Dykhuizen DE, Green L.. Recombination in Escherichia coli and the definition of biological species. J Bacteriol 173: 7257-7268

Department of Ecology and Evolution, State University of New York, Stony Brook 11794-5245.
Journal of Bacteriology (Impact Factor: 2.81). 12/1991; 173(22):7257-68.
Source: PubMed


The DNA sequence of part of the gnd (6-phosphogluconate dehydrogenase) gene was determined for eight wild strains of Escherichia coli and for Salmonella typhimurium. Since a region of the trp (tryptophan) operon and the phoA (alkaline phosphatase) gene have been sequenced from the same strains, the gene trees for these three regions were determined and compared. Gene trees are different from species or strain trees in that a gene tree is derived from a particular segment of DNA, whereas a species or strain tree should be derived from many such segments and is the tree that best represents the phylogenetic relationship of the species or strains. If there were no recombination in E. coli, the gene trees for different genes would not be statistically different from the strain tree or from each other. But, if the gene trees are significantly different, there must have been recombination. Methods are proposed that show these gene trees to be statistically different. Since the gene trees are different, we conclude that recombination is important in natural populations of E. coli. Finally, we suggest that gene trees can be used to create an operational means of defining bacterial species by using the biological species definition.

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Available from: Daniel E Dykhuizen, Oct 12, 2015
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    • "Recombination is an essential facilitator of adaptation, without which species would quickly go extinct due to accumulation of deleterious mutations (''Mueller's Ratchet'') as well as an inability to fix beneficial ones (''Hill–Robinson Effect'') (Barton, 1995; Hill and Robertson, 1966; Muller, 1964). Although reproducing asexually , bacterial species are no exception to a dependency on homologous recombination for long-term sustainability (Didelot and Maiden, 2010; Dykhuizen and Green, 1991; Fraser et al., 2007). "
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    ABSTRACT: Borrelia burgdorferi sensu lato (B. burgdorferi s.l.), the group of bacterial species represented by Lyme Disease pathogens, has one of the most complex and variable genomic architectures among prokaryotes. Showing frequent recombination within and limited gene flow among geographic populations, the B. burgdorferi s.l. genomes provides an excellent window into the processes of bacterial evolution at both within- and between-population levels. Comparative analyses of B. burgdorferi s.l. genomes revealed a highly dynamic plasmid composition but a conservative gene repertoire. Gene duplication and loss as well as sequence variations at loci encoding surface-localized lipoproteins (e.g., the PF54 genes) are strongly associated with adaptive differences between species. There are a great many conserved intergenic spacer sequences that are candidates for cis-regulatory elements and non-coding RNAs. Recombination among coexisting strains occurs at a rate approximately three times the mutation rate. The coexistence of a large number of genomic groups within local B. burgdorferi s.l. populations may be driven by immune-mediated diversifying selection targeting major antigen loci as well as by adaptation to multiple host species. Questions remain regarding the ecological causes (e.g., climate change, host movements, or new adaptations) of the ongoing range expansion of B. burgdorferi s.l. and on the genomic variations associated with its ecological and clinical variability. Anticipating an explosive growth of the number of B. burgdorferi s.l. genomes sampled from both within and among species, we propose genome-based methods to test adaptive mechanisms and to identify molecular bases of phenotypic variations. Genome sequencing is also necessary to monitor the ongoing genetic admixture of previously isolated species and populations in North America and elsewhere.
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    • "Escherichia coli is a highly diverse organism, which ranges from the intestinal commensal K12 strains, through to intestinal pathogenic variants such as ETEC, EAEC, and EPEC, to severe intestinal pathogens such as E. coli O157, and then extraintestinal pathogenic variants causing UTIs and bacteremia . This enormous diversity has made E. coli the subject of countless comparative and evolutionary studies attempting to determine the mechanisms by which each of the subgroups has diversified and specialized (Dykhuizen and Green 1991; Touchon et al. 2009). The recent emergence of the multidrugresistant E. coli O:25b:H4 ST131 as the globally dominant strain type isolated from extraintestinal infections (Peirano and Pitout 2010) provides a new and important dimension to the study of how E. coli evolves and diversifies. "
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    ABSTRACT: Escherichia coli is a highly diverse group of pathogens ranging from commensal of the intestinal tract, through to intestinal pathogen, and extra-intestinal pathogen. Here we present data on the population diversity of E. coli, using Bayesian analysis to identify thirteen distinct clusters within the population from MLST data, which map perfectly onto a whole genome derived phylogeny based on 62 genome sequences. Bayesian analysis of recombination within the core genome identified reduction in detectable core genome recombination as one moves from the commensals, through the intestinal pathogens down to the multi-drug resistant extra-intestinal pathogenic clone E. coli ST131. Our data shows that the emergence of a multi-drug resistant, extra-intestinal pathogenic lineage of E. coli is marked by substantial reduction in detectable core genome recombination, resulting in a "clone" which is phylogenetically distinct and sexually isolated in terms of core genome recombination.
    Genome Biology and Evolution 03/2013; 5(4). DOI:10.1093/gbe/evt038 · 4.23 Impact Factor
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    • "That is, evidence for HGT and subsequent recombination would further support the notion that SD vibrios are part of a larger panmictic group of Vibrio strains that spans disparate marine ecologies. Repeatedly, HGT has been cited as the source of incongruence (phylogenetic discordance) between nucleotide sequences (Dykhuizen and Green, 1991; Lecointre et al., 1998; Brown et al., 2002). Specifically , the ILD test is a parsimony-based phylogenetic method that evaluates statistically the null hypothesis of congruence between different genes or distinct domains within the same gene (Farris et al., 1994). "
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    ABSTRACT: Vibrio represents a diverse bacterial genus found in different niches of the marine environment, including numerous genera of marine sponges (phylum Porifera), inhabiting different depths and regions of benthic seas, that are potentially important in driving adaptive change among Vibrio spp. Using 16S rRNA gene sequencing, a previous study showed that sponge‐derived (SD) vibrios clustered with their mainstream counterparts present in shallow, coastal ecosystems, suggesting a genetic relatedness between these populations. Sequences from the topA, ftsZ, mreB, rpoD, rctB and toxR genes were used to investigate the degree of relatedness existing between these two separate populations by examining their phylogenetic and genetic disparity. Phylogenies were constructed from the concatenated sequences of the six housekeeping genes using maximum‐parsimony, maximum‐likelihood and neighbour‐joining algorithms. Genetic recombination was evaluated using the incongruence length difference test, Split decomposition and measuring overall compatibility of sites. This combined technical approach provided evidence that SD Vibrio strains are largely genetically homologous to their shallow‐water counterparts. Moreover, the analyses conducted support the existence of extensive horizontal gene transfer between these two groups, supporting the idea of a single panmictic population structure among vibrios from two seemingly distinct, marine environments.
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