Open Access Highly Accessed Research article

Comparative genomics of the Bifidobacterium breve taxon

Francesca Bottacini1, Mary O’Connell Motherway1, Justin Kuczynski3, Kerry Joan O’Connell1, Fausta Serafini2, Sabrina Duranti2, Christian Milani2, Francesca Turroni1, Gabriele Andrea Lugli2, Aldert Zomer4, Daria Zhurina5, Christian Riedel5, Marco Ventura2* and Douwe van Sinderen1*

Author Affiliations

1 Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland

2 Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy

3 Second Genome, Bioinformatics Department, San Bruno, CA, USA

4 Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands

5 Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany

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BMC Genomics 2014, 15:170  doi:10.1186/1471-2164-15-170

Published: 1 March 2014

Abstract

Background

Bifidobacteria are commonly found as part of the microbiota of the gastrointestinal tract (GIT) of a broad range of hosts, where their presence is positively correlated with the host’s health status. In this study, we assessed the genomes of thirteen representatives of Bifidobacterium breve, which is not only a frequently encountered component of the (adult and infant) human gut microbiota, but can also be isolated from human milk and vagina.

Results

In silico analysis of genome sequences from thirteen B. breve strains isolated from different environments (infant and adult faeces, human milk, human vagina) shows that the genetic variability of this species principally consists of hypothetical genes and mobile elements, but, interestingly, also genes correlated with the adaptation to host environment and gut colonization. These latter genes specify the biosynthetic machinery for sortase-dependent pili and exopolysaccharide production, as well as genes that provide protection against invasion of foreign DNA (i.e. CRISPR loci and restriction/modification systems), and genes that encode enzymes responsible for carbohydrate fermentation. Gene-trait matching analysis showed clear correlations between known metabolic capabilities and characterized genes, and it also allowed the identification of a gene cluster involved in the utilization of the alcohol-sugar sorbitol.

Conclusions

Genome analysis of thirteen representatives of the B. breve species revealed that the deduced pan-genome exhibits an essentially close trend. For this reason our analyses suggest that this number of B. breve representatives is sufficient to fully describe the pan-genome of this species. Comparative genomics also facilitated the genetic explanation for differential carbon source utilization phenotypes previously observed in different strains of B. breve.

Keywords:
Bifidobacterium breve; Evolutionary genomics; Core genome; Dispensable genome; Pan-genome