Phylogenomics of lactic acid bacteria: an insight from carbohydrate metabolism.

Lactic acid bacteria (LAB) are a functional group of bacteria with a prominent role in the production of fermented food products and in human health as commensals in the gut. Due to their biological and industrial properties, LAB have been extensively investigated and a number of genome sequences have been obtained. The aim of this study was to perform a comparative genomics of LAB and provide novel insights into their evolution through the analysis of the genetic background of carbohydrate metabolism. The analysis was based on 40 LAB genome sequences of strains belonging to Enterococcaceae, Lactobacillaceae, Leuconostocaceae and Streptococcaceae representatives. A phylogenetic tree was inferred from the concatenation of 42 ribosomal proteins and used as a reference to map the distribution of 45 genes of glycolysis and pentose phosphate (PP) pathway. These genes were analysed as phylogenetic markers and also in terms of presence/absence and number of paralogs. Main observations concerned the occurrence of lineage-specific trends of gene loss/acquisition, revealing the mosaicism of the two metabolic pathways in these bacteria. Moreover, the paraphyly of Lactobacillaceae family was confirmed and additional information was obtained on the genetic bases of heterofermentative/homofermentative metabolism. In this study, a modus operandi for comparative genomics was also delineated, in which different genes are given different weight in the analysis, depending on their strain-, subspecies- and species-specific distribution. As the number of available genome sequences increases, the underrepresentation of some taxa and the omission to fully consider the taxonomic framework are predicted to be the most crucial factors in comparative genomics and evolutionary analyses