Comparative genomics of the genus Lactobacillus reveals robust phylogroups that provide the basis for reclassification

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dc.contributor.author Salvetti, Elisa
dc.contributor.author Harris, Hugh M. B.
dc.contributor.author Felis, Giovanna E.
dc.contributor.author O'Toole, Paul W.
dc.date.accessioned 2021-08-24T11:43:18Z
dc.date.available 2021-08-24T11:43:18Z
dc.date.issued 2018-08-17
dc.identifier.citation Salvetti, E., Harris, H. M. B., Felis, G. E. and O'Toole, P. W (2018) 'Comparative genomics of the genus Lactobacillus reveals robust phylogroups that provide the basis for reclassification'. Applied and Environmental Microbiology, 84(17), e00993-18 (15pp). doi: 10.1128/AEM.00993-18 en
dc.identifier.volume 84 en
dc.identifier.issued 17 en
dc.identifier.startpage 1 en
dc.identifier.endpage 15 en
dc.identifier.issn 0099-2240
dc.identifier.uri http://hdl.handle.net/10468/11776
dc.identifier.doi 10.1128/AEM.00993-18 en
dc.description.abstract The genus Lactobacillus includes over 200 species that are widely used in fermented food preservation and biotechnology or that are explored for beneficial effects on health. Naming, classifying, and comparing lactobacilli have been challenging due to the high level of phenotypic and genotypic diversity that they display and because of the uncertain degree of relatedness between them and associated genera. The aim of this study was to investigate the feasibility of dividing the genus Lactobacillus into more homogeneous genera/clusters, exploiting genome-based data. The relatedness of 269 species belonging primarily to the families Lactobacillaceae and Leuconostocaceae was investigated through phylogenetic analysis (by the use of ribosomal proteins and housekeeping genes) and the assessment of the average amino acid identity (AAI) and the percentage of conserved proteins (POCP). For each subgeneric group that emerged, conserved signature genes were identified. Both distance-based and sequence-based metrics showed that the Lactobacillus genus was paraphyletic and revealed the presence of 10 methodologically consistent subclades, which were also characterized by a distinct distribution of conserved signature orthologues. We present two ways to reclassify lactobacilli: a conservative division into two subgeneric groups based on the presence/absence of a key carbohydrate utilization gene or a more radical subdivision into 10 groups that satisfy more stringent criteria for genomic relatedness. Importance: Lactobacilli have significant scientific and economic value, but their extraordinary diversity means that they are not robustly classified. The 10 homogeneous genera/subgeneric entities that we identify here are characterized by uniform patterns of the presence/absence of specific sets of genes which offer potential as discovery tools for understanding differential biological features. Reclassification/subdivision of the genus Lactobacillus into more uniform taxonomic nuclei will also provide accurate molecular markers that will be enabling for regulatory approval applications. Reclassification will facilitate scientific communication related to lactobacilli and prevent misidentification issues, which are still the major cause of mislabeling of probiotic and food products reported worldwide. en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher American Society for Microbiology en
dc.rights © 2018, American Society for Microbiology. All Rights Reserved. en
dc.subject Lactobacillus en
dc.subject Taxonomy en
dc.subject Phylogenomics en
dc.subject Phylogeny en
dc.subject Comparative genomics en
dc.subject Reclassification en
dc.title Comparative genomics of the genus Lactobacillus reveals robust phylogroups that provide the basis for reclassification en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Paul O'Toole, Microbiology, University College Cork, Cork, Ireland. +353-21-490-3000 Email: pwotoole@ucc.ie en
dc.internal.availability Full text available en
dc.date.updated 2021-08-24T11:27:18Z
dc.description.version Accepted Version en
dc.internal.rssid 451668186
dc.internal.wokid WOS:000441894000011
dc.contributor.funder Horizon 2020 en
dc.contributor.funder Science Foundation Ireland en
dc.description.status Peer reviewed en
dc.identifier.journaltitle Applied and Environmental Microbiology en
dc.internal.copyrightchecked Yes
dc.internal.licenseacceptance Yes en
dc.internal.IRISemailaddress pwotoole@ucc.ie en
dc.identifier.articleid e00993-18 en
dc.relation.project info:eu-repo/grantAgreement/EC/H2020::MSCA-IF-EF-ST/659801/EU/Consolidating a genomic framework for exploiting lactobacilli/GENOLACT en
dc.relation.project info:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/ en
dc.identifier.eissn 1098-5336


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