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Bacillus subtilis  and  B. velezensis  are frequently isolated from various niches, including fermented foods, water, and soil. Within the  Bacillus subtilis  group,  B. velezensis  and  B. subtilis  subsp.  subtilis  have received significant attention as biological resources for biotechnology-associated industries. Nevertheless, radical solutions are urgently needed to identify microbes during their ecological succession to accurately confirm their action at the species or subspecies level in diverse environments, such as fermented materials. Thus, in this study, previously published genome data of the  B. subtilis  group were compared to exploit species- or subspecies-specific genes for use as improved qPCR targets to detect  B. velezensis  and  B. subtilis  subsp.  subtilis  in kimchi samples.  In silico  analyses of the selected genes and designed primer sequences, in conjunction with SYBR Green real-time PCR, confirmed the robustness of this newly developed assay. Consequently, this study will allow for new insights into the ontogeny and succession of  B. velezensis  and  B. subtilis  subsp.  subtilis  in various niches. Interestingly, in white kimchi without red pepper powder, neither  B. subtilis  subsp.  subtilis  nor  B. velezensis  was detected.

Understanding the ontogeny and succession of Bacillus velezensis and B. subtilis subsp. subtilis by focusing on kimchi fermentation