Ecological dominance and genomic features of bacterial generalists during pit fermentation of three distinct baijiu types in Anhui Province.

Microbial generalists are pivotal for maintaining the stability of fermentation systems, yet their distribution across different Baijiu types remains poorly understood. This study identified generalists and specialists during the pit fermentation of strong-flavor, jian-flavor, and sesame-flavor Baijiu in Anhui Province, and further elucidated their genomic features. Results showed that bacterial communities in all three types are dominated by generalists, whereas fungal communities depend more on diverse specialists. Bacterial generalists were represented by OTUs classified as Acetilactobacillus, Lactobacillus, and Limosilactobacillus. Targeted removal of these generalists increased the robustness of time-series networks, as they correlated negatively with most other taxa and were strongly linked to physicochemical properties. The major species belonging to bacterial generalists included Acetilactobacillus jinshanensis, Lactobacillus acetotolerans, and Limosilactobacillus pontis. These generalists possessed specialized genomic features for niche dominance, characterized by: (i) a low-acquisition, high-growth life history strategy (A/Y < 1); (ii) a preference for sugar metabolism (SAP >0); (iii) a complete multi-layered defense system conferring tolerance to acid and ethanol; and (iv) a streamlined (< 2 Mb) and non-redundant (lacking the TCA cycle) genome that minimizes regulatory burden. This study provides a systematic analysis of generalists across distinct Baijiu types in Anhui Province, offering a theoretical framework for understanding the rules of microbial assembly in the brewing process.