Phylogenomics and comparative genomics of Lactobacillus salivarius, a mammalian gut commensal

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dc.contributor.author Harris, Hugh Michael B.
dc.contributor.author Bourin, Maxence J. B.
dc.contributor.author Claesson, Marcus J.
dc.contributor.author O'Toole, Paul W.
dc.date.accessioned 2017-10-18T09:40:12Z
dc.date.available 2017-10-18T09:40:12Z
dc.date.issued 2017
dc.identifier.citation Harris, H. M. B., Bourin, M. J. B., Claesson, M. J. and O'Toole, P. W. (2017) 'Phylogenomics and comparative genomics of Lactobacillus salivarius, a mammalian gut commensal', Microbial Genomics, 3, pp. 1-16. doi: 10.1099/mgen.0.000115 en
dc.identifier.volume 3
dc.identifier.startpage 1
dc.identifier.endpage 16
dc.identifier.issn 2057-5858
dc.identifier.uri http://hdl.handle.net/10468/4878
dc.identifier.doi 10.1099/mgen.0.000115
dc.description.abstract The genus Lactobacillus is a diverse group with a combined species count of over 200. They are the largest group within the lactic acid bacteria and one of the most important bacterial groups involved in food microbiology and human nutrition because of their fermentative and probiotic properties. Lactobacillus salivarius, a species commonly isolated from the gastrointestinal tract of humans and animals, has been described as having potential probiotic properties and results of previous studies have revealed considerable functional diversity existing on both the chromosomes and plasmids. Our study consists of comparative genomic analyses of the functional and phylogenomic diversity of 42 genomes of strains of L . salivarius using bioinformatic techniques. The main aim of the study was to describe intra-species diversity and to determine how this diversity is spread across the replicons. We found that multiple phylogenomic and non-phylogenomic methods used for reconstructing trees all converge on similar tree topologies, showing that different metrics largely agree on the evolutionary history of the species. The greatest genomic variation lies on the small plasmids, followed by the repA-type circular megaplasmid, with the chromosome varying least of all. Additionally, the presence of extra linear and circular megaplasmids is noted in several strains, while small plasmids are not always present. Glycosyl hydrolases, bacteriocins and proteases vary considerably on all replicons while two exopolysaccharide clusters and several clustered regularly interspaced short palindromic repeats-associated systems show a lot of variation on the chromosome. Overall, despite its reputation as a mammalian gastrointestinal tract specialist, the intra-specific variation of L. salivarius reveals potential strain-dependant effects on human health. en
dc.description.sponsorship Health Research Board (HRA_POR/2012/123) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher Microbiology Society en
dc.relation.uri http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000115
dc.rights © 2017, the Authors. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited. en
dc.rights.uri https://creativecommons.org/licenses/by/4.0/
dc.subject Bioinformatics en
dc.subject Comparative genomics en
dc.subject Lactobacillus salivarius en
dc.title Phylogenomics and comparative genomics of Lactobacillus salivarius, a mammalian gut commensal en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Hugh M.B. Harris, Microbiology, University College Cork, Cork, Ireland. +353-21-490-3000. Email: hughharris86@gmail.com en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.contributor.funder Health Research Board
dc.description.status Peer reviewed en
dc.identifier.journaltitle Microbial Genomics en
dc.internal.IRISemailaddress hughharris86@gmail.com en


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© 2017, the Authors. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited. Except where otherwise noted, this item's license is described as © 2017, the Authors. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited.
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