Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination

dc.contributor.authorConrad, Roth E.
dc.contributor.authorBrink, Catherine E.
dc.contributor.authorViver, Tomeu
dc.contributor.authorRodriguez-R, Luis M.
dc.contributor.authorAldeguer-Riquelme, Borja
dc.contributor.authorHatt, Janet K.
dc.contributor.authorVenter, S.N. (Stephanus Nicolaas)
dc.contributor.authorRossello-Mora, Ramon
dc.contributor.authorAmann, Rudolf I.
dc.contributor.authorKonstantinidis, Konstantinos T.
dc.date.accessioned2025-02-26T05:58:36Z
dc.date.available2025-02-26T05:58:36Z
dc.date.issued2024-11-15
dc.descriptionCODE AVAILABILITY : Our main analysis workflow is available at: https://github.com/ rotheconrad/F100_Prok_Recombination. (https://doi.org/10.5281/ zenodo.13922077) and https://github.com/rotheconrad/Population- Genome-Simulator (https://doi.org/10.5281/zenodo.13922083); and for Supplementary analysis/figures, https://github.com/catbrink/ Explaining-ANI-gaps-Code-for-supplementary-figures.git.en_US
dc.descriptionDATA AVAILABILITY : Accession codes for the genomic sequence datasets analyzed in this study are provided in Supplementary Data 1. Other data are available in the main text or the Supplementary Information document.en_US
dc.description.abstractRecent genomic analyses have revealed that microbial communities are predominantly composed of persistent, sequence-discrete species and intraspecies units (genomovars), but themechanisms that create andmaintain these units remain unclear. By analyzing closely-related isolate genomes from the same or related samples and identifying recent recombination events using a novel bioinformaticsmethodology,we showthat high ecological cohesiveness coupled to frequent-enough and unbiased (i.e., not selection-driven) horizontal gene flow, mediated by homologous recombination, often underlie these diversity patterns. Ecological cohesiveness was inferred based on greater similarity in temporal abundance patterns of genomes of the same vs. different units, and recombination was shown to affect all sizable segments of the genome (i.e., be genome-wide) and have two times or greater impact on sequence evolution than point mutations. These results were observed in both Salinibacter ruber, an environmental halophilic organism, and Escherichia coli, themodel gut-associated organism and an opportunistic pathogen, indicating that they may be more broadly applicable to the microbial world. Therefore, our results represent a departure compared to previous models of microbial speciation that invoke either ecology or recombination, but not necessarily their synergistic effect, and answer an important question for microbiology: what a species and a subspecies are.en_US
dc.description.departmentBiochemistry, Genetics and Microbiology (BGM)en_US
dc.description.librarianam2024en_US
dc.description.sdgSDG-15:Life on landen_US
dc.description.sponsorshipThe Office of Science of the U.S. Department of Energy; the US National Science Foundation; the research at the IMEDEA was funded by the Ministry of Science and Innovation supported—in part—by European Regional Development Fund; supported, in part, by the U.S. National Science Foundation; the Ministry of Science and Innovation; the “Margarita Salas” postdoctoral grant, funded by the Spanish Ministry of Universities; the European Union; the Max Planck Society. Open Access funding enabled and organized by Projekt DEAL.en_US
dc.description.urihttps://www.nature.com/ncomms/en_US
dc.identifier.citationConrad, R.E., Brink, C.E., Viver, T. et al. 2024, 'Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination', Nature Communications, vol. 15, art. 9906, pp. 1-12, https://DOI.org/10.1038/s41467-024-53787-0en_US
dc.identifier.issn2041-1723 (online)
dc.identifier.other10.1038/s41467-024-53787-0
dc.identifier.urihttp://hdl.handle.net/2263/101216
dc.language.isoenen_US
dc.publisherNature Researchen_US
dc.rights© The Author(s) 2024. Open access. This article is licensed under a Creative Commons Attribution 4.0 International License.en_US
dc.subjectGenomesen_US
dc.subjectRecombinationen_US
dc.subjectDiversity patternsen_US
dc.subjectMicrobial communitiesen_US
dc.subjectSDG-15: Life on landen_US
dc.titleMicrobial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombinationen_US
dc.typeArticleen_US

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