Local mobile gene pools rapidly cross species boundaries to create endemicity within global Vibrio cholerae populations.

PubWeight™: 1.47‹?› | Rank: Top 5%

🔗 View Article (PMC 3073641)

Published in MBio on April 12, 2011

Authors

Yan Boucher1, Otto X Cordero, Alison Takemura, Dana E Hunt, Klaus Schliep, Eric Bapteste, Philippe Lopez, Cheryl L Tarr, Martin F Polz

Author Affiliations

1: Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. yboucher@ualberta.ca

Articles citing this

Ecology drives a global network of gene exchange connecting the human microbiome. Nature (2011) 3.64

Horizontal gene transfer and the evolution of bacterial and archaeal population structure. Trends Genet (2013) 1.95

Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations. Proc Natl Acad Sci U S A (2012) 1.62

Integrons: past, present, and future. Microbiol Mol Biol Rev (2014) 1.23

The Vibrio cholerae type VI secretion system employs diverse effector modules for intraspecific competition. Nat Commun (2014) 1.15

Combining de novo and reference-guided assembly with scaffold_builder. Source Code Biol Med (2013) 1.11

Ordering microbial diversity into ecologically and genetically cohesive units. Trends Microbiol (2014) 1.10

Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution. ISME J (2014) 1.09

Evolutionary analyses of non-genealogical bonds produced by introgressive descent. Proc Natl Acad Sci U S A (2012) 1.07

Reproducibility of Vibrionaceae population structure in coastal bacterioplankton. ISME J (2012) 1.05

Fitness factors in vibrios: a mini-review. Microb Ecol (2013) 0.94

Indigenous Vibrio cholerae strains from a non-endemic region are pathogenic. Open Biol (2013) 0.89

Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees. Genome Biol Evol (2015) 0.86

Migration and horizontal gene transfer divide microbial genomes into multiple niches. Nat Commun (2015) 0.86

A model for the effect of homologous recombination on microbial diversification. Genome Biol Evol (2011) 0.86

High frequency of a novel filamentous phage, VCY φ, within an environmental Vibrio cholerae population. Appl Environ Microbiol (2011) 0.86

Shape and evolution of the fundamental niche in marine Vibrio. ISME J (2012) 0.83

Genomic and phenotypic characterization of Vibrio cholerae non-O1 isolates from a US Gulf Coast cholera outbreak. PLoS One (2014) 0.83

What Is Speciation? PLoS Genet (2016) 0.82

"Every Gene Is Everywhere but the Environment Selects": Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis. Genome Biol Evol (2016) 0.81

A genomic island integrated into recA of Vibrio cholerae contains a divergent recA and provides multi-pathway protection from DNA damage. Environ Microbiol (2014) 0.81

Grappling with Proteus: population level approaches to understanding microbial diversity. Front Microbiol (2012) 0.81

Integration of a laterally acquired gene into a cell network important for growth in a strain of Vibrio rotiferianus. BMC Microbiol (2011) 0.80

The Dynamics of Genetic Interactions between Vibrio metoecus and Vibrio cholerae, Two Close Relatives Co-Occurring in the Environment. Genome Biol Evol (2015) 0.79

Microbial Speciation. Cold Spring Harb Perspect Biol (2015) 0.78

A Small Number of Phylogenetically Distinct Clonal Complexes Dominate a Coastal Vibrio cholerae Population. Appl Environ Microbiol (2016) 0.78

Association mapping reveals novel serpentine adaptation gene clusters in a population of symbiotic Mesorhizobium. ISME J (2016) 0.78

Multiple Pathways of Genome Plasticity Leading to Development of Antibiotic Resistance. Antibiotics (Basel) (2013) 0.78

Sequential displacement of Type VI Secretion System effector genes leads to evolution of diverse immunity gene arrays in Vibrio cholerae. Sci Rep (2017) 0.78

Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions. BMC Genomics (2014) 0.77

The superintegron integrase and the cassette promoters are co-regulated in Vibrio cholerae. PLoS One (2014) 0.77

The evolutionary dynamics of integrons in changing environments. ISME J (2016) 0.77

Diversity of gene cassettes and the abundance of the class 1 integron-integrase gene in sediment polluted by metals. Extremophiles (2016) 0.76

Biogeography and evolution of Thermococcus isolates from hydrothermal vent systems of the Pacific. Front Microbiol (2015) 0.76

Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance. MBio (2017) 0.75

A genomic comparison of 13 symbiotic Vibrio fischeri isolates from the perspective of their host source and colonization behavior. ISME J (2016) 0.75

Ecological genomics of mutualism decline in nitrogen-fixing bacteria. Proc Biol Sci (2016) 0.75

Architecture of the superintegron in Vibrio cholerae: identification of core and unique genes. F1000Res (2013) 0.75

Bacterial Strain Diversity Within Wounds. Adv Wound Care (New Rochelle) (2015) 0.75

Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes. Front Microbiol (2017) 0.75

Articles cited by this

Basic local alignment search tool. J Mol Biol (1990) 659.07

MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (2006) 87.59

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res (2008) 52.43

The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics (2008) 29.20

Global climate and infectious disease: the cholera paradigm. Science (1996) 10.08

The general stochastic model of nucleotide substitution. J Theor Biol (1990) 9.25

Epidemiology, genetics, and ecology of toxigenic Vibrio cholerae. Microbiol Mol Biol Rev (1998) 8.36

Ecological relationships between Vibrio cholerae and planktonic crustacean copepods. Appl Environ Microbiol (1983) 7.52

Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures. Appl Environ Microbiol (2006) 6.45

Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science (2003) 6.42

Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature (2010) 5.08

Chitin induces natural competence in Vibrio cholerae. Science (2005) 5.00

Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae. Proc Natl Acad Sci U S A (2009) 4.80

Comparative genomics: the bacterial pan-genome. Curr Opin Microbiol (2008) 4.40

Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet (2005) 4.19

Explaining microbial population genomics through phage predation. Nat Rev Microbiol (2009) 3.87

A distinctive class of integron in the Vibrio cholerae genome. Science (1998) 3.86

Evolution of new variants of Vibrio cholerae O1. Trends Microbiol (2009) 3.75

Cholera transmission: the host, pathogen and bacteriophage dynamic. Nat Rev Microbiol (2009) 2.79

Characterization and pathogenic significance of Vibrio vulnificus antigens preferentially expressed in septicemic patients. Infect Immun (2003) 2.69

Genomic characterization of non-O1, non-O139 Vibrio cholerae reveals genes for a type III secretion system. Proc Natl Acad Sci U S A (2005) 2.65

Estimating the size of the bacterial pan-genome. Trends Genet (2009) 2.61

Off the hook--how bacteria survive protozoan grazing. Trends Microbiol (2005) 2.59

The SOS response controls integron recombination. Science (2009) 2.27

A statistical toolbox for metagenomics: assessing functional diversity in microbial communities. BMC Bioinformatics (2008) 2.17

Mosaic bacterial chromosomes: a challenge en route to a tree of genomes. Bioessays (1999) 2.04

Global impact of Vibrio cholerae interactions with chitin. Environ Microbiol (2008) 1.98

Biogeography of the Sulfolobus islandicus pan-genome. Proc Natl Acad Sci U S A (2009) 1.95

A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Res (2007) 1.85

Structural basis for broad DNA-specificity in integron recombination. Nature (2006) 1.79

Widespread metabolic potential for nitrite and nitrate assimilation among Prochlorococcus ecotypes. Proc Natl Acad Sci U S A (2009) 1.72

Evolutionary genetic analysis of the emergence of epidemic Vibrio cholerae isolates on the basis of comparative nucleotide sequence analysis and multilocus virulence gene profiles. J Clin Microbiol (2004) 1.46

Conservation of the chitin utilization pathway in the Vibrionaceae. Appl Environ Microbiol (2007) 1.40

Metapopulation structure of Vibrionaceae among coastal marine invertebrates. Environ Microbiol (2010) 1.34

Population genomics: diversity and virulence in the Neisseria. Curr Opin Microbiol (2008) 1.34

Identification of Vibrio isolates by a multiplex PCR assay and rpoB sequence determination. J Clin Microbiol (2006) 1.31

Integrons in Xanthomonas: a source of species genome diversity. Proc Natl Acad Sci U S A (2005) 1.30

Conjugative DNA transfer induces the bacterial SOS response and promotes antibiotic resistance development through integron activation. PLoS Genet (2010) 1.28

Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio. BMC Evol Biol (2006) 1.23

Use of recA as an alternative phylogenetic marker in the family Vibrionaceae. Int J Syst Evol Microbiol (2004) 1.20

On the origins of a Vibrio species. Microb Ecol (2010) 1.13

Maximum-likelihood analysis using TREE-PUZZLE. Curr Protoc Bioinformatics (2007) 1.08

Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae. BMC Microbiol (2010) 1.08

Use of chromosomal integron arrays as a phylogenetic typing system for Vibrio cholerae pandemic strains. Microbiology (2007) 1.02

Biogeography of the ubiquitous marine bacterium Alteromonas macleodii determined by multilocus sequence analysis. Mol Ecol (2008) 1.01

ACID: annotation of cassette and integron data. BMC Bioinformatics (2009) 0.93

Articles by these authors

Fine-scale phylogenetic architecture of a complex bacterial community. Nature (2004) 8.99

Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol (2004) 7.98

Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'. Nucleic Acids Res (2002) 6.07

PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl Environ Microbiol (2005) 5.97

Phylogenomics revives traditional views on deep animal relationships. Curr Biol (2009) 5.89

Population genomics of early events in the ecological differentiation of bacteria. Science (2012) 4.67

Genotypic diversity within a natural coastal bacterioplankton population. Science (2005) 4.06

Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol Biol Evol (2004) 3.65

Ecology drives a global network of gene exchange connecting the human microbiome. Nature (2011) 3.64

Pattern pluralism and the Tree of Life hypothesis. Proc Natl Acad Sci U S A (2007) 3.56

Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science (2008) 3.46

The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils? Proc Natl Acad Sci U S A (2004) 3.33

The bacterial species challenge: making sense of genetic and ecological diversity. Science (2009) 2.88

Rapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches. Proc Natl Acad Sci U S A (2008) 2.70

The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc Natl Acad Sci U S A (2002) 2.64

Ecological populations of bacteria act as socially cohesive units of antibiotic production and resistance. Science (2012) 2.28

Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti. MBio (2013) 2.24

High overall diversity and dominance of microdiverse relationships in salt marsh sulphate-reducing bacteria. Environ Microbiol (2004) 2.15

Eubacterial phylogeny based on translational apparatus proteins. Trends Genet (2002) 1.95

Diversity and dynamics of a north atlantic coastal Vibrio community. Appl Environ Microbiol (2004) 1.79

Network analyses structure genetic diversity in independent genetic worlds. Proc Natl Acad Sci U S A (2009) 1.73

DNA phosphorothioation is widespread and quantized in bacterial genomes. Proc Natl Acad Sci U S A (2011) 1.69

Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Philos Trans R Soc Lond B Biol Sci (2006) 1.65

A simple and efficient method for concentration of ocean viruses by chemical flocculation. Environ Microbiol Rep (2011) 1.64

Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations. Proc Natl Acad Sci U S A (2012) 1.62

Pyrococcus genome comparison evidences chromosome shuffling-driven evolution. Nucleic Acids Res (2002) 1.58

Multistate outbreak of listeriosis associated with cantaloupe. N Engl J Med (2013) 1.49

Effects of temperature and salinity on Vibrio vulnificus population dynamics as assessed by quantitative PCR. Appl Environ Microbiol (2004) 1.45

Spatial distribution and stability of the eight microbial species of the altered schaedler flora in the mouse gastrointestinal tract. Appl Environ Microbiol (2004) 1.45

Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement. BMC Evol Biol (2005) 1.43

Conservation of the chitin utilization pathway in the Vibrionaceae. Appl Environ Microbiol (2007) 1.40

Establishment and maintenance of planar epithelial cell polarity by asymmetric cadherin bridges: a computer model. Dev Dyn (2006) 1.35

Metapopulation structure of Vibrionaceae among coastal marine invertebrates. Environ Microbiol (2010) 1.34

A selective barrier to horizontal gene transfer in the T4-type bacteriophages that has preserved a core genome with the viral replication and structural genes. Mol Biol Evol (2006) 1.29

Genome sequence of Vibrio splendidus: an abundant planctonic marine species with a large genotypic diversity. Environ Microbiol (2009) 1.29

Colonization dynamics of altered Schaedler flora is influenced by gender, aging, and Helicobacter hepaticus infection in the intestines of Swiss Webster mice. Appl Environ Microbiol (2006) 1.29

Homeodomain proteins belong to the ancestral molecular toolkit of eukaryotes. Evol Dev (2007) 1.26

The potential value of indels as phylogenetic markers: position of trichomonads as a case study. Mol Biol Evol (2002) 1.24

Evaluation of 23S rRNA PCR primers for use in phylogenetic studies of bacterial diversity. Appl Environ Microbiol (2006) 1.22

Solar disinfection (SODIS): simulation of solar radiation for global assessment and application for point-of-use water treatment in Haiti. Water Res (2003) 1.22

The coastal environment and human health: microbial indicators, pathogens, sentinels and reservoirs. Environ Health (2008) 1.18

Toxigenic Vibrio cholerae O1 in water and seafood, Haiti. Emerg Infect Dis (2011) 1.16

Merging taxonomy with ecological population prediction in a case study of Vibrionaceae. Appl Environ Microbiol (2011) 1.14

Gene similarity networks provide tools for understanding eukaryote origins and evolution. Proc Natl Acad Sci U S A (2013) 1.12

Extensive variation in intracellular symbiont community composition among members of a single population of the wood-boring bivalve Lyrodus pedicellatus (Bivalvia: Teredinidae). Appl Environ Microbiol (2006) 1.11

Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sediments. Environ Microbiol (2008) 1.11

Natural selection of the major histocompatibility complex (Mhc) in Hawaiian honeycreepers (Drepanidinae). Mol Ecol (2004) 1.08

Evolutionary analyses of non-genealogical bonds produced by introgressive descent. Proc Natl Acad Sci U S A (2012) 1.07

Adaptation and spectral tuning in divergent marine proteorhodopsins from the eastern Mediterranean and the Sargasso Seas. ISME J (2007) 1.06

Reproducibility of Vibrionaceae population structure in coastal bacterioplankton. ISME J (2012) 1.05

Competition-dispersal tradeoff ecologically differentiates recently speciated marine bacterioplankton populations. Proc Natl Acad Sci U S A (2014) 1.05

HF2: a double-stranded DNA tailed haloarchaeal virus with a mosaic genome. Mol Microbiol (2002) 1.05

Sequencing-independent method to generate oligonucleotide probes targeting a variable region in bacterial 16S rRNA by PCR with detachable primers. Appl Environ Microbiol (2002) 1.02

Evolution of the RNA polymerase B' subunit gene (rpoB') in Halobacteriales: a complementary molecular marker to the SSU rRNA gene. Mol Biol Evol (2004) 1.02

Molecular phylogeny in mytilids supports the wooden steps to deep-sea vents hypothesis. C R Biol (2007) 1.02

Evolution of rhodopsin ion pumps in haloarchaea. BMC Evol Biol (2007) 1.00

Population structure of Listeria monocytogenes serotype 4b isolates from sporadic human listeriosis cases in the United States from 2003 to 2008. Appl Environ Microbiol (2014) 0.99

Harvesting evolutionary signals in a forest of prokaryotic gene trees. Mol Biol Evol (2010) 0.98

The Public Goods Hypothesis for the evolution of life on Earth. Biol Direct (2011) 0.96

Accurately quantifying low-abundant targets amid similar sequences by revealing hidden correlations in oligonucleotide microarray data. Proc Natl Acad Sci U S A (2006) 0.95

Vibrio chromosomes share common history. BMC Microbiol (2010) 0.95

Molecular phylogeny: reconstructing the forest. C R Biol (2008) 0.94

O-antigen diversity and lateral transfer of the wbe region among Vibrio splendidus isolates. Environ Microbiol (2010) 0.94

ACID: annotation of cassette and integron data. BMC Bioinformatics (2009) 0.93

A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment. BMC Genomics (2009) 0.93

Let them fall where they may: congruence analysis in massive phylogenetically messy data sets. Mol Biol Evol (2011) 0.91

Heterotachy and functional shift in protein evolution. IUBMB Life (2003) 0.91

Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli. Biol Direct (2011) 0.90

Diversity of active marine picoeukaryotes in the Eastern Mediterranean Sea unveiled using photosystem-II psbA transcripts. ISME J (2010) 0.90

Evolutionary plasticity of methionine biosynthesis. Gene (2005) 0.90

Microbial taxonomy in the post-genomic era: rebuilding from scratch? Arch Microbiol (2014) 0.90

Emerging contaminant or an old toxin in disguise? Silver nanoparticle impacts on ecosystems. Environ Sci Technol (2014) 0.89

A pluralistic account of homology: adapting the models to the data. Mol Biol Evol (2013) 0.89

Horizontal gene transfer and the evolution of cnidarian stinging cells. Curr Biol (2008) 0.89

Distinct dissolved organic matter sources induce rapid transcriptional responses in coexisting populations of Prochlorococcus, Pelagibacter and the OM60 clade. Environ Microbiol (2013) 0.89

Some considerations for analyzing biodiversity using integrative metagenomics and gene networks. Biol Direct (2010) 0.89

Functional divergence prediction from evolutionary analysis: a case study of vertebrate hemoglobin. Mol Biol Evol (2003) 0.89

The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea. J Bacteriol (2009) 0.88

EGN: a wizard for construction of gene and genome similarity networks. BMC Evol Biol (2013) 0.87

High frequency of a novel filamentous phage, VCY φ, within an environmental Vibrio cholerae population. Appl Environ Microbiol (2011) 0.86

Clanistics: a multi-level perspective for harvesting unrooted gene trees. Trends Microbiol (2010) 0.85