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Fu J, Chen L, Yang S, Li Y, Jin L, He X, He L, Ao X, Liu S, Liu A, Yang Y, Ma B, Cui X, Chen S, Zou L. Metagenome and analysis of metabolic potential of the microbial community in pit mud used for Chinese strong-flavor liquor production. Food Res Int 2021; 143:110294. [PMID: 33992393 DOI: 10.1016/j.foodres.2021.110294] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/29/2021] [Accepted: 03/03/2021] [Indexed: 12/31/2022]
Abstract
Complex microbiomes of pit mud (PM) play significant roles in imbuing flavors and qualities of Chinese strong-flavor liquor (CSFL) during fermentation. However, understanding both of the taxonomic and functional diversity of the whole microorganisms in PM still remain a major challenge. Here, PM microbiomes were investigated based on metagenomic sequencing, assembly and binning. Metagenomic data revealed that Euryarchaeota was the predominant phylum, followed by Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria. For further functional exploration, 703 metagenome-assembled genomes (MAGs), including 304 novel strains, 197 novel species, and 94 novel genera were reconstructed. Three primary groups of Firmicutes (n = 406), Euryarchaeota (n = 130) and Bacteroidetes (n = 74), particularly genus of them Syntrophomonas, Thermacetogenium and Clostridium, methanogens (Methanobacterium, Methanoculleus, and Methanosarcina), Proteiniphilum and Prevotella, contained most of metabolic potential genes. Additionally, Chloroflexi was firstly reported to have potential to be involved in the caproic acid (CA) production. Bacteroidetes could be the key phylum to synthesize terpenes, and Armatimonadetes, Firmicutes, Ignavibacteriae and Verrucomicrobia may possess the same metabolic potential as well. Overall, this study will significantly improve our understanding of the diverse PM microbiome and help guide the future exploration of microbial resources for modifying PM fermentation processes.
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Affiliation(s)
- Jingxia Fu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Li Chen
- Yibin Products Quality Supervision and Inspection Institute, Yibin, Sichuan 644000, PR China
| | - Shengzhi Yang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Yuzhu Li
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Lei Jin
- College of Resources, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Xueping He
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Li He
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Xiaoling Ao
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Shuliang Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Aiping Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Yong Yang
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China
| | - Bingcun Ma
- Microbiological Inspection Center, Sichuan Institute for Food and Drug Control, Chengdu 611731, PR China
| | - Xuewen Cui
- Microbiological Inspection Center, Sichuan Institute for Food and Drug Control, Chengdu 611731, PR China
| | - Shujuan Chen
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, PR China.
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Chengdu 611130, PR China.
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Lu M, Zhou W, Ji F, Wu J, Nie Y, Ren C, Xu Y. Profiling prokaryotic community in pit mud of Chinese strong-aroma type liquor by using oligotrophic culturing. Int J Food Microbiol 2020; 337:108951. [PMID: 33202299 DOI: 10.1016/j.ijfoodmicro.2020.108951] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 10/11/2020] [Accepted: 10/24/2020] [Indexed: 02/08/2023]
Abstract
Pit mud microbiota plays a key role in flavour production for Chinese strong-aroma type liquor. However, the pit mud microbiota cannot be cultured in laboratory. In this study, an oligotrophic medium with acetate as carbon source was used to enrich pit mud microbiota. The 16S rRNA gene amplicon sequencing was applied to examine the microbial dynamics of the enrichment consortia. Both methanogens and bacteria were simultaneously enriched. Euryarchaeota, Bacteroidetes and Firmicutes were the top 3 enriched phyla, and 31 genera were successfully enriched. More specifically, 11 genera (65%) out of the 17 dominant genera in pit mud were successfully enriched, including Petrimonas, Proteiniphilum, Anaerocella, Hydrogenispora, Methanosarcina, Fermentimonas, LNR_A2-18, Sedimentibacter, Lutispora, Syntrophomonas and Aminobacterium. Furthermore, 20 rare genera in the analyzed pit mud samples were also enriched. Aceticlastic Methanosaeta and Methanosarcina were found to be dominant methanogens in the enrichment consortia. Metagenomic sequencing was then applied to the enriched microbial consortia to explore the metabolic potentials of pit mud microbes. Aceticlastic methanogenesis pathway of Methanosaeta was reconstructed. Furthermore, 26 high-quality metagenome-assembled genomes (MAGs) were obtained based on the metagenomic binning analysis. Moreover, nutrients in pit mud were found to be crucial to sustain the methanogenesis of the enriched microbial consortia. These results suggested that the enrichment approach by using oligotrophic culturing can effectively cultivate the pit mud microbiota. Combined with metagenomics, the oligotrophic culturing will be greatly helpful to decipher the community composition and metabolic potentials of pit mud microbiota.
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Affiliation(s)
- Mengmeng Lu
- Key Laboratory of Industrial Biotechnology of Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Weicheng Zhou
- Key Laboratory of Industrial Biotechnology of Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Fang Ji
- Jiangsu King's Luck Brewery Co., Ltd., Huaian 223001, China
| | - Jianfeng Wu
- Jiangsu King's Luck Brewery Co., Ltd., Huaian 223001, China
| | - Yao Nie
- Key Laboratory of Industrial Biotechnology of Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Cong Ren
- Key Laboratory of Industrial Biotechnology of Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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St. James AR, Richardson RE. Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions. FEMS Microbiol Ecol 2020; 96:5809959. [DOI: 10.1093/femsec/fiaa050] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/17/2020] [Indexed: 01/13/2023] Open
Abstract
ABSTRACT
The anaerobic digestion of wastes is globally important in the production of methane (CH4) as a biofuel. When sulfate is present, sulfate-reducing bacteria (SRB) are stimulated, competing with methanogens for common substrates, which decreases CH4 production and results in the formation of corrosive, odorous hydrogen sulfide gas (H2S). Here, we show that a population of SRB within a methanogenic bioreactor fed only butyrate for years immediately (within hours) responded to sulfate availability and shifted the microbial community dynamics within the bioreactor. By mapping shotgun metatranscriptomes to metagenome-assembled genomes, we shed light on the transcriptomic responses of key community members in response to increased sulfate provision. We link these short-term transcriptional responses to long-term niche partitioning using comparative metagenomic analyses. Our results suggest that sulfate provision supports a syntrophic butyrate oxidation community that disfavors poly-β-hydroxyalkanoate storage and that hydrogenotrophic SRB populations effectively exclude obligately hydrogenotrophic, but not aceticlastic, methanogens when sulfate is readily available. These findings elucidate key ecological dynamics between SRB, methanogens and syntrophic butyrate-oxidizing bacteria, which can be applied to a variety of engineered and natural systems.
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Affiliation(s)
- Andrew R St. James
- School of Civil and Environmental Engineering, Cornell University, 527 College Ave, Hollister Hall, Ithaca, NY, USA 14853
| | - Ruth E Richardson
- School of Civil and Environmental Engineering, Cornell University, 527 College Ave, Hollister Hall, Ithaca, NY, USA 14853
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Gan SH, Yang F, Sahu SK, Luo RY, Liao SL, Wang HY, Jin T, Wang L, Zhang PF, Liu X, Xu J, Xu J, Wang YY, Liu H. Deciphering the Composition and Functional Profile of the Microbial Communities in Chinese Moutai Liquor Starters. Front Microbiol 2019; 10:1540. [PMID: 31333631 PMCID: PMC6620787 DOI: 10.3389/fmicb.2019.01540] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/20/2019] [Indexed: 11/13/2022] Open
Abstract
Moutai is a world-famous traditional Chinese liquor with complex taste and aroma, which are considered to be strongly influenced by the quality of fermentation starters (Daqu). However, the role of microbial communities in the starters has not been fully understood. In this study, we revealed the microbial composition of 185 Moutai starter samples, covering three different types of starters across immature and mature phases, and functional gene composition of mature starter microbiome. Our results showed that microbial composition patterns of immature starters varied, but they eventually were similar and steady when they became mature starters, after half-year storage and subsequent mixing. To help identify two types of immature starters, we selected seven operational taxonomic unit (OTU) markers by leave-one-out cross validation (LOOCV) and an OTU classified as Saccharopolyspora was the most decisive one. For mature starters, we identified a total of 16 core OTUs, one of which annotated as Bacillus was found positively associated with saccharifying power. We also identified the functional gene and microbial composition in starch and cellulose hydrolysis pathways. Microbes with higher abundances of alpha-glucosidase, alpha-amylase, and glucoamylase probably contributed to high saccharifying power. Overall, this study reveals the features of Moutai starter microbial communities in different phases and improves understanding of the relationships between microbiota and functional properties of the starters.
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Affiliation(s)
- Shu-Heng Gan
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Fan Yang
- China Kweichow Moutai Distillery Co., Ltd., Zunyi, China
| | - Sunil Kumar Sahu
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Ru-Ye Luo
- China Kweichow Moutai Distillery Co., Ltd., Zunyi, China
| | - Shui-Lin Liao
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - He-Yu Wang
- China Kweichow Moutai Distillery Co., Ltd., Zunyi, China
| | - Tao Jin
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Li Wang
- China Kweichow Moutai Distillery Co., Ltd., Zunyi, China
| | - Peng-Fan Zhang
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Jin Xu
- BGI-Shenzhen, Shenzhen, China
| | - Jing Xu
- BGI-Shenzhen, Shenzhen, China
| | - Ya-Yu Wang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Copenhagen, Denmark
| | - Huan Liu
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
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Speth DR, Orphan VJ. Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales. PeerJ 2018; 6:e5614. [PMID: 30245936 PMCID: PMC6147122 DOI: 10.7717/peerj.5614] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/21/2018] [Indexed: 01/24/2023] Open
Abstract
Over the past years, metagenomics has revolutionized our view of microbial diversity. Moreover, extracting near-complete genomes from metagenomes has led to the discovery of known metabolic traits in unsuspected lineages. Genome-resolved metagenomics relies on assembly of the sequencing reads and subsequent binning of assembled contigs, which might be hampered by strain heterogeneity or low abundance of a target organism. Here we present a complementary approach, metagenome marker gene mining, and use it to assess the global diversity of archaeal methane metabolism through the mcrA gene. To this end, we have screened 18,465 metagenomes for the presence of reads matching a database representative of all known mcrA proteins and reconstructed gene sequences from the matching reads. We use our mcrA dataset to assess the environmental distribution of the Methanomassiliicoccales and reconstruct and analyze a draft genome belonging to the ‘Lake Pavin cluster’, an uncultivated environmental clade of the Methanomassiliicoccales. Analysis of the ‘Lake Pavin cluster’ draft genome suggests that this organism has a more restricted capacity for hydrogenotrophic methylotrophic methanogenesis than previously studied Methanomassiliicoccales, with only genes for growth on methanol present. However, the presence of the soluble subunits of methyltetrahydromethanopterin:CoM methyltransferase (mtrAH) provide hypothetical pathways for methanol fermentation, and aceticlastic methanogenesis that await experimental verification. Thus, we show that marker gene mining can enhance the discovery power of metagenomics, by identifying novel lineages and aiding selection of targets for in-depth analyses. Marker gene mining is less sensitive to strain heterogeneity and has a lower abundance threshold than genome-resolved metagenomics, as it only requires short contigs and there is no binning step. Additionally, it is computationally cheaper than genome resolved metagenomics, since only a small subset of reads needs to be assembled. It is therefore a suitable approach to extract knowledge from the many publicly available sequencing projects.
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Affiliation(s)
- Daan R Speth
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States of America
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States of America
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Zou W, Zhao C, Luo H. Diversity and Function of Microbial Community in Chinese Strong-Flavor Baijiu Ecosystem: A Review. Front Microbiol 2018; 9:671. [PMID: 29686656 PMCID: PMC5900010 DOI: 10.3389/fmicb.2018.00671] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/21/2018] [Indexed: 11/13/2022] Open
Abstract
Strong flavor baijiu (SFB), also called Luzhou-flavor liquor, is the most popular Chinese baijiu. It is manufactured via solid fermentation, with daqu as the starter. Microbial diversity of the SFB ecosystem and the synergistic effects of the enzymes and compounds produced by them are responsible for the special flavor and mouthfeel of SFB. The present review covers research studies focused on microbial community analysis of the SFB ecosystem, including the culturable microorganisms, their metabolic functions, microbial community diversity and their interactions. The review specifically emphasizes on the most recently conducted culture-independent analysis of SFB microbial community diversity. Furthermore, the possible application of systems biology approaches for elucidating the molecular mechanisms of SFB production were also reviewed and prospected.
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Affiliation(s)
- Wei Zou
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong, China
| | | | - Huibo Luo
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong, China
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