The microbiome beyond the horizon of ecological and evolutionary theory

Salivary mucins promote the coexistence of competing oral bacterial species

(2017) Erica Shapiro Frenkel et al.   ISME Journal

Ecology of the Oral Microbiome: Beyond Bacteria

(2017) Jonathon L. Baker et al.   TRENDS IN MICROBIOLOGY

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

(2017) Mathieu Groussin et al.   Nature Communications

Rapid adaptation drives invasion of airway donor microbiota by Pseudomonas after lung transplantation

(2017) M. Beaume et al.   Scientific Reports

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

(2016) Tommi Vatanen et al.   CELL

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility

(2016) Mahesh S. Desai 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

The Host Shapes the Gut Microbiota via Fecal MicroRNA

(2016) Shirong Liu et al.   Cell Host & Microbe

Genetic Determinants of the Gut Microbiome in UK Twins

(2016) Julia K. Goodrich et al.   Cell Host & Microbe

Ecological similarity is related to phylogenetic distance between species in a cross-niche field transplant experiment

(2016) Brian L. Anacker et al.   ECOLOGY

Prevalence and genetic diversity of Blastocystis in family units living in the United States

(2016) Pauline D. Scanlan et al.   INFECTION GENETICS AND EVOLUTION

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

(2016) Stefanie Widder et al.   ISME Journal

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

(2016) Hilary P. Browne et al.   NATURE

Biogeography of a human oral microbiome at the micron scale

(2016) Jessica L. Mark Welch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

How colonization by microbiota in early life shapes the immune system

(2016) Thomas Gensollen et al.   SCIENCE

Adapting Koch's postulates

(2016) A. L. Byrd et al.   SCIENCE

Cospeciation of gut microbiota with hominids

(2016) A. H. Moeller et al.   SCIENCE

Functional Redundancy-Induced Stability of Gut Microbiota Subjected to Disturbance

(2016) Andrés Moya et al.   TRENDS IN MICROBIOLOGY

Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

(2016) Matthew T. Agler et al.   PLOS BIOLOGY

Species–function relationships shape ecological properties of the human gut microbiome

(2016) Sara Vieira-Silva 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

Exploring Vertical Transmission of Bifidobacteria from Mother to Child

(2015) Christian Milani et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The cystic fibrosis microbiome in an ecological perspective and its impact in antibiotic therapy

(2015) Andreia P. Magalhães et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Determining the Long-term Effect of Antibiotic Administration on the Human Normal Intestinal Microbiota Using Culture and Pyrosequencing Methods

(2015) Mamun-Ur Rashid et al.   CLINICAL INFECTIOUS DISEASES

The cost of phage resistance in a plant pathogenic bacterium is context-dependent

(2015) Sean Meaden et al.   EVOLUTION

Bacterial predation in a marine host-associated microbiome

(2015) Rory M Welsh et al.   ISME Journal

Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development

(2015) Adam R Burns et al.   ISME Journal

Patterns, causes and consequences of defensive microbiome dynamics across multiple scales

(2015) Andrew H. Smith et al.   MOLECULAR ECOLOGY

The importance of the microbiome of the plant holobiont

(2015) Philippe Vandenkoornhuyse et al.   NEW PHYTOLOGIST

Library preparation methodology can influence genomic and functional predictions in human microbiome research

(2015) Marcus B. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Backbones of evolutionary history test biodiversity theory for microbes

(2015) James P. O’Dwyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antimicrobial peptide resistance mediates resilience of prominent gut commensals during inflammation

(2015) T. W. Cullen et al.   SCIENCE

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

Interchange of entire communities: microbial community coalescence

(2015) Matthias C. Rillig et al.   TRENDS IN ECOLOGY & EVOLUTION

Application of a Neutral Community Model To Assess Structuring of the Human Lung Microbiome

(2015) Arvind Venkataraman et al.   mBio

The Upper Respiratory Tract as a Microbial Source for Pulmonary Infections in Cystic Fibrosis. Parallels from Island Biogeography

(2014) Katrine L. Whiteson et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

Bacteria from Diverse Habitats Colonize and Compete in the Mouse Gut

(2014) Henning Seedorf et al.   CELL

Adhesion as a weapon in microbial competition

(2014) Jonas Schluter et al.   ISME Journal

A single genus in the gut microbiome reflects host preference and specificity

(2014) A Murat Eren et al.   ISME Journal

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Rapid changes in the gut microbiome during human evolution

(2014) Andrew H. Moeller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tipping elements in the human intestinal ecosystem

(2014) Leo Lahti et al.   Nature Communications

Microbial Succession in the Gut: Directional Trends of Taxonomic and Functional Change in a Birth Cohort of Spanish Infants

(2014) Yvonne Vallès et al.   PLoS Genetics

Phage-Mediated Selection on Microbiota of a Long-Lived Host

(2013) Britt Koskella   CURRENT BIOLOGY

Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome

(2013) Sheetal R. Modi et al.   NATURE

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

(2013) R. Levy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut

(2013) A. Reyes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacteriophage adhering to mucus provide a non-host-derived immunity

(2013) J. J. Barr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development of intestinal microbiota in infants and its impact on health

(2013) Sebastien Matamoros et al.   TRENDS IN MICROBIOLOGY

Ecological interactions drive evolutionary loss of traits

(2012) Jacintha Ellers et al.   ECOLOGY LETTERS

Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood

(2012) S. S. Stahringer et al.   GENOME RESEARCH

The human microbiome: A hot spot of microbial horizontal gene transfer

(2012) Li Liu et al.   GENOMICS

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes

(2012) P. Jeraldo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Density-dependent fitness benefits in quorum-sensing bacterial populations

(2012) S. E. Darch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Application of Ecological Theory Toward an Understanding of the Human Microbiome

(2012) E. K. Costello et al.   SCIENCE

Kinetic modelling of lactate utilization and butyrate production by key human colonic bacterial species

(2011) Rafael Muñoz-Tamayo et al.   FEMS MICROBIOLOGY ECOLOGY

Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome

(2011) David T Pride et al.   ISME Journal

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

(2011) Chris S. Smillie et al.   NATURE

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

(2011) S. Greenblum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial community assembly based on functional genes rather than species

(2011) C. Burke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Antibacterial Lectin RegIII  Promotes the Spatial Segregation of Microbiota and Host in the Intestine

(2011) S. Vaishnava et al.   SCIENCE

Phenotypic and genotypic analyses of lactic acid bacteria in local fermented food, breast milk and faeces of mothers and their babies

(2011) Rima Albesharat et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Human milk glycobiome and its impact on the infant gastrointestinal microbiota

(2010) A. M. Zivkovic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Succession of microbial consortia in the developing infant gut microbiome

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

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

(2010) M. G. Dominguez-Bello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

What are the consequences of the disappearing human microbiota?

(2009) Martin J. Blaser et al.   NATURE REVIEWS MICROBIOLOGY