Selection Is a Significant Driver of Gene Gain and Loss in the Pangenome of the Bacterial Genus Sulfurovum in Geographically Distinct Deep-Sea Hydrothermal Vents

Fluid geochemistry, local hydrology, and metabolic activity define methanogen community size and composition in deep-sea hydrothermal vents

(2019) Lucy C. Stewart et al.   ISME Journal

Genome‐resolved metagenomics and metatranscriptomics reveal niche differentiation in functionally redundant microbial communities at deep‐sea hydrothermal vents

(2019) David Galambos et al.   ENVIRONMENTAL MICROBIOLOGY

Linking pangenomes and metagenomes: the Prochlorococcus metapangenome

(2018) Tom O. Delmont et al.   PeerJ

Spatially distinct, temporally stable microbial populations mediate biogeochemical cycling at and below the seafloor in hydrothermal vent fluids

(2017) Caroline S. Fortunato et al.   ENVIRONMENTAL MICROBIOLOGY

Structured Populations of Sulfolobus acidocaldarius with Susceptibility to Mobile Genetic Elements

(2017) Rika E. Anderson et al.   Genome Biology and Evolution

Prokaryote genome fluidity is dependent on effective population size

(2017) Nadia Andrea Andreani et al.   ISME Journal

Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents

(2017) Dimitri V Meier et al.   ISME Journal

Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents

(2017) Rika E. Anderson et al.   Nature Communications

Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species

(2016) Jeanneth Mosquera-Rendón et al.   BMC GENOMICS

Flexible genomic islands as drivers of genome evolution

(2016) Francisco Rodriguez-Valera et al.   CURRENT OPINION IN MICROBIOLOGY

Subseafloor microbial communities in hydrogen-rich vent fluids from hydrothermal systems along the Mid-Cayman Rise

(2016) Julie Reveillaud et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2016) Matthew L Bendall et al.   ISME Journal

Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection

(2015) Nobuto Takeuchi et al.   BMC BIOLOGY

Ten years of pan-genome analyses

(2015) George Vernikos et al.   CURRENT OPINION IN MICROBIOLOGY

Pathways for abiotic organic synthesis at submarine hydrothermal fields

(2015) Jill M. McDermott et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biogeography and evolution of Thermococcus isolates from hydrothermal vent systems of the Pacific

(2015) Mark T. Price et al.   Frontiers in Microbiology

Metagenomic insights into S(0) precipitation in a terrestrial subsurface lithoautotrophic ecosystem

(2015) Trinity L. Hamilton et al.   Frontiers in Microbiology

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

ITEP: An integrated toolkit for exploration of microbial pan-genomes

(2014) Matthew N Benedict et al.   BMC GENOMICS

Microbial consumption of zero-valence sulfur in marine benthic habitats

(2014) Petra Pjevac et al.   ENVIRONMENTAL MICROBIOLOGY

Explaining microbial genomic diversity in light of evolutionary ecology

(2014) Otto X. Cordero et al.   NATURE REVIEWS MICROBIOLOGY

Evolutionary Strategies of Viruses, Bacteria and Archaea in Hydrothermal Vent Ecosystems Revealed through Metagenomics

(2014) Rika E. Anderson et al.   PLoS One

Antibacterial gene transfer across the tree of life

(2014) Jason A Metcalf et al.   eLife

Pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria

(2014) Ying Zhang et al.   Frontiers in Microbiology

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano

(2013) Julie L Meyer et al.   ISME Journal

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology

(2013) A. Murat Eren et al.   PLoS One

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

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

Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote

(2013) G. Schonknecht et al.   SCIENCE

Phylogenetic diversity and functional gene patterns of sulfur-oxidizing subseafloor Epsilonproteobacteria in diffuse hydrothermal vent fluids

(2013) Nancy H. Akerman et al.   Frontiers in Microbiology

Biogeography of Persephonella in deep-sea hydrothermal vents of the Western Pacific

(2013) Sayaka Mino et al.   Frontiers in Microbiology

Microbiological characterization of post-eruption “snowblower” vents at Axial Seamount, Juan de Fuca Ridge

(2013) Julie L. Meyer et al.   Frontiers in Microbiology

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Microbial community structure across fluid gradients in the Juan de Fuca Ridge hydrothermal system

(2012) Rika E. Anderson et al.   FEMS MICROBIOLOGY ECOLOGY

How Bacterial Lineages Emerge

(2012) R. T. Papke et al.   SCIENCE

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

Feedback Interactions between Trace Metal Nutrients and Phytoplankton in the Ocean

(2012) William G. Sunda   Frontiers in Microbiology

Bacterial species may exist, metagenomics reveal

(2011) Alejandro Caro-Quintero et al.   ENVIRONMENTAL MICROBIOLOGY

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

(2011) O. Popa et al.   GENOME RESEARCH

Core and Panmetabolism in Escherichia coli

(2011) G. Vieira et al.   JOURNAL OF BACTERIOLOGY

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

(2011) Chris S. Smillie et al.   NATURE

Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones

(2011) J. Grote et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

(2011) Todd J. Treangen et al.   PLoS Genetics

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries

(2010) Wei Xie et al.   ISME Journal

Genetic diversity and connectivity of deep-sea hydrothermal vent metapopulations

(2010) ROBERT C. VRIJENHOEK   MOLECULAR ECOLOGY

Metagenomic Comparison of Two Thiomicrospira Lineages Inhabiting Contrasting Deep-Sea Hydrothermal Environments

(2010) William J. Brazelton et al.   PLoS One

Ecosystem-specific selection pressures revealed through comparative population genomics

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

Diverse styles of submarine venting on the ultraslow spreading Mid-Cayman Rise

(2010) C. R. German et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High Frequency of Horizontal Gene Transfer in the Oceans

(2010) L. D. McDaniel et al.   SCIENCE

Why Genes Evolve Faster on Secondary Chromosomes in Bacteria

(2010) Vaughn S. Cooper et al.   PLoS Computational Biology

Phylogenetic diversity of transition and anoxic zone bacterial communities within a near-shore anoxic basin: Nitinat Lake

(2009) Jana Schmidtova et al.   ENVIRONMENTAL MICROBIOLOGY

Individual hydrothermal vents at Axial Seamount harbor distinct subseafloor microbial communities

(2009) Andrew D. Opatkiewicz et al.   FEMS MICROBIOLOGY ECOLOGY

Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm

(2009) William J Brazelton et al.   ISME Journal

Explaining microbial population genomics through phage predation

(2009) Francisco Rodriguez-Valera et al.   NATURE REVIEWS MICROBIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY

Graph Clustering Via a Discrete Uncoupling Process

(2008) Stijn Van Dongen   SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS

The Population Genetics of dN/dS

(2008) Sergey Kryazhimskiy et al.   PLoS Genetics