Phylogenetic analysis of the genus Lactobacillus and related lactic acid bacteria as determined by reverse transcriptase sequencing of 16S rRNA

Abstract The small subunit rRNA sequences of 55 species of the genus Lactobacillus were determined by reverse transcription in an attempt to elucidate their natural interrelationships. Comparative analysis of the sequence data revealed the presence of 3 phylogenetically distinct clusters. Cluster 1 (designated) the L. delbrueckii group) included L. delbrueckii the type species of the genus and 11 other obligately homofermentative species. Cluster 2 (designated the L. casei group) comprised 32 Lactobacillus species and 5 Pediococcus species (including P. damnosus , the type species of the genus). With the exception of 5 obligately homofermentative species ( L. animalis, L. ruminis, L. salivarius, L. sharpeae, L. yamanashiensis ) most members of cluster 2 were heterofermentative. Cluster 3 (designated the Leuconostoc paramesenteroides group) included the atypical heterofermentative lactobacilli, L. confusus L. kandleri, L. minor, L. viridescens and Leu. paramesenteroides . The sequence data clearly demonstrate that the genus Lactobacillus as presently constituted is phylogenetically very heterogeneous. Further, the rRNA groups identified in the present study do not correspond to the classical division of Lactobacillus into the subgenera Thermobacterium, Streptobacterium and Betabacterium established on the basis of phenotype.