How does long-term artificial intervention select the microbial community? A case study of the cellar mud chronosequence in the Chinese liquor brewing ecosystem

Abstract Background: Despite artificial selection being proposed to engineer microbiome from the top down to obtain the desired practical phenotypes, we lack the empirical evidence regarding the feasibility of the community-level selection. Chinese liquor fermentation for centuries caused sustained shifts of the diversity and structure of the microbial community within the cellar mud, thus providing an ideal ecosystem to study the microbiome evolution under long-term artificial selection. While multiple previous studies have reported the microbial diversity of cellar mud microbiome, few have resolved the metabolic roles of the microbial community and their relationships with cellar mud aging. Results: We used genome-centric metagenomics to analyze the microbial community of cellar mud samples (n=120) for four ages spanning 100 years. Our results showed that cellar mud microbiota was dominated by Bacteroidota, Firmicutes, and Halobacteriota lineages, with the discovery of diverse novel species. Metabolic reconstruction of these microorganisms indicated that macromolecules hydrolysis, fatty acid chain elongation, syntrophic fatty acid oxidation, and methanogenesis pathways were core functions of the cellar mud microbial ecosystem. During cellar mud initiation, we identified Bacteroidota with high hydrolysis capability as the dominant community members. Contrastingly, the proportion of Bacteroidota in mature and deep aging cellar mud decreased, while that of Firmicutes with potential of syntrophic fatty acids oxidation and methanogens increased. Metabolic potential of fatty acid chain elongation was stable throughout the development of cellar mud, with taxonomic variation being observed against environmental change. Conclusions: This study unravels the structure, function, and succession of microbial communities inhabiting the cellar mud, with changing metabolic cross-feeding interactions for environmental adaption. Our findings provide fundamental and comprehensive knowledge for exploring the impact of artificial ecosystem selection on the microbial community.