Conserved accessory genes link phylogenetically distinct Bacillus subtilis from Japanese and Indian fermented soyfoods

Bacillus subtilis is central to the production of many fermented soybean foods across Asia, yet the relationship between its phylogeny and niche adaptation remains unclear. To address this, we performed a pangenome analysis on 55 B. subtilis strains, including isolates from Japanese natto and Indian bekang. Our analysis revealed a striking evolutionary paradox: a bekang-producing strain, while phylogenetically distant from the homogeneous B. subtilis var. natto clade, shares a highly conserved accessory gene repertoire with it. This accessory genome profile defines a "natto-type" adaptive strategy, clustering the bekang isolate with the natto strains (Group A) and separating them from other successful soybean-fermenting strains, such as those from Korean cheonggukjang (Group B), which possess a different set of adaptive genes. Analysis of the Group A-specific repertoire revealed an enrichment of transcriptional regulators and metabolic enzymes, representing one successful evolutionary solution for soybean fermentation. The presence of this adaptive module in phylogenetically disparate lineages is consistent with an evolutionary history shaped by events such as horizontal gene transfer. This study highlights a model of polygenic adaptation, in which the acquisition of a large, co-evolved functional module provides a powerful shortcut for rapid adaptation to a complex nutritional niche.