Genetic marker gene, recQ, differentiating Bacillus subtilis and the closely related Bacillus species

RecQ, which encodes a DNA helicase, was selected in searching for a marker gene of Bacillus subtilis and related species via genome mining. RecQ gene sequence similarity of type strains among Bacillus species used in this study ranged from 66.2% to 96.6%, whereas orthologous average nucleotide identity ranged from 72.6% to 95.8%. According to the phylogenetic tree based on recQ sequences, each type strain of all Bacillus species or subspecies used in this study was placed in a unique taxonomic position. Four B. subtilis subspecies, Bacillus tequilensis and Bacillus vallismortis were grouped in one cluster (cluster A). Strains of B. subtilis subsp. subtilis were classified into A1 cluster, and divided into subgroups. Isolates from Natto, Japanese fermented bean food, were classified into one subgroup, whereas those from Cheonggukjang, Korean fermented bean food, were divided into several subgroups within A1. Type strains of Bacillus halotolerans and Bacillus mojavensis were grouped into another cluster (cluster B), related to cluster A. Bacillus siamensis, Bacillus velezensis and Bacillus amyloliquefaciens were grouped into an independent cluster (cluster E). Sequencing of recQ was useful for the classification or differentiation of B. subtilis and closely related species. Therefore, recQ gene can be applied to the classification of these taxa.