Population genomics of Aspergillus sojae is shaped by the food environment

Traditional fermented foods often contain specialized microorganisms adapted to the unique food environment. For example, the filamentous mold Aspergillus oryzae, used in sake fermentation, has evolved to thrive in starch-rich conditions compared to its wild ancestor, Aspergillus flavus. Similarly, Aspergillus sojae is used in soybean-based food fermentations (e.g. miso and shochu) and is closely related to Aspergillus parasiticus. Here, we investigated the impact of long-term A. sojae usage in soybean fermentation on population structure, genome variation, and phenotypic traits. We analyzed 12 A. sojae and 10 A. parasiticus genomes, along with phenotypic characteristics of 15 isolates. Our results revealed that A. sojae isolates formed a distinct population separate from A. parasiticus and displayed remarkably low levels of genetic diversity, indicative of a recent clonal expansion. Genome comparisons revealed numerous loss-of-function mutations in A. sojae, notably in genes responsible for secondary metabolite production, including genes in the aflatoxin encoding gene cluster. Consequently, A. sojae lacked aflatoxin production, while it varied among A. parasiticus isolates. No other significant differences were observed in growth rates or other measured phenotypic traits between A. sojae and A. parasiticus. These findings suggest that A. sojae may have evolved from a population of A. parasiticus and lost the ability to produce some secondary metabolites. To elucidate the phenotypic differences between A. sojae and A. parasiticus, future work should focus on the influence of wild and food-associated strains on the sensory aspects and microbial community dynamics of fermented soy products.