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

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

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Adaptive Evolution within Gut Microbiomes of Healthy People

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

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

(2019) Li Xie et al.   PLOS BIOLOGY

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

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

Assessing the benefits of horizontal gene transfer by laboratory evolution and genome sequencing

(2018) Hoi Yee Chu et al.   BMC EVOLUTIONARY BIOLOGY

Anti-CRISPR Phages Cooperate to Overcome CRISPR-Cas Immunity

(2018) Mariann Landsberger et al.   CELL

Current understanding of the human microbiome

(2018) Jack A Gilbert et al.   NATURE MEDICINE

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

It Takes a Village: Microbial Communities Thrive through Interactions and Metabolic Handoffs

(2018) Laura A. Hug et al.   mSystems

Function and functional redundancy in microbial systems

(2018) Stilianos Louca et al.   Nature Ecology & Evolution

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

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

Evolution of copper resistance in the kiwifruit pathogenPseudomonas syringaepv.actinidiaethrough acquisition of integrative conjugative elements and plasmids

(2017) Elena Colombi et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria

(2017) James P. J. Hall et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Carriage of type II toxin-antitoxin systems by the growing group of IncX plasmids

(2017) Paula Bustamante et al.   PLASMID

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

(2017) Martial Marbouty et al.   Science Advances

The microbiome beyond the horizon of ecological and evolutionary theory

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

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

(2016) Stefanie Widder et al.   ISME Journal

Sex speeds adaptation by altering the dynamics of molecular evolution

(2016) Michael J. McDonald et al.   NATURE

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Marine microbial community dynamics and their ecological interpretation

(2015) Jed A. Fuhrman et al.   NATURE REVIEWS MICROBIOLOGY

The MG-RAST metagenomics database and portal in 2015

(2015) Andreas Wilke et al.   NUCLEIC ACIDS RESEARCH

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

CDD: NCBI's conserved domain database

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

(2014) Martial Marbouty et al.   eLife

A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity

(2013) Kimberley D. Seed et al.   NATURE

Horizontal gene transfer and the evolution of bacterial and archaeal population structure

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Role and significance of beta-glucosidases in the hydrolysis of cellulose for bioethanol production

(2012) Reeta Rani Singhania et al.   BIORESOURCE TECHNOLOGY

Species Interactions Alter Evolutionary Responses to a Novel Environment

(2012) Diane Lawrence et al.   PLOS BIOLOGY

FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes

(2011) Beifang Niu et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Microbial diversity of cellulose hydrolysis

(2011) David B Wilson   CURRENT OPINION IN MICROBIOLOGY

Selfish genetic elements, genetic conflict, and evolutionary innovation

(2011) J. H. Werren   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Horizontal Gene Exchange in Environmental Microbiota

(2011) Rustam I. Aminov   Frontiers in Microbiology

Microbial Nitrogen Cycling Processes in Oxygen Minimum Zones

(2010) Phyllis Lam et al.   Annual Review of Marine Science

Darwinian evolution in the light of genomics

(2009) E. V. Koonin   NUCLEIC ACIDS RESEARCH

Horizontal gene transfer in evolution: facts and challenges

(2009) L. Boto   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Microbial contributions to climate change through carbon cycle feedbacks

(2008) Richard D Bardgett et al.   ISME Journal

Resistance, resilience, and redundancy in microbial communities

(2008) S. D. Allison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA