Metagenome and analysis of metabolic potential of the microbial community in pit mud used for Chinese strong-flavor liquor production

Fu, Jingxia; Chen, Li; Yang, Sheng; Li, Yuzhu; Jin, Lan; He, Xueping; He, Li; Ao, Xiaoling; Liu, Shuliang; Liu, Aiping; Yang, Yong; Ma, Bing-cun; Cui, Xuewen; Chen, Shujuan; Zou, Likou

doi:10.1016/j.foodres.2021.110294

Cited by 47 publications

(26 citation statements)

References 60 publications

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“…The HB group harbored generalists that most abundantly encoded the peptidase, lipase, and CAZYmes in the present study, thus suggesting their ability to hydrolyze biopolymers (e.g., starch and protein) into monomers (sugars and amino acids), which were then metabolized to H 2 , CO 2 , and SCFAs. Consistent with previous metagenomics analysis [11], members of genera Proteiniphilum (e.g. MAG254.1) and Petrimonas (MAG246.1) belonging to phylum Bacteroidota, dominantly occupied the niches and encoded the highest relative abundance of peptidase, lipase, and CAZYmes in the present study, thereby indicating that they were major HB within the cellar mud.…”

Section: Diverse Novel Microorganisms Contributed To Carbon Cycling W...supporting

confidence: 91%

“…However, sensitive amplicon sequencing still reported numerous unknown species within cellar mud [17]. Previous metagenomic analysis of the cellar mud found that only 32.97% of the DNA sequences were taxonomically classi ed [11]. Consistently, our metagenomic data showed that more than half of the rMAGs (436 of 634 rMAGs) were de ned as the uncultured species according to the taxonomic classi cation of GTDBtk, thus implying the large knowledge gaps in microorganisms within CSFL fermentation.…”

Section: Diverse Novel Microorganisms Contributed To Carbon Cycling W...supporting

confidence: 74%

“…Industry experience shows that the quality and yield of CSFL positively correlate with cellar mud usage duration, thereby suggesting that cellar mud microbiome achieved a highfunctioning community during the long-term fermentation. Consequently, cellar muds represent chronosequences of distinct development stages, thus offering an ideal ecosystem to study the evolution of functional microbial communities under long-term arti cial selection [8, [10][11][12].…”

Section: Introductionmentioning

confidence: 99%

“…Among them, Bacteroidetes, Firmicutes and Euryarchaeota are frequently the dominant microorganisms within cellar mud, with some members being able to convert the metabolites to the expected butyrate and caproate, both major avoring compounds of CSFL [12,13,18,19]. Such pioneering studies have recognized that the microbial communities inhabiting the cellar mud noticeably change under the long-term impact of the jiupei fermentation batches, with a decrease in Bacteroidetes but an increase in Firmicutes and Euryarchaeota [8, [10][11][12]. Microbial interactions and environmental variables are assumed to be vital in driving niche differentiation and higher-level microbial community assembly within cellar mud [8,10,16,20].…”

Section: Introductionmentioning

confidence: 99%

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

Zhong

Chai

Zeng

et al. 2022

Preprint

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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.

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Section: Diverse Novel Microorganisms Contributed To Carbon Cycling W...supporting

confidence: 91%

Section: Diverse Novel Microorganisms Contributed To Carbon Cycling W...supporting

confidence: 74%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

Zhong

Chai

Zeng

et al. 2022

Preprint

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“…Acetotrophic Methanosarcinales was the predominant archaea in both the APMs and was more abundant in FPM. Methanosarcina has been considered the vital indicator of pit age and has a high potential for flavor production, including hexanoic acid and ethyl hexanoate [ 34 , 35 ]. Moreover, hydrogenotrophic methanogen ( Methanomicrobiales and Methanobacteriales ) and the functional bacteria ( Clostridium and C. kluyveri ) in the FPM were also higher than that in the CPM ( Figure 1 and Table S2 ).…”

Section: Resultsmentioning

confidence: 99%

Effects of Daqu Attributes on Distribution and Assembly Patterns of Microbial Communities and Their Metabolic Function of Artificial Pit Mud

Huang

Zhou

et al. 2022

Foods

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Daqu provides functional microbiota and various nutrients for artificial pit mud (APM) cultivation. However, little is known about whether its attributes affect the microbiome and metabolome of APM. Here, two types of APM were manufactured by adding fortified Daqu (FD) and conventional Daqu (CD); they were comprehensively compared by polyphasic detection methods after being used for two years. The results showed that FD altered the prokaryotic communities rather than the fungal ones, resulting in increased archaea and Clostridium_sensu_stricto_12 and decreased eubacteria and Lactobacillus. Correlation analysis suggested that these variations in community structure promoted the formation of hexanoic acid, butyric acid, and the corresponding ethyl esters, whereas they inhibited that of lactic acid and ethyl lactate and thus improved the flavor quality of the APM. Notably, pH was the main driving factor for the bacterial community variation, and the total acid mediated the balance between the stochastic and the deterministic processes. Furthermore, the results of the network analysis and PICRUSt2 indicated that FD also enhanced the modularity and robustness of the co-occurrence network and the abundance of enzymes related to hexanoic acid and butyric acid production. Our study highlights the importance of Daqu attributes in APM cultivation, which are of great significance for the production of high-quality strong-flavor Baijiu.

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Metagenomic analysis of the relationship between the microorganisms and the volatiles' development in the wines during spontaneous fermentation from the eastern foothills of the Ningxia Helan mountains in China

Yang

et al. 2023

J Sci Food Agric

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BACKGROUNDThe natural fermentation of multispecies microbial communities is responsible for unique flavors of winery regions of the eastern foothills of the Ningxia Helan Mountains in China. However, the participation of different microorganisms in the metabolic network for the development of important flavor substances is not clearly defined. Microbial population and diversity on different fermentation phases of Ningxia wine were analyzed by metagenomic sequencing approach.RESULTSGas chromatography–mass spectrometry and ion chromatography were used to identify flavor components, and 13 esters, 13 alcohols, nine aldehydes and seven ketones were detected in volatile substances with odor activity values > 1, and eight organic acids were detected as important flavor components in young wine. Thus, 52 238 predicted protein‐coding genes from 24 genera were identified in the Kyoto Encyclopedia of Genes and Genomes level 2 pathways of global and overview maps, and the genes were primarily involved in amino acid metabolism and carbohydrate metabolism. Major microbial genera (Saccharomyces, Tatumella, Hanseniaspora, Lactobacillus, and Lachancea) were closely related to self‐characteristic compound metabolism and further contributed to wine flavor.CONCLUSIONThis study clarifies the different metabolic roles of microorganisms in flavor formation during Ningxia wine spontaneous fermentation. Saccharomyces, dominant fungi involved in glycolysis and pyruvate metabolism, produces not only ethanol but also two important precursors, pyruvate and acetyl‐CoA, which are necessary for the tricarboxylic acid cycle, fatty acid metabolism, amino acid metabolism, and flavor formation. Lactobacillus and Lachancea, dominant bacteria involved in lactic acid metabolism. Tatumella, dominant bacteria involved in amino acid metabolism, fatty acid metabolism, and acetic acid metabolism to produce esters in the Shizuishan City region samples. These findings provide insights into the use of local functional strains to generate unique flavor formation, as well as improved stability and quality, in wine production. © 2023 Society of Chemical Industry.

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Metagenome and analysis of metabolic potential of the microbial community in pit mud used for Chinese strong-flavor liquor production

Cited by 47 publications

References 60 publications

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

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

Effects of Daqu Attributes on Distribution and Assembly Patterns of Microbial Communities and Their Metabolic Function of Artificial Pit Mud

Metagenomic analysis of the relationship between the microorganisms and the volatiles' development in the wines during spontaneous fermentation from the eastern foothills of the Ningxia Helan mountains in China

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