Integrated Metagenomics and Network Analysis of Metabolic Functional Genes in the Microbial Community of Chinese Fermentation Pits

Traditional Chinese strong-aroma baijiu (CSAB) fermentation technology has been used for thousands of years. Microbial communities that are enriched in continuous and uninterrupted fermentation pits (FPs) are important for fermentation. However, changes in the metabolic functional genes in microbial communities of FPs are still under-characterized. High-throughput sequencing technology was applied to comprehensively analyze the diversity, function, and dynamics of the metabolic genes among FPs of different ages, positions, and geographical regions. Approximately 1,375,660 microbial genes derived from 259 Gb metagenomic sequences of FPs were assembled and characterized to understand the impact of FP microorganisms on the quality of CSAB and to assess their genetic potential. The core functional gene catalog of FPs, consisting of 3379 ubiquitously known gene clusters, was established using Venn analysis. The functional profile confirmed that the flavor compounds in CSAB mainly originate from the metabolism of carbohydrates and amino acids. Approximately 17 key gene clusters that determine the yield and quality of CSAB were identified. The potential mechanism was associated with the biosynthesis of host compounds in CSAB, which relies on the abundance of species, such as Lactobacillus, Clostridium, Saccharomycetales, and the abundance of functional genes, such as CoA dehydrogenase, CoA transferase, and NAD dehydrogenase. Furthermore, the detailed metabolic pathways for the production of main flavor compounds of CSAB were revealed. This study provides a theoretical reference for a deeper understanding of substance metabolism during CSAB brewing and may help guide the future exploration of novel gene resources for biotechnological applications.