Comparative genomics for the taxonomy of the family Lactobacillaceae

The bacterial family of Lactobacillaceae is constituted by two genera, Lactobacillus and Pediococcus, and 153 species, including some taxa of utmost importance in food science and technology. Most of Lactobacillaceae species are grouped into 14 phylogenetic groups that are not coherent with the 3 traditional groups derived from the analysis of carbohydrate metabolism (homofermentative-A, facultatively-B, obligately heterofermentative-C). The aim of this study was to apply, for the first time for this family, a genomic approach to try to find a consistency between phylogeny and the genetic background related to metabolic data. The comparative analysis of the pathways involved in glucose metabolism (glycolysis and pentose phosphate pathway) was performed on the 24 genomic sequences available and revealed genotypic differences typical for members of the 3 metabolic groups in term of presence/absence of 5 genes of glycolysis. In silico predictions were subsequently verified on different species belonging to several phylogenetic groups, starting from every species of L. delbrueckii and L. casei clades: the former includes members of the three different metabolisms (A, B and C), the latter only facultatively heterofermentative species (B). Results showed that metabolic similarities among groups were due to distinguishable genetic backgrounds. Moreover, from a genetic viewpoint, intra-group homogeneity and inter-group heterogeneity correlated with the phylogenetic subdivision, demonstrating the validity of the proposed approach to understand diversity and evolution of lactobacilli and related genera. These data represent a key-step for the resolution of the incongruence of Lactobacillaceae taxonomy and they could sustain the creation of more homogeneous genera inside it.