Quantitative metaproteomics reveals composition and metabolism characteristics of microbial communities in Chinese liquor fermentation starters

Abstract

IntroductionDaqu, the Chinese liquor fermentation starter, contains complex microbial communities that are important for the yield, quality, and unique flavor of produced liquor. However, the composition and metabolism of microbial communities in the different types of high-temperature Daqu (i.e., white, yellow, and black Daqu) have not been well understood.MethodsHerein, we used quantitative metaproteomics based on data-independent acquisition (DIA) mass spectrometry to analyze a total of 90 samples of white, yellow, and black Daqu collected in spring, summer, and autumn, revealing the taxonomic and metabolic profiles of different types of Daqu across seasons.ResultsTaxonomic composition differences were explored across types of Daqu and seasons, where the under-fermented white Daqu showed the higher microbial diversity and seasonal stability. It was demonstrated that yellow Daqu had higher abundance of saccharifying enzymes for raw material degradation. In addition, considerable seasonal variation of microbial protein abundance was discovered in the over-fermented black Daqu, suggesting elevated carbohydrate and amino acid metabolism in autumn black Daqu.DiscussionWe expect that this study will facilitate the understanding of the key microbes and their metabolism in the traditional fermentation process of Chinese liquor production.

Critical steps in an environmental metaproteomics workflow

“…Spectronaut is a popular, commercial software package (https://biognosys.com/software/spectronaut/), designed for the analysis of DIA datasets. It features directDIA, a proprietary, library‐free DIA method which has been successfully applied to metaproteomics samples (Zhao et al, 2022; Zhao, Yang, et al, 2023), and also offers options for the simple integration of DDA libraries to guide DIA analysis, as well as hybrid approaches which combine directDIA and library‐based methods for comprehensive and reliable quantification. Spectronaut also offers visual reports for post‐analysis, including interpretable identification and quantification results, differential abundance testing, and GO enrichment analysis.…”

Metaproteomics profiling of the microbial communities in fermentation starters (Daqu) during multi-round production of Chinese liquor

“…Recently, data-independent acquisition (DIA) mass spectrometry (MS) has shown the applicability to the analysis of complex metaproteomic samples ( 16 , 21 , 22 ). In particular, the latest library-free DIA data analysis methods ( 22 – 24 ), e.g., directDIA ( 23 ), can achieve deep proteome coverage and reproducible quantification without the need of pre-built spectral libraries ( 25 , 26 ), showing great potential in metaproteome profiling of large cohorts of samples.…”