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

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dc.contributor.authorSalvetti, Elisa
dc.contributor.authorHarris, Hugh M. B.
dc.contributor.authorFelis, Giovanna E.
dc.contributor.authorO'Toole, Paul W.
dc.contributor.funderHorizon 2020en
dc.contributor.funderScience Foundation Irelanden
dc.date.accessioned2021-08-24T11:43:18Z
dc.date.available2021-08-24T11:43:18Z
dc.date.issued2018-08-17
dc.date.updated2021-08-24T11:27:18Z
dc.description.abstractThe 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.description.statusPeer revieweden
dc.description.versionAccepted Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleide00993-18en
dc.identifier.citationSalvetti, 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.00993-18en
dc.identifier.doi10.1128/AEM.00993-18en
dc.identifier.eissn1098-5336
dc.identifier.endpage15en
dc.identifier.issn0099-2240
dc.identifier.issued17en
dc.identifier.journaltitleApplied and Environmental Microbiologyen
dc.identifier.startpage1en
dc.identifier.urihttps://hdl.handle.net/10468/11776
dc.identifier.volume84en
dc.language.isoenen
dc.publisherAmerican Society for Microbiologyen
dc.relation.projectinfo:eu-repo/grantAgreement/EC/H2020::MSCA-IF-EF-ST/659801/EU/Consolidating a genomic framework for exploiting lactobacilli/GENOLACTen
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/en
dc.rights© 2018, American Society for Microbiology. All Rights Reserved.en
dc.subjectLactobacillusen
dc.subjectTaxonomyen
dc.subjectPhylogenomicsen
dc.subjectPhylogenyen
dc.subjectComparative genomicsen
dc.subjectReclassificationen
dc.titleComparative genomics of the genus Lactobacillus reveals robust phylogroups that provide the basis for reclassificationen
dc.typeArticle (peer-reviewed)en
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