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Chen L, Wang G, Teng M, Wang L, Yang F, Jin G, Du H, Xu Y. Non-gene-editing microbiome engineering of spontaneous food fermentation microbiota-Limitation control, design control, and integration. Compr Rev Food Sci Food Saf 2023; 22:1902-1932. [PMID: 36880579 DOI: 10.1111/1541-4337.13135] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/01/2023] [Accepted: 02/17/2023] [Indexed: 03/08/2023]
Abstract
Non-gene-editing microbiome engineering (NgeME) is the rational design and control of natural microbial consortia to perform desired functions. Traditional NgeME approaches use selected environmental variables to force natural microbial consortia to perform the desired functions. Spontaneous food fermentation, the oldest kind of traditional NgeME, transforms foods into various fermented products using natural microbial networks. In traditional NgeME, spontaneous food fermentation microbiotas (SFFMs) are typically formed and controlled manually by the establishment of limiting factors in small batches with little mechanization. However, limitation control generally leads to trade-offs between efficiency and the quality of fermentation. Modern NgeME approaches based on synthetic microbial ecology have been developed using designed microbial communities to explore assembly mechanisms and target functional enhancement of SFFMs. This has greatly improved our understanding of microbiota control, but such approaches still have shortcomings compared to traditional NgeME. Here, we comprehensively describe research on mechanisms and control strategies for SFFMs based on traditional and modern NgeME. We discuss the ecological and engineering principles of the two approaches to enhance the understanding of how best to control SFFM. We also review recent applied and theoretical research on modern NgeME and propose an integrated in vitro synthetic microbiota model to bridge gaps between limitation control and design control for SFFM.
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Affiliation(s)
- Liangqiang Chen
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Kweichow Moutai Distillery Co., Ltd., Zunyi, China
| | | | | | - Li Wang
- Kweichow Moutai Distillery Co., Ltd., Zunyi, China
| | - Fan Yang
- Kweichow Moutai Distillery Co., Ltd., Zunyi, China
| | - Guangyuan Jin
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Hai Du
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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Yao Z, Zhu Y, Wu Q, Xu Y. Challenges and perspectives of quantitative microbiome profiling in food fermentations. Crit Rev Food Sci Nutr 2022; 64:4995-5015. [PMID: 36412251 DOI: 10.1080/10408398.2022.2147899] [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] [Indexed: 11/23/2022]
Abstract
Spontaneously fermented foods are consumed and appreciated for thousands of years although they are usually produced with fluctuated productivity and quality, potentially threatening both food safety and food security. To guarantee consistent fermentation productivity and quality, it is essential to control the complex microbiota, the most crucial factor in food fermentations. The prerequisite for the control is to comprehensively understand the structure and function of the microbiota. How to quantify the actual microbiota is of paramount importance. Among various microbial quantitative methods evolved, quantitative microbiome profiling, namely to quantify all microbial taxa by absolute abundance, is the best method to understand the complex microbiota, although it is still at its pioneering stage for food fermentations. Here, we provide an overview of microbial quantitative methods, including the development from conventional methods to the advanced quantitative microbiome profiling, and the application examples of these methods. Moreover, we address potential challenges and perspectives of quantitative microbiome profiling methods, as well as future research needs for the ultimate goal of rational and optimal control of microbiota in spontaneous food fermentations. Our review can serve as reference for the traditional food fermentation sector for stable fermentation productivity, quality and safety.
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Affiliation(s)
- Zhihao Yao
- Lab 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
| | - Yang Zhu
- Bioprocess Engineering, Wageningen University and Research, Wageningen, The Netherlands
| | - Qun Wu
- Lab 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
- Lab 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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Chen J, Yan R, Hu Y, Zhang N, Hu H. Compositional shifts in the fungal diversity of garlic scapes during postharvest transportation and cold storage. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2019.108453] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Xiong T, Chen J, Huang T, Xie M, Xiao Y, Liu C, Peng Z. Fast evaluation by quantitative PCR of microbial diversity and safety of Chinese Paocai inoculated with Lactobacillus plantarum NCU116 as the culture starter. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2018.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Amplicon and shotgun metagenomic sequencing indicates that microbial ecosystems present in cheese brines reflect environmental inoculation during the cheese production process. Int Dairy J 2018. [DOI: 10.1016/j.idairyj.2018.07.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Liang H, Chen H, Ji C, Lin X, Zhang W, Li L. Dynamic and Functional Characteristics of Predominant Species in Industrial Paocai as Revealed by Combined DGGE and Metagenomic Sequencing. Front Microbiol 2018; 9:2416. [PMID: 30356774 PMCID: PMC6189446 DOI: 10.3389/fmicb.2018.02416] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/20/2018] [Indexed: 01/12/2023] Open
Abstract
The microbial community during the fermentation of industrial paocai, a lactic acid fermented vegetable food, was investigated via combined denaturing gradient gel electrophoresis (DGGE) and metagenomic sequencing. Firmicutes and Proteobacteria were identified as the dominant phyla during the fermentation. DGGE results of the bacterial community analysis showed that many genera were observed during the fermentation of industrial paocai, but the same predominant genus and species were observed: Lactobacillus and Lactobacillus (L.) alimentarius/L. paralimentarius. The abundance of L. alimentarius/L. paralimentarius increased fast during the initial stage of fermentation and approximately remained constant during the later stage. Metagenomic sequencing was used to finally identify the predominant species and their genetic functions. Metabolism was the primary functions of the microbial community in industrial paocai fermentation, including carbohydrate metabolism (CM), overview (OV), amino acid metabolism (AAM), nucleotide metabolism (NM), energy metabolism (EM), etc. The predominant species L. alimentarius and L. paralimentarius were involved in plenty of pathways in metabolism and played different roles in the metabolism of carbohydrate, amino acid, lipid to form flavor compounds during industrial paocai fermentation. This study provided valuable information about the predominant species in industrial paocai and its functional properties, which could enable us to advance our understanding of the fermentation mechanism during fermentation of industrial paocai. Our results will advance the understanding of the microbial roles in the industrial paocai fermentation and provide a theoretical basis for improving the quality of industrial paocai products.
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Affiliation(s)
- Huipeng Liang
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
| | - Huiying Chen
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
| | - Chaofan Ji
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
| | - Xinping Lin
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
| | - Wenxue Zhang
- Food Eco-engineering and Biotechnology Lab, College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu, China
| | - Li Li
- College of Biotechnology Engineering, Sichuan University of Science and Engineering, Zigong, China
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Liang H, Chen H, Zhang W, Yu C, Ji C, Lin X. Investigation on microbial diversity of industrial Zhacai paocai during fermentation using high-throughput sequencing and their functional characterization. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2018.01.088] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Du R, Song G, Zhao D, Sun J, Ping W, Ge J. Lactobacillus caseistarter culture improves vitamin content, increases acidity and decreases nitrite concentration during sauerkraut fermentation. Int J Food Sci Technol 2018. [DOI: 10.1111/ijfs.13779] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Renpeng Du
- Key Laboratory of Microbiology; College of Life Science; Heilongjiang University; Harbin 150080 China
| | - Gang Song
- Key Laboratory of Microbiology; College of Life Science; Heilongjiang University; Harbin 150080 China
- Engineering Research Center of Agricultural Microbiology Technology; Ministry of Education; Heilongjiang University; Harbin 150500 China
| | - Dan Zhao
- Key Laboratory of Microbiology; College of Life Science; Heilongjiang University; Harbin 150080 China
- Engineering Research Center of Agricultural Microbiology Technology; Ministry of Education; Heilongjiang University; Harbin 150500 China
| | - Jian Sun
- Key Laboratory of Microbiology; College of Life Science; Heilongjiang University; Harbin 150080 China
| | - Wenxiang Ping
- Key Laboratory of Microbiology; College of Life Science; Heilongjiang University; Harbin 150080 China
- Engineering Research Center of Agricultural Microbiology Technology; Ministry of Education; Heilongjiang University; Harbin 150500 China
| | - Jingping Ge
- Key Laboratory of Microbiology; College of Life Science; Heilongjiang University; Harbin 150080 China
- Engineering Research Center of Agricultural Microbiology Technology; Ministry of Education; Heilongjiang University; Harbin 150500 China
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Dynamics and diversity of a microbial community during the fermentation of industrialized Qingcai paocai, a traditional Chinese fermented vegetable food, as assessed by Illumina MiSeq sequencing, DGGE and qPCR assay. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-017-1321-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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