Time series comparative genomics analysis reveals the adaptive evolution of caproic acid-producing bacteria to the long-term liquor brewing environment

Abstract

Caproic acid is a significant flavor compound of strong-flavor Baijiu, which is primarily produced by microorganisms inhabiting pit mud. The adaptive evolution mechanisms during the long-term brewing process for decades even centuries of three caproic acid-producing bacterial genera, Caproicibacter, Caproicibacterium, and Caproiciproducens (CAP), which were challenging to cultivate from the pit mud, were examined in this study utilizing metagenomics and comparative genomics. The results indicated that CAPs progressively acclimated to the pit mud environment and took over as the dominant microorganisms in the community with continuous brewing. CAPs in the aged pit mud contained more genes linked to the synthesis of short-chain fatty acids, a greater capacity to metabolize small molecules, and a decreased capacity to metabolize starch macromolecules. More ethanol and lactic acid metabolism-related gene types were evolved by CAPs in the aged pit mud, and their capacity to metabolize these substances was greater. In order to assist them adjust to the high alcohol and high acid environment, CAPs in the aged pit mud possessed additional defense mechanisms and genes linked to environmental adaptability. The adaptive evolutionary mechanism of caproic acid-producing bacteria during long-term fermentation was examined in this study. This analysis served as a foundation for additional regulation of the metabolic activity of these bacteria and offered theoretical support for preserving and enhancing pit mud quality.