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

Lugli, Gabriele A.; Milani, Christian; Duranti, Sabrina; Mancabelli, Leonardo; Mangifesta, Marta; Turroni, Francesca; Viappiani, Alice; van Sinderen, Douwe; Ventura, Marco

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

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Tracking the Taxonomy of the Genus Bifidobacterium.pdf(4.07 MB)

Published Version

Date

2018

Authors

Lugli, Gabriele A.

Milani, Christian

Duranti, Sabrina

Mancabelli, Leonardo

Mangifesta, Marta

Turroni, Francesca

Viappiani, Alice

van Sinderen, Douwe

Ventura, Marco

Publisher

American Society for Microbiology

Published Version

10.1128/AEM.02249-17

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.

Keywords

Genomics , Phylogenomics , Its , Next generation sequencing , Bifidobacteria , Bifidobacterium

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