Rejection of reclassification of Lactobacillus kimchii and Lactobacillus bobalius as later subjective synonyms of Lactobacillus paralimentarius using comparative genomics

Abstract

Lactobacillus bobalius, Lactobacillus kimchii and Lactobacillus paralimentarius belong to the genus Lactobacillus and show close phylogenetic relationships. In a previous study, L. bobalius and L. kimchii were proposed to be reclassified as later heterotypic synonyms of L. paralimentarius using high 16S rRNA gene sequence similarities (>= 99.5 %) and DNA-DNA hybridization values (>= 82 %). We determined high quality whole genome assemblies of the type strains of L. bobalius and L. kimchii, which were then compared with that of L. paralimentarius. Average nucleotide identity values among three genomes ranged from 91.4 to 92.3% which are clearly below 95 similar to 96 %, the generally recognized cutoff value for bacterial species boundaries. On the basis of comparative genomic evidence, L. bobalius, L. kimchii, and L. paralimentarius should stand as separate species in the genus Lactobacillus. We therefore suggest rejecting the previous proposal to combine these three species into a single species.