McCarthy, C. M. | bioRxiv Science

bioRxiv2025

Divergent Volatile Metabolomes and Flavor Attributes in Rice Fermented by Aspergillus oryzae and Aspergillus flavus

The generally recognized as safe (GRAS) fungus Aspergillus oryzae has been used for millennia in the production of traditional Asian fermented foods and beverages. This prolonged domestication has led to phenotypic adaptations that distinguish A. oryzae from its wild relative, Aspergillus flavus. While genomic and phenotypic differences between these species have been partially characterized, their comparative production of volatile compounds during food fermentation remains poorly understood. Here, we evaluated alpha-amylase activity, aflatoxin production, taste attributes (via electronic tongue), and volatile profiles (via dynamic headspace gas chromatography-mass spectrometry) of the food-grade strain A. oryzae RIB40 and two wild A. flavus strains, NPK13tox and AflaGuard. A. oryzae RIB40 exhibited significantly higher alpha-amylase activity during rice fermentation, and only A. flavus NPK13tox produced aflatoxin. Sensory analysis revealed that rice fermented by A. oryzae RIB40 exhibited more favorable taste attributes, including significantly lower astringency, aftertaste, and bitterness, as well as significantly higher richness (defined as umami aftertaste). Additionally, A. oryzae RIB40 produced a greater number and higher concentrations of volatile compounds, with 20 compounds significantly elevated compared to rice fermented by A. flavus. Many of these volatiles, including 2-methyl-3-buten-2-ol, 3-octen-2-one, 2-methyl-butanal, and 3-methyl-butanal, are associated with pleasant sensory attributes and have previously been linked to A. oryzae-fermented foods. These findings suggest that the volatilome of A. oryzae RIB40 has been shaped by domestication to produce a more desirable sensory profile, enriched in alcohols, aldehydes, ketones, and heterocyclic compounds contributing fruity, umami, and malty notes.

evolutionary biology↗

bioRxiv2023

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. Significance StatementLike plants and animals, microbes were also domesticated by humans, however relatively little is known about how the process of domestication shapes microbial genomes and traits. We found that isolates of Aspergillus sojae, a mold used in the production of miso and soy sauce, makeup a less toxic group that is genetically distinct from its closely related wild ancestor Aspergillus parasiticus. Our analyses shed new light on commonalities observed across filamentous molds adapted to the food environment.

evolutionary biology↗