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Han D, Yang Y, Guo Z, Chen K, Dai S, Zhu Y, Wang Y, Yu Z, Wang K, Liu P, Rong C, Yu Y. Metagenomics profiling of the microbial community and functional differences in solid-state fermentation vinegar starter (seed Pei) from different Chinese regions. Front Microbiol 2024; 15:1389737. [PMID: 38756727 PMCID: PMC11096547 DOI: 10.3389/fmicb.2024.1389737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/01/2024] [Indexed: 05/18/2024] Open
Abstract
Introduction The starter used in solid-state fermentation (SSF) vinegar, known as seed Pei is a microbial inoculant from the previous batch that is utilized during the acetic acid fermentation stage. The seed Pei, which has a notable impact on vinegar fermentation and flavor, is under-researched with comparative studies on microorganisms. Methods Herein metagenomics was employed to reveal the microbes and their potential metabolic functions of four seed Pei from three regions in China. Results The predominant microbial taxa in all four starters were bacteria, followed by viruses, eukaryotes, and archaea, with Lactobacillus sp. or Acetobacter sp. as main functional taxa. The seed Pei used in Shanxi aged vinegar (SAV) and Sichuan bran vinegar (SBV) exhibited a higher similarity in microbial composition and distribution of functional genes, while those used in two Zhenjiang aromatic vinegar (ZAV) differed significantly. Redundancy analysis (RDA) of physicochemical factors and microbial communities indicated that moisture content, pH, and reducing sugar content are significant factors influencing microbial distribution. Moreover, seven metagenome-assembled genomes (MAGs) that could potentially represent novel species were identified. Conclusions There are distinctions in the microbiome and functional genes among different seed Pei. The vinegar starters were rich in genes related to carbohydrate metabolism. This research provides a new perspective on formulating vinegar fermentation starters and developing commercial fermentation agents for vinegar production.
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Affiliation(s)
- Dong Han
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yunsong Yang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zhantong Guo
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Ken Chen
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Shuwen Dai
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yuanyuan Zhu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yuqin Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zhen Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Ke Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Peng Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Chunchi Rong
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yongjian Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
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Ma J, Qian C, Hu Q, Zhang J, Gu G, Liang X, Zhang L. The bacteriome-coupled phage communities continuously contract and shift to orchestrate the traditional rice vinegar fermentation. Food Res Int 2024; 184:114244. [PMID: 38609223 DOI: 10.1016/j.foodres.2024.114244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 04/14/2024]
Abstract
Amounts of microbiome studies have uncovered the microbial communities of traditional food fermentations, while in which the phageome development with time is poorly understood. Here, we conducted a study to decipher both phageome and bacteriome of the traditional rice vinegar fermentation. The vinegar phageomes showed significant differences in the alpha diversity, network density and clustering coefficient over time. Peduoviridae had the highest relative abundance. Moreover, the phageome negatively correlated to the cognate bacteriome in alpha diversity, and undergone constantly contracting and shifting across the temporal scale. Nevertheless, 257 core virial clusters (VCs) persistently occurred with time whatever the significant impacts imposed by the varied physiochemical properties. Glycoside hydrolase (GH) and glycosyltransferase (GT) families genes displayed the higher abundances across all samples. Intriguingly, diversely structuring of toxin-antitoxin systems (TAs) and CRISPR-Cas arrays were frequently harbored by phage genomes. Their divergent organization and encoding attributes underlie the multiple biological roles in modulation of network and/or contest of phage community as well as bacterial host community. This phageome-wide mapping will fuel the current insights of phage community ecology in other traditional fermented ecosystems that are challenging to decipher.
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Affiliation(s)
- Jiawen Ma
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province 310018, China
| | - Chenggong Qian
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province 310018, China
| | - Qijie Hu
- Huzhou Institute of Food and Drug Control, Huzhou, Zhejiang Province 313002, China
| | - Jianping Zhang
- Haining Yufeng Brewing Co., Ltd, Haining, Zhejiang Province 314408, China
| | - Guizhang Gu
- Huzhou Institute of Food and Drug Control, Huzhou, Zhejiang Province 313002, China
| | - Xinle Liang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province 310018, China.
| | - Lei Zhang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province 310018, China.
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Shen L, Wang Y, Li X, Hou Z, Mao J, Shi J, Battino M, Routledge MN, Gong Y, Zou X, Zhang D. Spatial-temporal distribution of deoxynivalenol, aflatoxin B 1, and zearalenone in the solid-state fermentation basin of traditional vinegar and their potential correlation with microorganisms. Food Chem 2024; 433:137317. [PMID: 37683481 DOI: 10.1016/j.foodchem.2023.137317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/16/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
This study revealed the spatial-temporal distribution of deoxynivalenol (DON), aflatoxin B1 (AFB1), and zearalenone (ZEN) during the acetic acid fermentation (AAF) of aromatic vinegar and the corresponding correlation with the microbial community. A total of 324 samples were collected during the AAF process to analyze the mycotoxin content. The average DON content fluctuated during the first 7 d, while the average AFB1 and ZEN levels increased at 5-7 d and 7-11 d, respectively, remaining stable until the end of fermentation. In addition, the significant AFB1 and ZEN content variation was limited to the cross-sectional sampling planes in the fermentation basin, while DON was heterogeneously distributed on the cross-sectional, horizontal, and vertical sampling planes. Furthermore, the redundancy analysis and Spearman correlation coefficients revealed close relationships between three mycotoxins and certain bacterial and fungal species. This study provides new information regarding the mycotoxins during solid-state fermentation of traditional vinegar.
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Affiliation(s)
- Lingqin Shen
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yifan Wang
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xin Li
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Ziqing Hou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jin Mao
- National Reference Laboratory for Agricultural Testing, Key Laboratory of Detection for Mycotoxins, Laboratory of Quality & Safety Risk Assessment for Oilseed Products (Wuhan), Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jiyong Shi
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Maurizio Battino
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China; Department of Clinical Sciences, Faculty of Medicine, Polytechnic University of Marche, Ancona, Italy
| | - Michael N Routledge
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; Leicester Medical School, University of Leicester, Leicester, UK
| | - Yunyun Gong
- School of Food Science and Nutrition, University of Leeds, Leeds, UK
| | - Xiaobo Zou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Di Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
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Zhang H, Zhang H, Du H, Yu X, Xu Y. The insights into the phage communities of fermented foods in the age of viral metagenomics. Crit Rev Food Sci Nutr 2024:1-13. [PMID: 38214674 DOI: 10.1080/10408398.2023.2299323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Phages play a critical role in the assembly and regulation of fermented food microbiome through lysis and lysogenic lifestyle, which in turn affects the yield and quality of fermented foods. Therefore, it is important to investigate and characterize the diversity and function of phages under complex microbial communities and nutrient substrate conditions to provide novel insights into the regulation of traditional spontaneous fermentation. Viral metagenomics has gradually garnered increasing attention in fermented food research to elucidate phage functions and characterize the interactions between phages and the microbial community. Advances in this technology have uncovered a wide range of phages associated with the production of traditional fermented foods and beverages. This paper reviews the common methods of viral metagenomics applied in fermented food research, and summarizes the ecological functions of phages in traditional fermented foods. In the future, combining viral metagenomics with culturable methods and metagenomics will broaden the scope of research on fermented food systems, revealing the complex role of phages and intricate phage-bacterium interactions.
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Affiliation(s)
- Huadong Zhang
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hongxia Zhang
- College of Life Sciences, Shanxi Normal University, Taiyuan, Shanxi, China
| | - Hai Du
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiaowei Yu
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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Tan G, Qi S, Wang Y, Li X, Li X, Li M, Li L, Zhao L, Hu M. Uncovering differences in the composition and function of phage communities and phage-bacterium interactions in raw soy sauce. Front Microbiol 2023; 14:1328158. [PMID: 38188564 PMCID: PMC10766790 DOI: 10.3389/fmicb.2023.1328158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/05/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction Although the composition and succession of microbial communities in soy sauce fermentation have been well-characterized, the understanding of phage communities in soy sauce remains limited. Methods This study determined the diversity, taxonomic composition, and predicted function of phage communities and the phage-host interactions in two types of raw soy sauce (Cantonese-type fermentation, NJ; Japanese-type fermentation, PJ) using shotgun metagenomics. Results and discussion These two raw soy sauces showed differences in phage composition (121 viral operational taxonomic units (vOTUs) in NJ and 387 vOTUs in PJ), with a higher abundance of the family Siphoviridae (58.50%) in the NJ phage community and a higher abundance of Myoviridae (33.01%) in PJ. Auxiliary metabolic functional annotation analyses showed that phages in the raw soy sauces mostly encoded genes with unknown functions (accounting for 66.33% of COG profiles), but the NJ sample contained genes mostly annotated to conventional functions related to carbohydrate metabolism (0.74%) and lipid metabolism (0.84%), while the PJ sample presented a higher level of amino acid metabolism functions (0.12%). Thirty auxiliary metabolism genes (AMGs) were identified in phage genomes, which were associated with carbohydrate utilization, cysteine and methionine metabolism, and aspartic acid biosynthesis for the host. To identify phage-host interactions, 30 host genomes (affiliated with 22 genera) were also recruited from the metagenomic dataset. The phage-host interaction analysis revealed a wide range of phage hosts, for which a total of 57 phage contigs were associated with 17 host genomes, with Shewanella fodinae and Weissella cibaria infected by the most phages. This study provides a comprehensive understanding of the phage community composition, auxiliary metabolic functions, and interactions with hosts in two different types of raw soy sauce.
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Affiliation(s)
- Guiliang Tan
- School of Material Science and Food Engineering, University of Electronic Science and Technology of China, Zhongshan Institute, Zhongshan, China
| | - Shaohan Qi
- College of Food Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yi Wang
- School of Material Science and Food Engineering, University of Electronic Science and Technology of China, Zhongshan Institute, Zhongshan, China
| | - Xueyan Li
- School of Material Science and Food Engineering, University of Electronic Science and Technology of China, Zhongshan Institute, Zhongshan, China
| | - Xiangli Li
- School of Health Industry, Zhongshan Torch Polytechnic, Zhongshan, China
| | - Mei Li
- School of Material Science and Food Engineering, University of Electronic Science and Technology of China, Zhongshan Institute, Zhongshan, China
| | - Lin Li
- School of Material Science and Food Engineering, University of Electronic Science and Technology of China, Zhongshan Institute, Zhongshan, China
| | - Lichao Zhao
- College of Food Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Min Hu
- School of Environmental Science and Engineering, Changzhou University, Changzhou, China
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Sáenz JS, Rios-Galicia B, Rehkugler B, Seifert J. Dynamic Development of Viral and Bacterial Diversity during Grass Silage Preservation. Viruses 2023; 15:v15040951. [PMID: 37112930 PMCID: PMC10146946 DOI: 10.3390/v15040951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/31/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Ensilaging is one of the most common feed preservation processes using lactic acid bacteria to stabilize feed and save feed quality. The silage bacterial community is well known but the role of the virome and its relationship with the bacterial community is scarce. In the present study, metagenomics and amplicon sequencing were used to describe the composition of the bacterial and viral community during a 40-day grass silage preservation. During the first two days, we observed a rapid decrease in the pH and a shift in the bacterial and viral composition. The diversity of the dominant virus operational taxonomic units (vOTUs) decreased throughout the preservation. The changes in the bacterial community resembled the predicted putative host of the recovered vOTUs during each sampling time. Only 10% of the total recovered vOTUs clustered with a reference genome. Different antiviral defense mechanisms were found across the recovered metagenome-assembled genomes (MAGs); however, only a history of bacteriophage infection with Lentilactobacillus and Levilactobacillus was observed. In addition, vOTUs harbored potential auxiliary metabolic genes related to carbohydrate metabolism, organic nitrogen, stress tolerance, and transport. Our data suggest that vOTUs are enriched during grass silage preservation, and they could have a role in the establishment of the bacterial community.
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Affiliation(s)
- Johan S Sáenz
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- HoLMiR-Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, 70593 Stuttgart, Germany
| | - Bibiana Rios-Galicia
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- HoLMiR-Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, 70593 Stuttgart, Germany
| | - Bianca Rehkugler
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- HoLMiR-Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, 70593 Stuttgart, Germany
| | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- HoLMiR-Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, 70593 Stuttgart, Germany
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