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

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dc.contributor.author Lugli, Gabriele A.
dc.contributor.author Milani, Christian
dc.contributor.author Duranti, Sabrina
dc.contributor.author Mancabelli, Leonardo
dc.contributor.author Mangifesta, Marta
dc.contributor.author Turroni, Francesca
dc.contributor.author Viappiani, Alice
dc.contributor.author van Sinderen, Douwe
dc.contributor.author Ventura, Marco
dc.date.accessioned 2018-09-24T12:36:58Z
dc.date.available 2018-09-24T12:36:58Z
dc.date.issued 2018
dc.identifier.citation Lugli, 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.02249-17 en
dc.identifier.volume 84
dc.identifier.issued 4
dc.identifier.startpage 1
dc.identifier.endpage 14
dc.identifier.issn 0099-2240
dc.identifier.uri http://hdl.handle.net/10468/6875
dc.identifier.doi 10.1128/AEM.02249-17
dc.description.abstract For 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.sponsorship Joint 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.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher American Society for Microbiology en
dc.relation.uri http://aem.asm.org/content/84/4/e02249-17
dc.rights © 2018, American Society for Microbiology. All rights reserved. en
dc.subject Genomics en
dc.subject Phylogenomics en
dc.subject Its en
dc.subject Next generation sequencing en
dc.subject Bifidobacteria en
dc.subject Bifidobacterium en
dc.title Tracking the taxonomy of the genus Bifidobacterium based on a phylogenomic approach en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Douwe Van Sinderen, Microbiology, University College Cork, Cork, Ireland. +353-21-490-3000 Email: d.vansinderen@ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.contributor.funder Joint Programming Initiative A healthy diet for a healthy life
dc.contributor.funder Ministero dell’Istruzione, dell’Università e della Ricerca
dc.contributor.funder Università degli Studi di Parma
dc.contributor.funder Fondazione Cariparma
dc.contributor.funder European Regional Development Fund
dc.description.status Peer reviewed en
dc.identifier.journaltitle Applied and Environmental Microbiology en
dc.internal.IRISemailaddress d.vansinderen@ucc.ie en
dc.identifier.articleid UNSP e02249-17
dc.relation.project info:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/


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