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

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

Selective maternal seeding and environment shape the human gut microbiome

(2018) Katri Korpela et al.   GENOME RESEARCH

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

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

Recombination-Driven Genome Evolution and Stability of Bacterial Species

(2017) Purushottam D. Dixit et al.   GENETICS

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates

(2017) Matthew R. Olm et al.   GENOME RESEARCH

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Subspecies in the global human gut microbiome

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

The dynamics of molecular evolution over 60,000 generations

(2017) Benjamin H. Good et al.   NATURE

Collective Phase in Resource Competition in a Highly Diverse Ecosystem

(2017) Mikhail Tikhonov et al.   PHYSICAL REVIEW LETTERS

Microbial consortia at steady supply

(2017) Thibaud Taillefumier et al.   eLife

Parallel evolution of influenza across multiple spatiotemporal scales

(2017) Katherine S Xue et al.   eLife

Recombination-Driven Genome Evolution and Stability of Bacterial Species

(2017) Purushottam D. Dixit et al.   GENETICS

Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling

(2017) Francesco Asnicar et al.   mSystems

The microbiome beyond the horizon of ecological and evolutionary theory

(2017) Britt Koskella et al.   Nature Ecology & Evolution

Bacterial Speciation: Genetic Sweeps in Bacterial Species

(2016) Frederick M. Cohan   CURRENT BIOLOGY

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

(2016) Stephen Nayfach et al.   GENOME RESEARCH

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

(2016) Matthew L Bendall et al.   ISME Journal

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

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

(2016) Hilary P. Browne et al.   NATURE

The evolution of cooperation within the gut microbiota

(2016) Seth Rakoff-Nahoum et al.   NATURE

Mobile genes in the human microbiome are structured from global to individual scales

(2016) I. L. Brito et al.   NATURE

Tempo and mode of genome evolution in a 50,000-generation experiment

(2016) Olivier Tenaillon et al.   NATURE

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

(2016) Matthias Scholz et al.   NATURE METHODS

Within-host evolution of bacterial pathogens

(2016) Xavier Didelot et al.   NATURE REVIEWS MICROBIOLOGY

MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples

(2016) Moreno Zolfo et al.   NUCLEIC ACIDS RESEARCH

Cospeciation of gut microbiota with hominids

(2016) A. H. Moeller et al.   SCIENCE

Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome

(2016) Hailiang Xie et al.   Cell Systems

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

(2015) Sharon Greenblum et al.   CELL

Genomic investigations of evolutionary dynamics and epistasis in microbial evolution experiments

(2015) Elizabeth R Jerison et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

ConStrains identifies microbial strains in metagenomic datasets

(2015) Chengwei Luo et al.   NATURE BIOTECHNOLOGY

Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome

(2015) Volodymyr Kuleshov et al.   NATURE BIOTECHNOLOGY

Gut biogeography of the bacterial microbiota

(2015) Gregory P. Donaldson et al.   NATURE REVIEWS MICROBIOLOGY

Recombinant transfer in the basic genome ofEscherichia coli

(2015) Purushottam D. Dixit et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche

(2015) M. J. Rosen et al.   SCIENCE

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

A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota

(2015) David J. Roach et al.   PLoS Genetics

Population genomics of intrapatient HIV-1 evolution

(2015) Fabio Zanini et al.   eLife

Temporal and technical variability of human gut metagenomes

(2015) Anita Y Voigt et al.   GENOME BIOLOGY

Inter-individual differences in the gene content of human gut bacterial species

(2015) Ana Zhu et al.   GENOME BIOLOGY

Bacteria from Diverse Habitats Colonize and Compete in the Mouse Gut

(2014) Henning Seedorf et al.   CELL

Deleterious Passengers in Adapting Populations

(2014) B. H. Good et al.   GENETICS

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

(2014) Mikhail Tikhonov et al.   ISME Journal

Ordering microbial diversity into ecologically and genetically cohesive units

(2014) B. Jesse Shapiro et al.   TRENDS IN MICROBIOLOGY

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

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

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

(2013) Gregory I. Lang et al.   NATURE

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures

(2013) Tami D Lieberman et al.   NATURE GENETICS

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli

(2013) Matthew D. Herron et al.   PLOS BIOLOGY

Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli

(2012) Xavier Didelot et al.   BMC GENOMICS

A framework for human microbiome research

(2012)   NATURE

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections

(2012) C. C. Traverse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Drift-barrier hypothesis and mutation-rate evolution

(2012) W. Sung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

In Situ Evolutionary Rate Measurements Show Ecological Success of Recently Emerged Bacterial Hybrids

(2012) V. J. Denef et al.   SCIENCE

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

Statistical genetics and evolution of quantitative traits

(2011) Richard A. Neher et al.   REVIEWS OF MODERN PHYSICS

Evidence that Adaptation in Drosophila Is Not Limited by Mutation at Single Sites

(2010) Talia Karasov 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

A comparison of homologous recombination rates in bacteria and archaea

(2008) Michiel Vos et al.   ISME Journal

Linkage disequilibrium — understanding the evolutionary past and mapping the medical future

(2008) Montgomery Slatkin   NATURE REVIEWS GENETICS

Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics

(2008) A. Koeppel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA