Pais et al.   PLOS BIOLOGY

Evolution of a Dominant Natural Isolate of Escherichia coli in the Human Gut over the Course of a Year Suggests a Neutral Evolution with Reduced Effective Population Size

(2018) Mohamed Ghalayini et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Dietary trehalose enhances virulence of epidemic Clostridium difficile

(2018) J. Collins et al.   NATURE

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization

(2018) Patrick H. Bradley et al.   PLoS Computational Biology

Adaptation limits ecological diversification and promotes ecological tinkering during the competition for substitutable resources

(2018) Benjamin H. Good et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The evolution of the host microbiome as an ecosystem on a leash

(2017) Kevin R. Foster et al.   NATURE

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Mutator genomes decay, despite sustained fitness gains, in a long-term experiment with bacteria

(2017) Alejandro Couce et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

(2017) Mathieu Groussin et al.   Nature Communications

Using long-term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin-treated mouse gut

(2016) Mathilde Lescat et al.   MOLECULAR ECOLOGY

The evolution of cooperation within the gut microbiota

(2016) Seth Rakoff-Nahoum et al.   NATURE

The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism

(2016) Peter Spanogiannopoulos et al.   NATURE REVIEWS MICROBIOLOGY

Within-host evolution of bacterial pathogens

(2016) Xavier Didelot et al.   NATURE REVIEWS MICROBIOLOGY

Cospeciation of gut microbiota with hominids

(2016) A. H. Moeller et al.   SCIENCE

Quantitative evolutionary dynamics using high-resolution lineage tracking

(2015) Sasha F. Levy et al.   NATURE

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

(2015) M. Wu et al.   SCIENCE

Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria

(2015) João Barroso-Batista et al.   Nature Communications

Bacteria from Diverse Habitats Colonize and Compete in the Mouse Gut

(2014) Henning Seedorf et al.   CELL

The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps

(2014) João Barroso-Batista et al.   PLoS Genetics

Interspecies Interactions Determine the Impact of the Gut Microbiota on Nutrient Allocation in Drosophila melanogaster

(2013) Peter D. Newell et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

(2013) Yukihiro Furusawa et al.   NATURE

Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations

(2012) B. H. Good et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Species Interactions Alter Evolutionary Responses to a Novel Environment

(2012) Diane Lawrence et al.   PLOS BIOLOGY

Commensal Bacteroides Species Induce Colitis in Host-Genotype-Specific Fashion in a Mouse Model of Inflammatory Bowel Disease

(2011) Seth M. Bloom et al.   Cell Host & Microbe

Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts

(2011) Eric C. Martens et al.   PLOS BIOLOGY

Trade-Off between Bile Resistance and Nutritional Competence Drives Escherichia coli Diversification in the Mouse Gut

(2011) Marianne De Paepe et al.   PLoS Genetics

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

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

Dissecting the Genetic Components of Adaptation of Escherichia coli to the Mouse Gut

(2008) Antoine Giraud et al.   PLoS Genetics