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  • 1
    Publication Date: 2012-04-12
    Description: Genetic exchange is common among bacteria, but its effect on population diversity during ecological differentiation remains controversial. A fundamental question is whether advantageous mutations lead to selection of clonal genomes or, as in sexual eukaryotes, sweep through populations on their own. Here, we show that in two recently diverged populations of ocean bacteria, ecological differentiation has occurred akin to a sexual mechanism: A few genome regions have swept through subpopulations in a habitat-specific manner, accompanied by gradual separation of gene pools as evidenced by increased habitat specificity of the most recent recombinations. These findings reconcile previous, seemingly contradictory empirical observations of the genetic structure of bacterial populations and point to a more unified process of differentiation in bacteria and sexual eukaryotes than previously thought.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337212/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337212/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shapiro, B Jesse -- Friedman, Jonathan -- Cordero, Otto X -- Preheim, Sarah P -- Timberlake, Sonia C -- Szabo, Gitta -- Polz, Martin F -- Alm, Eric J -- U54 GM088558/GM/NIGMS NIH HHS/ -- U54 GM088558-02/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Apr 6;336(6077):48-51. doi: 10.1126/science.1218198.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22491847" target="_blank"〉PubMed〈/a〉
    Keywords: Chromosomes, Bacterial/genetics ; *Ecosystem ; *Evolution, Molecular ; Gene Flow ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; *Genome, Bacterial ; Models, Genetic ; Molecular Sequence Data ; Mutation ; Oceans and Seas ; Phylogeny ; Polymorphism, Single Nucleotide ; *Recombination, Genetic ; Seawater/*microbiology ; *Selection, Genetic ; Vibrio/classification/*genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2012-09-08
    Description: In animals and plants, social structure can reduce conflict within populations and bias aggression toward competing populations; however, for bacteria in the wild it remains unknown whether such population-level organization exists. Here, we show that environmental bacteria are organized into socially cohesive units in which antagonism occurs between rather than within ecologically defined populations. By screening approximately 35,000 possible mutual interactions among Vibrionaceae isolates from the ocean, we show that genotypic clusters known to have cohesive habitat association also act as units in terms of antibiotic production and resistance. Genetic analyses show that within populations, broad-range antibiotics are produced by few genotypes, whereas all others are resistant, suggesting cooperation between conspecifics. Natural antibiotics may thus mediate competition between populations rather than solely increase the success of individuals.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cordero, Otto X -- Wildschutte, Hans -- Kirkup, Benjamin -- Proehl, Sarah -- Ngo, Lynn -- Hussain, Fatima -- Le Roux, Frederique -- Mincer, Tracy -- Polz, Martin F -- New York, N.Y. -- Science. 2012 Sep 7;337(6099):1228-31. doi: 10.1126/science.1219385.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22955834" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/*biosynthesis ; *Antibiosis ; DNA Transposable Elements ; *Drug Resistance, Bacterial ; *Ecosystem ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Genotype ; *Microbial Interactions ; Molecular Sequence Data ; Oceans and Seas ; Polyketide Synthases/genetics ; Seawater/*microbiology ; Vibrio/*drug effects/genetics/metabolism/*physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2011-11-01
    Description: Horizontal gene transfer (HGT), the acquisition of genetic material from non-parental lineages, is known to be important in bacterial evolution. In particular, HGT provides rapid access to genetic innovations, allowing traits such as virulence, antibiotic resistance and xenobiotic metabolism to spread through the human microbiome. Recent anecdotal studies providing snapshots of active gene flow on the human body have highlighted the need to determine the frequency of such recent transfers and the forces that govern these events. Here we report the discovery and characterization of a vast, human-associated network of gene exchange, large enough to directly compare the principal forces shaping HGT. We show that this network of 10,770 unique, recently transferred (more than 99% nucleotide identity) genes found in 2,235 full bacterial genomes, is shaped principally by ecology rather than geography or phylogeny, with most gene exchange occurring between isolates from ecologically similar, but geographically separated, environments. For example, we observe 25-fold more HGT between human-associated bacteria than among ecologically diverse non-human isolates (P = 3.0 x 10(-270)). We show that within the human microbiome this ecological architecture continues across multiple spatial scales, functional classes and ecological niches with transfer further enriched among bacteria that inhabit the same body site, have the same oxygen tolerance or have the same ability to cause disease. This structure offers a window into the molecular traits that define ecological niches, insight that we use to uncover sources of antibiotic resistance and identify genes associated with the pathology of meningitis and other diseases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smillie, Chris S -- Smith, Mark B -- Friedman, Jonathan -- Cordero, Otto X -- David, Lawrence A -- Alm, Eric J -- England -- Nature. 2011 Oct 30;480(7376):241-4. doi: 10.1038/nature10571.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22037308" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/*genetics/isolation & purification/metabolism/pathogenicity ; *Biological Evolution ; Drug Resistance, Microbial/genetics ; *Ecosystem ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Genome, Bacterial/genetics ; Humans ; Metagenome/*genetics ; Organ Specificity ; Phylogeny ; Phylogeography ; RNA, Ribosomal, 16S/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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