Toward a dynamical understanding of microbial communities

Ecological scaffolding and the evolution of individuality

(2020) Andrew J. Black et al.   Nature Ecology & Evolution

Experimental manipulation of selfish genetic elements links genes to microbial community function

(2020) Steven D. Quistad et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

Adaptive Evolution within Gut Microbiomes of Healthy People

(2019) Shijie Zhao et al.   Cell Host & Microbe

Ultra-deep, long-read nanopore sequencing of mock microbial community standards

(2019) Samuel M Nicholls et al.   GigaScience

Simulations reveal challenges to artificial community selection and possible strategies for success

(2019) Li Xie et al.   PLOS BIOLOGY

The Landscape of Genetic Content in the Gut and Oral Human Microbiome

(2019) Braden T. Tierney et al.   Cell Host & Microbe

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

Artificially selecting microbial communities: If we can breed dogs, why not microbiomes?

(2019) Flor I. Arias-Sánchez et al.   PLOS BIOLOGY

High-order interactions distort the functional landscape of microbial consortia

(2019) Alicia Sanchez-Gorostiaga et al.   PLOS BIOLOGY

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

Processes and patterns of interaction as units of selection: An introduction to ITSNTS thinking

(2018) W. Ford Doolittle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Advantages of meta-total RNA sequencing (MeTRS) over shotgun metagenomics and amplicon-based sequencing in the profiling of complex microbial communities

(2018) Fabien Cottier et al.   npj Biofilms and Microbiomes

Model Microbial Consortia as Tools for Understanding Complex Microbial Communities

(2018) Shin Haruta et al.   CURRENT GENOMICS

Experimental bacterial adaptation to the zebrafish gut reveals a primary role for immigration

(2018) Catherine D. Robinson et al.   PLOS BIOLOGY

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease

(2017) Giovanni Bacci et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Coupling between distant biofilms and emergence of nutrient time-sharing

(2017) Jintao Liu et al.   SCIENCE

Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium

(2017) Elham Karimi et al.   Frontiers in Microbiology

Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay

(2017) Martial Marbouty et al.   Science Advances

Diverse modes of eco-evolutionary dynamics in communities of antibiotic-producing microorganisms

(2017) Kalin Vetsigian   Nature Ecology & Evolution

Predicting evolution

(2017) Michael Lässig et al.   Nature Ecology & Evolution

It’s the song, not the singer: an exploration of holobiosis and evolutionary theory

(2016) W. Ford Doolittle et al.   BIOLOGY & PHILOSOPHY

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

(2016) Stephen Nayfach et al.   GENOME RESEARCH

Sex speeds adaptation by altering the dynamics of molecular evolution

(2016) Michael J. McDonald et al.   NATURE

Not So Simple After All: Bacteria, Their Population Genetics, and Recombination

(2016) William P. Hanage   Cold Spring Harbor Perspectives in Biology

VIP: an integrated pipeline for metagenomics of virus identification and discovery

(2016) Yang Li et al.   Scientific Reports

Quantitative evolutionary dynamics using high-resolution lineage tracking

(2015) Sasha F. Levy et al.   NATURE

ConStrains identifies microbial strains in metagenomic datasets

(2015) Chengwei Luo et al.   NATURE BIOTECHNOLOGY

Metagenome Analysis Exploiting High-Throughput Chromosome Conformation Capture (3C) Data

(2015) Martial Marbouty et al.   TRENDS IN GENETICS

The pan-genome as a shared genomic resource: mutual cheating, cooperation and the black queen hypothesis

(2015) Matthew S. Fullmer et al.   Frontiers in Microbiology

Resolving Conflicts During the Evolutionary Transition to Multicellular Life

(2014) Paul B. Rainey et al.   Annual Review of Ecology Evolution and Systematics

Life cycles, fitness decoupling and the evolution of multicellularity

(2014) Katrin Hammerschmidt et al.   NATURE

Pervasive domestication of defective prophages by bacteria

(2014) L.-M. Bobay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms

(2014) Martial Marbouty et al.   eLife

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

(2013) Tomáš Větrovský et al.   PLoS One

Comparative Metagenomics of Two Microbial Mats at Cuatro Ciénegas Basin II: Community Structure and Composition in Oligotrophic Environments

(2012) Germán Bonilla-Rosso et al.   ASTROBIOLOGY

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

Species Interactions Alter Evolutionary Responses to a Novel Environment

(2012) Diane Lawrence et al.   PLOS BIOLOGY

Microbial control over carbon cycling in soil

(2012) Joshua P. Schimel et al.   Frontiers in Microbiology

Structure and Evolution of Streptomyces Interaction Networks in Soil and In Silico

(2011) Kalin Vetsigian et al.   PLOS BIOLOGY

Bacterial competition: surviving and thriving in the microbial jungle

(2009) Michael E. Hibbing et al.   NATURE REVIEWS MICROBIOLOGY