Taxonomic analysis of genera including probiotic bacteria

Background The recent development of “probiogenomics” is starting to reveal the potential common genetic basis for the health-promoting activities of probiotic bacteria (Ventura et al., 2008). Besides exhibiting the same features, these bacteria are characterised, taxonomically speaking, by a marked diversity: they belong to different species and genera and are assigned to two distinct Families, the Lactobacillaceae and the Bifidobacteriaceae Objectives The aim of this study was to present updated information on the taxonomy of these Families, revaluating and refining their phylogenetic structure. Moreover genetic and phenotypic data available were collected and integrated in order to pose the basis for a novel taxonomic approach to comprehend the evolution and the diversity of the two Families. Methods 16S rRNA gene sequence analysis was applied to determine the phylogenetic structure of Lactobacillaceae and Bifidobacteriaceae, and the method of split decomposition was applied to detect conflicting phylogenetic signals in the tree-like structure obtained. Public databases and historical literature were exploited to explore and combine both phenotypic and genotypic data. Conclusions Phylogenetic analyses led to the recognition of a number of robust clades, but the presence of network-like structures suggests a complex evolutionary history of the Families. The integration of phenotypic and genotypic data effectively completed and enriched the phylogenetic analyses. The information obtained appears to be very important to unravel the evolution of the species of lactobacilli and bifidobacteria, including probiotics. These results can be considered as a starting point for the improvement of the existing taxonomic schemes.