Tracking the taxonomy of the genus Bifidobacterium based on a phylogenomic approach
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.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.date.accessioned | 2018-09-24T12:36:58Z | |
dc.date.available | 2018-09-24T12:36:58Z | |
dc.date.issued | 2018 | |
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.description.status | Peer reviewed | en |
dc.description.version | Published Version | en |
dc.format.mimetype | application/pdf | en |
dc.identifier.articleid | UNSP e02249-17 | |
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.doi | 10.1128/AEM.02249-17 | |
dc.identifier.endpage | 14 | |
dc.identifier.issn | 0099-2240 | |
dc.identifier.issued | 4 | |
dc.identifier.journaltitle | Applied and Environmental Microbiology | en |
dc.identifier.startpage | 1 | |
dc.identifier.uri | https://hdl.handle.net/10468/6875 | |
dc.identifier.volume | 84 | |
dc.language.iso | en | en |
dc.publisher | American Society for Microbiology | en |
dc.relation.project | info:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/ | |
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 |
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