Tracking the taxonomy of the genus Bifidobacterium based on a phylogenomic approach

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dc.contributor.authorLugli, Gabriele A.
dc.contributor.authorMilani, Christian
dc.contributor.authorDuranti, Sabrina
dc.contributor.authorMancabelli, Leonardo
dc.contributor.authorMangifesta, Marta
dc.contributor.authorTurroni, Francesca
dc.contributor.authorViappiani, Alice
dc.contributor.authorvan Sinderen, Douwe
dc.contributor.authorVentura, Marco
dc.contributor.funderJoint Programming Initiative A healthy diet for a healthy life
dc.contributor.funderMinistero dell’Istruzione, dell’Università e della Ricerca
dc.contributor.funderUniversità degli Studi di Parma
dc.contributor.funderFondazione Cariparma
dc.contributor.funderEuropean Regional Development Fund
dc.date.accessioned2018-09-24T12:36:58Z
dc.date.available2018-09-24T12:36:58Z
dc.date.issued2018
dc.description.abstractFor decades, bacterial taxonomy has been based on in vitro molecular biology techniques and comparison of molecular marker sequences to measure the degree of genetic similarity and deduce phylogenetic relatedness of novel bacterial species to reference microbial taxa. Due to the advent of the genomic era, access to complete bacterial genome contents has become easier, thereby presenting the opportunity to precisely investigate the overall genetic diversity of microorganisms. Here, we describe a high-accuracy phylogenomic approach to assess the taxonomy of members of the genus Bifidobacterium and identify apparent misclassifications in current bifidobacterial taxonomy. The developed method was validated by the classification of seven novel taxa belonging to the genus Bifidobacterium by employing their overall genetic content. The results of this study demonstrate the potential of this whole-genome approach to become the gold standard for phylogenomics-based taxonomic classification of bacteria. IMPORTANCE Nowadays, next-generation sequencing has given access to genome sequences of the currently known bacterial taxa. The public databases constructed by means of these new technologies allowed comparison of genome sequences between microorganisms, providing information to perform genomic, phylogenomic, and evolutionary analyses. In order to avoid misclassifications in the taxonomy of novel bacterial isolates, new (bifido) bacterial taxons should be validated with a phylogenomic assessment like the approach presented here.en
dc.description.sponsorshipJoint Programming Initiative A healthy diet for a healthy life/Science Foundation Ireland/Ministero dell’Istruzione, dell’Università e della Ricerca(15/JP-HDHL/3280); Università degli Studi di Parma (GenProbio srl, Laboratory of Probiogenomics)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleidUNSP e02249-17
dc.identifier.citationLugli, G. A., Milani, C., Duranti, S., Mancabelli, L., Mangifesta, M., Turroni, F., Viappiani, A., van Sinderen, D. and Ventura, M. (2018) 'Tracking the taxonomy of the genus Bifidobacterium based on a phylogenomic approach', Applied and Environmental Microbiology, 84(4), e02249-17 (14pp). doi: 10.1128/AEM.02249-17en
dc.identifier.doi10.1128/AEM.02249-17
dc.identifier.endpage14
dc.identifier.issn0099-2240
dc.identifier.issued4
dc.identifier.journaltitleApplied and Environmental Microbiologyen
dc.identifier.startpage1
dc.identifier.urihttps://hdl.handle.net/10468/6875
dc.identifier.volume84
dc.language.isoenen
dc.publisherAmerican Society for Microbiologyen
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/
dc.relation.urihttp://aem.asm.org/content/84/4/e02249-17
dc.rights© 2018, American Society for Microbiology. All rights reserved.en
dc.subjectGenomicsen
dc.subjectPhylogenomicsen
dc.subjectItsen
dc.subjectNext generation sequencingen
dc.subjectBifidobacteriaen
dc.subjectBifidobacteriumen
dc.titleTracking the taxonomy of the genus Bifidobacterium based on a phylogenomic approachen
dc.typeArticle (peer-reviewed)en
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