Sabri M. Naser, Peter Dawyndt, Bart Hoste, Dirk Gevers, Katrien Vandemeulebroecke, Ilse Cleenwerck, Marc Vancanneyt& Jean Swings

The aim of our study was to evaluate the use of the phenylalanyl-tRNA synthase alpha subunit (pheS) and the RNA polymerase alpha subunit (rpoA) partial gene sequences for species identification of Lactobacillus. Two hundred and one strains representing the validly named species (98) and their subspecies (17) were examined. The pheS gene sequence analysis provides an interspecies gap, which normally exceeds 10% divergence and an intraspecies variation up to 3%. The rpoA gene sequences revealed a somewhat lower resolution with an interspecies gap normally exceeding 5% and an intraspecies variation up to 2%. The combined use of pheS and rpoA gene sequences offers a reliable identification system for nearly all Lactobacillus species. The pheS and rpoA gene sequences provide a powerful tool for detection of the potential novel Lactobacillus species and synonymous taxa. In conclusion, pheS and rpoA gene sequences provide alternative genomic markers to 16S rRNA gene with higher discriminatory power for reliable identification of Lactobacillus species.