The evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract

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

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

(2017) Mathieu Groussin et al.   Nature Communications

Microbial Reconstitution Reverses Maternal Diet-Induced Social and Synaptic Deficits in Offspring

(2016) Shelly A. Buffington et al.   CELL

Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome

(2016) María X. Maldonado-Gómez et al.   Cell Host & Microbe

Distinct gene expression profile of Xanthomonas retroflexus engaged in synergistic multispecies biofilm formation

(2016) Lea Benedicte Skov Hansen et al.   ISME Journal

The evolution of cooperation within the gut microbiota

(2016) Seth Rakoff-Nahoum et al.   NATURE

Cospeciation of gut microbiota with hominids

(2016) A. H. Moeller et al.   SCIENCE

Evolving Perspectives on Monopolization and Priority Effects

(2016) Luc De Meester et al.   TRENDS IN ECOLOGY & EVOLUTION

Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History

(2016) Andrew W. Brooks et al.   PLOS BIOLOGY

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

(2016) Ilias Lagkouvardos et al.   Nature Microbiology

Historical Contingency in Community Assembly: Integrating Niches, Species Pools, and Priority Effects

(2015) Tadashi Fukami   Annual Review of Ecology Evolution and Systematics

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Interspecies interactions result in enhanced biofilm formation by co-cultures of bacteria isolated from a food processing environment

(2015) Henriette L. Røder et al.   FOOD MICROBIOLOGY

The ImageJ ecosystem: An open platform for biomedical image analysis

(2015) Johannes Schindelin et al.   MOLECULAR REPRODUCTION AND DEVELOPMENT

Lactobacilli with probiotic potential in the prairie vole (Microtus ochrogaster)

(2015) Senait Assefa et al.   Gut Pathogens

The Gut Microbiota of Wild Mice

(2015) Laura Weldon et al.   PLoS One

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Lactobacillus rodentium sp. nov., from the digestive tract of wild rodents

(2014) J. Killer et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

High prevalence of biofilm synergy among bacterial soil isolates in cocultures indicates bacterial interspecific cooperation

(2014) Dawei Ren et al.   ISME Journal

Synergistic interactions in mixed-species biofilms of pathogenic bacteria from the respiratory tract

(2014) Maryam Varposhti et al.   Revista da Sociedade Brasileira de Medicina Tropical

Ecological opportunity and the adaptive diversification of lineages

(2014) Gary A. Wellborn et al.   Ecology and Evolution

Gene expression of lactobacilli in murine forestomach biofilms

(2014) Clarissa Schwab et al.   Microbial Biotechnology

The Gastrointestinal Tract of the White-Throated Woodrat (Neotoma albigula) Harbors Distinct Consortia of Oxalate-Degrading Bacteria

(2013) Aaron W. Miller et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

BayesHammer: Bayesian clustering for error correction in single-cell sequencing

(2013) Sergey I Nikolenko et al.   BMC GENOMICS

Drivers of population genetic differentiation in the wild: isolation by dispersal limitation, isolation by adaptation and isolation by colonization

(2013) Luisa Orsini et al.   MOLECULAR ECOLOGY

The role of biogeography in shaping diversity of the intestinal microbiota in house mice

(2013) Miriam Linnenbrink et al.   MOLECULAR ECOLOGY

Porphyromonas gingivalis and Treponema denticola Synergistic Polymicrobial Biofilm Development

(2013) Ying Zhu et al.   PLoS One

Molecular Characterization of Host-Specific Biofilm Formation in a Vertebrate Gut Symbiont

(2013) Steven A. Frese et al.   PLoS Genetics

A glimpse on the pattern of rodent diversification: a phylogenetic approach

(2012) Pierre-Henri Fabre et al.   BMC EVOLUTIONARY BIOLOGY

Indication for Co-evolution of Lactobacillus johnsonii with its hosts

(2012) Keren Buhnik-Rosenblau et al.   BMC MICROBIOLOGY

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

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

Familial transmission rather than defective innate immunity shapes the distinct intestinal microbiota of TLR-deficient mice

(2012) Carles Ubeda et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Resource partitioning in relation to cohabitation of Lactobacillus species in the mouse forestomach

(2011) Gerald W Tannock et al.   ISME Journal

Phylogeny and fitness of Vibrio fischeri from the light organs of Euprymna scolopes in two Oahu, Hawaii populations

(2011) Michael S Wollenberg et al.   ISME Journal

An Improved Likelihood Ratio Test for Detecting Site-Specific Functional Divergence among Clades of Protein-Coding Genes

(2011) Cameron J. Weadick et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Evolution of Host Specialization in the Vertebrate Gut Symbiont Lactobacillus reuteri

(2011) Steven A. Frese et al.   PLoS Genetics

The population genetics of commensal Escherichia coli

(2010) Olivier Tenaillon et al.   NATURE REVIEWS MICROBIOLOGY

Gut Microbiota in Health and Disease

(2010) Inna Sekirov et al.   PHYSIOLOGICAL REVIEWS

Host-microbial symbiosis in the vertebrate gastrointestinal tract and the Lactobacillus reuteri paradigm

(2010) J. Walter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A species concept for bacteria based on adaptive divergence

(2010) Michiel Vos   TRENDS IN MICROBIOLOGY

Evolutionary Relationships of Wild Hominids Recapitulated by Gut Microbial Communities

(2010) Howard Ochman et al.   PLOS BIOLOGY

Lactobacillus taiwanensis sp. nov., isolated from silage

(2009) L.-T. Wang et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution

(2009) Phaik Lyn Oh et al.   ISME Journal

The evolution of facilitation and mutualism

(2009) Judith L. Bronstein   JOURNAL OF ECOLOGY

Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations

(2008) Jukka Corander et al.   BMC BIOINFORMATICS

Glucosyltransferase A (GtfA) and inulosucrase (Inu) of Lactobacillus reuteri TMW1.106 contribute to cell aggregation, in vitro biofilm formation, and colonization of the mouse gastrointestinal tract

(2008) J. Walter et al.   MICROBIOLOGY-SGM

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE