Phylogeny of lactic acid bacteria based on recA and 16S rDNAs sequence analysis

Current delineation of the evolutionary relationships among bacteria and, in particular, among lactic acid bacteria (LAB) is largely stated on 16S RNA sequence analysis. Based on branching patterns in the 16S rRNA trees, LAB belong to the Gram-positive low GC division (Firmicutes) and are separated in several genera, phylogenetically intermixed (Lactobacillus and Pediococcus) and/or internally subdivided (Lactobacillus). In addition, they exhibit different morphology, GC content, metabolic and phenotypic traits, that only partially correlate with their phylogenetic placement. Such premises support the opportunity of a deeper investigation on genealogical inter-relationships among LAB, to depict a more robust taxonomic scheme for this bacteria of relevant ecological and food interest. The present study addressed a comprehensive phylogenetic analysis of several LAB genera and species by integrating the information deriving from different molecular markers, i.e. recA gene and 16S rDNAs. Partial sequences of RecA protein and its coding gene have successfully been used to perform phylogenetic analysis of many bacterial genera, but rarely on LAB. Complete recA primary structures, available from databases or directly sequenced, were analysed for a major number of species belonging to the genera Lactobacillus, Pediococcus, Enterococcus, Leuconostoc, Oenococcus, Lactococcus, Carnobacterium and Weissella. A comparison of 16S rDNAs and recA phylogenetic trees obtained by the same bioinformatic methods was carried out. Statistical robustness of the deduced trees, influence of genome GC content on tree reconstruction and correlation among phylogenetic, phenotypic and genotypic classification schemes of LAB were discussed in a polyphasic scenario.