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Koide RT, Kanauchi M, Hashimoto Y. Variation Among Japanese Miso Breweries in Indoor Microbiomes is Mainly Ascribed to Variation in Type of Indoor Surface. Curr Microbiol 2024; 81:68. [PMID: 38236285 PMCID: PMC10796754 DOI: 10.1007/s00284-023-03591-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024]
Abstract
Miso is a microbially-fermented soybean food. The miso brewery indoor microbiome contributes to miso fermentation. Japanese breweries are not climate-controlled, so indoor spaces are strongly affected by the prevailing climate. Because climate influences microorganism distribution, our first hypothesis is that latitude, as a proxy for climate, is a major determinant of brewery indoor microbiome structure. Breweries vary in interior surface materials and in the way operations (steaming, processing, fermenting) are apportioned among rooms. Therefore, our second hypothesis is that more variability in indoor microbiomes exists among breweries than can be ascribed to a latitudinal gradient. Most miso produced today is inoculated with commercial microbial strains to standardize fermentation. If commercial strains outcompete indigenous microbes for membership in the indoor microbiome, this practice may homogenize indoor microbiomes among regions or breweries. Therefore, our third hypothesis is that inoculant fungal species dominate indoor fungal communities and make it impossible to distinguish communities among breweries or across their latitudinal gradient. We tested these hypotheses by sampling indoor surfaces in several breweries across a latitudinal gradient in Japan. We found that latitude had a significant but relatively small impact on indoor fungal and bacterial communities, that the effect of brewery was large relative to latitude, and that inoculant fungi made such small contributions to the indoor microbiome that distinctions among breweries and along the latitudinal gradient remained apparent. Recently, the Japanese Ministry of Agriculture, Forestry and Fisheries specified fungal inoculants to standardize miso production. However, this may not be possible so long as the indoor microbiome remains uncontrolled.
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Affiliation(s)
- Roger T Koide
- Department of Biology, Brigham Young University, Provo, UT, USA.
| | - Makoto Kanauchi
- Department of Food Management, Miyagi University, Sendai, Japan
| | - Yasushi Hashimoto
- Section of Ecology and Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
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2
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Zhu LX, Wang H, Han PJ, Lan YB. Identification of dominant functional microbes that contribute to the characteristic aroma of Msalais, traditional wine fermented from boiled local grape juice in China. Food Chem X 2023; 19:100778. [PMID: 37780303 PMCID: PMC10534102 DOI: 10.1016/j.fochx.2023.100778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 06/10/2023] [Accepted: 06/28/2023] [Indexed: 10/03/2023] Open
Abstract
Msalais is a traditional wine produced from naturally fermented boiled local grape juice in China. It has characteristic dried fruit and caramel odors, mainly attributed to aromatic compounds, such as furaneol and 5-methylfurfural. However, it is unclear how microbes involved in the natural fermentation of Msalais contribute to this characteristic aroma. Here, we analyzed the Msalais-fermenting microbes and aromatic compounds formed during natural Msalais fermentation by using high-throughput sequencing and gas chromatography-mass spectrometry, respectively. The analysis revealed that Saccharomyces cerevisiae, Kazachstania humilis, Lactobacillus plantarum, and Lactobacillus farraginis are the dominant and key functional species that produce high amounts of furaneol and 5-methylfurfural during Msalais fermentation. Of these, K. humilis and L. farraginis are rarely detected during regular wine fermentation. The identified functional species could be used to control typical aromatic characteristics of Msalais.
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Affiliation(s)
- Li-Xia Zhu
- Production and Construction Group, Key Laboratory of High-Quality Agricultural Product Extensive Processing in Southern Xinjiang, Tarim University, Alar, Xinjiang 843300, PR China
| | - Hui Wang
- Production and Construction Group, Key Laboratory of High-Quality Agricultural Product Extensive Processing in Southern Xinjiang, Tarim University, Alar, Xinjiang 843300, PR China
| | - Pei-jie Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yi-Bin Lan
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China
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3
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Lee HY, Cho DY, Jung JG, Kim MJ, Jeong JB, Lee JH, Lee GY, Jang MY, Lee JH, Haque MA, Cho KM. Comparisons of Physicochemical Properties, Bacterial Diversities, Isoflavone Profiles and Antioxidant Activities on Household and Commercial doenjang. Molecules 2023; 28:molecules28083516. [PMID: 37110750 PMCID: PMC10144870 DOI: 10.3390/molecules28083516] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/08/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
In this study, the physicochemical properties (pH, acidity, salinity, and soluble protein), bacterial diversities, isoflavone contents, and antioxidant activities of doenjang (fermented soy paste), household doenjang (HDJ), and commercial doenjang (CDJ), were assessed and compared. The values of pH 5.14-5.94 and acidity 1.36-3.03%, indicated a similar level in all doenjang. The salinity was high in CDJ at 12.8-14.6%, and the protein contents (25.69-37.54 mg/g) were generally high in HDJ. Forty-three species were identified from the HDJ and CDJ. The main species were verified to be Bacillus amyloliquefaciens (B. amyloliquefaciens), B. amyloliquefaciens subsp. plantarum, Bacillus licheniformis, Bacillus sp. and Bacillus subtilis. Comparing the ratios of isoflavone types, the HDJ has an aglycone ratio of >80%, and 3HDJ indicates a ratio of isoflavone to aglycone of 100%. In the CDJ, except 4CDJ, glycosides account for a high proportion of more than 50%. The results of antioxidant activities and DNA protection effects were variedly confirmed regardless of HDJs and CDJs. Through these results, it is judged that HDJs have a variety of bacterial species compared to CDJs, and these are biologically active and converted from glycoside to aglycone. Bacterial distribution and isoflavone contents could be used as basic data.
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Affiliation(s)
- Hee Yul Lee
- Department of Green Bio Science and Agri-Food Bio Convergence Institute, Gyeongsang National University, Jinju 52725, Republic of Korea
| | - Du Yong Cho
- Department of Green Bio Science and Agri-Food Bio Convergence Institute, Gyeongsang National University, Jinju 52725, Republic of Korea
| | - Jea Gack Jung
- Department of Green Bio Science and Agri-Food Bio Convergence Institute, Gyeongsang National University, Jinju 52725, Republic of Korea
| | - Min Ju Kim
- Department of Green Bio Science and Agri-Food Bio Convergence Institute, Gyeongsang National University, Jinju 52725, Republic of Korea
| | - Jong Bin Jeong
- Department of Green Bio Science and Agri-Food Bio Convergence Institute, Gyeongsang National University, Jinju 52725, Republic of Korea
| | - Ji Ho Lee
- Department of Green Bio Science and Agri-Food Bio Convergence Institute, Gyeongsang National University, Jinju 52725, Republic of Korea
| | - Ga Young Lee
- Department of Green Bio Science and Agri-Food Bio Convergence Institute, Gyeongsang National University, Jinju 52725, Republic of Korea
| | - Mu Yeun Jang
- Department of Food Science, Gyeongsang National University, Naedongro 139-8, Jinju 52849, Gyeongnam, Republic of Korea
| | - Jin Hwan Lee
- Department of Life Resource Industry, Dong-A University, 37, Nakdong-daero 550 beon-gil, Saha-gu, Busan 49315, Republic of Korea
| | - Md Azizul Haque
- Department of Biochemistry and Molecular Biology, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Kye Man Cho
- Department of Green Bio Science and Agri-Food Bio Convergence Institute, Gyeongsang National University, Jinju 52725, Republic of Korea
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Xiao L, Lapu M, Kang S, Jiang P, Li J, Liu Y, Liu D, Liu M. Effects of Tartary buckwheat on physicochemical properties and microbial community of low salt natural fermented soybean paste. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108953] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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5
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Ling H, Shi H, Chen X, Cheng K. Detection of the microbial diversity and flavour components of northeastern Chinese soybean paste during storage. Food Chem 2022; 374:131686. [PMID: 34906801 DOI: 10.1016/j.foodchem.2021.131686] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/05/2021] [Accepted: 11/23/2021] [Indexed: 11/17/2022]
Abstract
A combination of 16S rDNA and GC-IMS was used to study the changes in the composition of microorganisms and volatile organic compounds (VOCs) during the storage of northeastern Chinese soybean paste. Firmicutes and Actinobacteriota dominated the microbial communities of the soybean paste at the phylum level, bacterial profiles of different samples were different at genus level. Fifty-one VOCs were identified from soybean paste, most of which existed in the early storage stage. Most esters and alcohols decreased with the extension of the storage time, while acids and pyrazines accumulated in the later period of storage. Esters, alcohols, acids and aldehyde compounds are the key substances in the volatile components of soybean paste, which give the soybean paste the sour, sweet, rose, mushroom and smoky flavor characteristics. The biomarker Bacillus-velezensis in soybean paste is directly related to ester features; Kroppenstedtia, Sporolactobacillus-nakayamae, and Corynebacterium-stationis are positively associated with the biosynthesis of aldehydes.
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Affiliation(s)
- Hongzhi Ling
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China
| | - Huiling Shi
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China
| | - Xiaochun Chen
- Engineering Research Center of Health Food Design & Nutrition Regulation, School of Chemical Engineering and Energy Technology, Dongguan University of Technology, Dongguan 523808, China; Dongguan Institute of Technology Innovation, Dongguan 523000, China
| | - Keke Cheng
- Engineering Research Center of Health Food Design & Nutrition Regulation, School of Chemical Engineering and Energy Technology, Dongguan University of Technology, Dongguan 523808, China.
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Correlation between the quality and microbial community of natural-type and artificial-type Yongchuan Douchi. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110788] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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7
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Liu L, Chen X, Hao L, Zhang G, Jin Z, Li C, Yang Y, Rao J, Chen B. Traditional fermented soybean products: processing, flavor formation, nutritional and biological activities. Crit Rev Food Sci Nutr 2020; 62:1971-1989. [PMID: 33226273 DOI: 10.1080/10408398.2020.1848792] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Traditional fermented soybean food has emerged as an important part of people's dietary structure because of the unique flavors and improved health benefit. During fermentation, the nutrients in soybean undergo a series of biochemical reactions catalyzed naturally by microorganism secreted enzymes. Thereafter, many functional and bioactive substances such as bioactive peptides, unsaturated fatty acids, free soy isoflavones, vitamins and minerals are produced, making fermented soy products more advantageous in nutrition and health. This review comprehensively discusses the historical evolution, distribution, traditional fermentation processing, main sources and characteristics of fermented strains, flavor components, nutritional properties, and biological activities of four traditional fermented soybean foods including douchi, sufu, dajiang, and soy sauce. In the end, we introduce four major challenges encountered by traditional fermented soybean foods including high salt content, formation of biogenic amine, the presence of pathogenic microorganisms and mycotoxins, and quality inconsistency. We conclude that the establishment of scientific quality standard and innovated fermentation processing is the potential solutions to combat the issues and improve the safety of traditional fermented soybean products.
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Affiliation(s)
- Libo Liu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Xiaoqian Chen
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Linlin Hao
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Guofang Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Zhao Jin
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Chun Li
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Yuzhuo Yang
- Heilongjiang Green Food Research Institute, Harbin, China
| | - Jiajia Rao
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Bingcan Chen
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA
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8
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Sang X, Li K, Zhu Y, Ma X, Hao H, Bi J, Zhang G, Hou H. The Impact of Microbial Diversity on Biogenic Amines Formation in Grasshopper Sub Shrimp Paste During the Fermentation. Front Microbiol 2020; 11:782. [PMID: 32390997 PMCID: PMC7193991 DOI: 10.3389/fmicb.2020.00782] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/01/2020] [Indexed: 01/02/2023] Open
Abstract
Biogenic amines (BAs) and microbial diversity are important factors affecting food quality and safety in fermented foods. In this study, the bacterial and fungal diversity in grasshopper sub shrimp paste taken at different fermentation times were comprehensively analyzed, while the pH, colony counts, salinity, total volatile base nitrogen (TVB-N) and BA contents were quantitatively determined. In addition, the correlations among the samples with respect to microbial communities and the different parameters investigated especially BAs were also established. By combining the results of spearman correlation heatmap with the contents of BAs produced by the 102 halotolerant bacteria isolated from the grasshopper sub shrimp paste, six major genera of bacteria (Jeotgalibaca, Jeotgalicoccus, Lysinibacillus, Sporosarcina, Staphylococcus, and Psychrobacter) were found to be positively correlated with BA production level, suggesting that these bacteria might have a strong tendency to produce BAs. Other bacteria such as Lentibacillus, Pseudomonas, and Salinicoccus were considered as poor BA producers. The grasshopper sub shrimp paste was characterized by a relatively high abundance of Tetragenococcus, which was the dominant genus during the fermentation process, and it also produced a relatively high level of BAs but the spearman correlation heatmap revealed a negative correlation between T. muriaticus and BA level. Analysis of the species relevance network in grasshopper sub shrimp explained that the actual production of BAs by a certain strain was closely related to other species present in the complex fermentation system.
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Affiliation(s)
- Xue Sang
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian Polytechnic University, Dalian, China
| | - Kexin Li
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian Polytechnic University, Dalian, China
| | - Yaolei Zhu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian Polytechnic University, Dalian, China
| | - Xinxiu Ma
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian Polytechnic University, Dalian, China
| | - Hongshun Hao
- Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian Polytechnic University, Dalian, China
| | - Jingran Bi
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian Polytechnic University, Dalian, China
| | - Gongliang Zhang
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian Polytechnic University, Dalian, China
| | - Hongman Hou
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian Polytechnic University, Dalian, China
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9
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Lu Y, Tan X, Lv Y, Yang G, Chi Y, He Q. Physicochemical properties and microbial community dynamics during Chinese horse bean-chili-paste fermentation, revealed by culture-dependent and culture-independent approaches. Food Microbiol 2020; 85:103309. [PMID: 31500715 DOI: 10.1016/j.fm.2019.103309] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 07/31/2019] [Accepted: 08/20/2019] [Indexed: 02/06/2023]
Abstract
The production of Chinese horse bean-chili-paste (CHCP) involves three fermentation phases: chili-to-moromi fermentation (CF) phase, horse bean-to-meju fermentation (HF) phase and moromi-meju mixed fermentation (MF) phase. To understand the microbial dynamics among these three phases and the potential roles of viable microbes for fermentation, microbial community dynamics was investigated by using culture-dependent and culture-independent methods. Furthermore, the capacities of enzyme-producing of the isolates were determined. During the CF phase, reducing sugar content increased from 3.1% to 3.49%, while pH declined from 4.85 to 4.5. The protein content in the HF phase and MF phase reduced sharply from 22.23% to 10.29% and 4.39%-1.19%, respectively. Bacillus sp., Staphylococcus sp., Oceanobacillus sp., Candida sp., Zygosaccharomyces sp. and Aspergillus sp. dominated the CF phase, while Bacillus sp., Candida sp. and Zygosaccharomyces sp. were the dominant microorganisms in both the HF and MF phases. B. amyloliquefaciens, B. methylotrophicus, B. subtilis, B. licheniformis and A. oryzae possessed strong capacities of producing enzymes, i.e. α-amylase, cellulase and xylanase, acid protease and leucine aminopeptidase, and could make a great contribution to CHCP fermentation.
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Affiliation(s)
- Yunhao Lu
- College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, PR China
| | - Xinyi Tan
- College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, PR China
| | - Yuanping Lv
- College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, PR China
| | - Guohua Yang
- Sichuan Dandan Pixian-douban Co., Ltd., Chengdu, 610065, PR China
| | - Yuanlong Chi
- College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, PR China.
| | - Qiang He
- College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, PR China.
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10
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Wu J, Tian T, Liu Y, Shi Y, Tao D, Wu R, Yue X. The dynamic changes of chemical components and microbiota during the natural fermentation process in Da-Jiang, a Chinese popular traditional fermented condiment. Food Res Int 2018; 112:457-467. [DOI: 10.1016/j.foodres.2018.06.021] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 05/14/2018] [Accepted: 06/08/2018] [Indexed: 12/20/2022]
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11
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Gu J, Liu T, Sadiq FA, Yang H, Yuan L, Zhang G, He G. Biogenic amines content and assessment of bacterial and fungal diversity in stinky tofu – A traditional fermented soy curd. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2017.08.085] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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12
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Zhu L, Fan Z, Kuai H, Li Q. Batch-batch stable microbial community in the traditional fermentation process of huyumei broad bean pastes. Lett Appl Microbiol 2017; 65:226-233. [PMID: 28613417 DOI: 10.1111/lam.12765] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/08/2017] [Accepted: 06/08/2017] [Indexed: 11/29/2022]
Abstract
During natural fermentation processes, a characteristic microbial community structure (MCS) is naturally formed, and it is interesting to know about its batch-batch stability. This issue was explored in a traditional semi-solid-state fermentation process of huyumei, a Chinese broad bean paste product. The results showed that this MCS mainly contained four aerobic Bacillus species (8 log CFU per g), including B. subtilis, B. amyloliquefaciens, B. methylotrophicus, and B. tequilensis, and the facultative anaerobe B. cereus with a low concentration (4 log CFU per g), besides a very small amount of the yeast Zygosaccharomyces rouxii (2 log CFU per g). The dynamic change of the MCS in the brine fermentation process showed that the abundance of dominant species varied within a small range, and in the beginning of process the growth of lactic acid bacteria was inhibited and Staphylococcus spp. lost its viability. Also, the MCS and its dynamic change were proved to be highly reproducible among seven batches of fermentation. Therefore, the MCS naturally and stably forms between different batches of the traditional semi-solid-state fermentation of huyumei. SIGNIFICANCE AND IMPACT OF THE STUDY Revealing microbial community structure and its batch-batch stability is helpful for understanding the mechanisms of community formation and flavour production in a traditional fermentation. This issue in a traditional semi-solid-state fermentation of huyumei broad bean paste was firstly explored. This fermentation process was revealed to be dominated by a high concentration of four aerobic species of Bacillus, a low concentration of B. cereus and a small amount of Zygosaccharomyces rouxii. Lactic acid bacteria and Staphylococcus spp. lost its viability at the beginning of fermentation. Such the community structure was proved to be highly reproducible among seven batches.
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Affiliation(s)
- Linjiang Zhu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Institute of Fermentation Engineering, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Zihao Fan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Hui Kuai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Qi Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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13
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Lee MH, Li FZ, Lee J, Kang J, Lim SI, Nam YD. Next-Generation Sequencing Analyses of Bacterial Community Structures in Soybean Pastes Produced in Northeast China. J Food Sci 2017; 82:960-968. [PMID: 28253439 DOI: 10.1111/1750-3841.13665] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 01/07/2017] [Accepted: 01/25/2017] [Indexed: 12/11/2022]
Abstract
Fermented soybean foods contain nutritional components including easily digestible peptides, cholesterol-free oils, minerals, and vitamins. Various fermented soybean foods have been developed and are consumed as flavoring condiments in Asian regions. While the quality of fermented soybean foods is largely affected by microorganisms that participate in the fermentation process, our knowledge about the microorganisms in soybean pastes manufactured in Northeast China is limited. The current study used a culture-independent barcoded pyrosequencing method targeting hypervariable V1/V2 regions of the 16S rRNA gene to evaluate Korean doenjang and soybean pastes prepared by the Hun Chinese (SPHC) and Korean minority (SPKM) populations in Northeast China. In total, 63399 high-quality sequences were derived from 16 soybean paste samples collected in Northeast China. Each bacterial species-level taxon of SPHC, SPKM, and Korean doenjang was clustered separately. Each paste contained representative bacterial species that could be distinguished from each other: Bacillus subtilis in SPKM, Tetragenococcus halophilus in SPHC, and Enterococcus durans in Korean doenjang. This is the 1st massive sequencing-based study analyzing microbial communities in soybean pastes manufactured in Northeast China, compared to Korean doenjang. Our results clearly showed that each soybean paste contained unique microbial communities that varied depending on the manufacturing process and location.
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Affiliation(s)
- Mi-Hwa Lee
- Gut Microbiome Research Group, Korea Food Research Inst., Baekhyun-Dong, Bundang-Ku, Sungnam-Si, Gyeonggi-Do, 463-746, Republic of Korea
- Nakdonggang Natl. Inst. of Biological Resources, 137, Donam2-gil, Sangju-si, Gyeongsangbuk-do, 742-350, Republic of Korea
| | - Fan-Zhu Li
- Dept. of Food Science and Technology, Agricultural College of Yanbian Univ., Yanji, Jilin, 133002, P. R. China
| | - Jiyeon Lee
- Gut Microbiome Research Group, Korea Food Research Inst., Baekhyun-Dong, Bundang-Ku, Sungnam-Si, Gyeonggi-Do, 463-746, Republic of Korea
| | - Jisu Kang
- Gut Microbiome Research Group, Korea Food Research Inst., Baekhyun-Dong, Bundang-Ku, Sungnam-Si, Gyeonggi-Do, 463-746, Republic of Korea
- Korea Univ. of Science and Technology, Daejeon, 305-350, Republic of Korea
| | - Seong-Il Lim
- Gut Microbiome Research Group, Korea Food Research Inst., Baekhyun-Dong, Bundang-Ku, Sungnam-Si, Gyeonggi-Do, 463-746, Republic of Korea
| | - Young-Do Nam
- Gut Microbiome Research Group, Korea Food Research Inst., Baekhyun-Dong, Bundang-Ku, Sungnam-Si, Gyeonggi-Do, 463-746, Republic of Korea
- Korea Univ. of Science and Technology, Daejeon, 305-350, Republic of Korea
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14
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Yang L, Yang HL, Tu ZC, Wang XL. High-Throughput Sequencing of Microbial Community Diversity and Dynamics during Douchi Fermentation. PLoS One 2016; 11:e0168166. [PMID: 27992473 PMCID: PMC5167551 DOI: 10.1371/journal.pone.0168166] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 11/24/2016] [Indexed: 12/02/2022] Open
Abstract
Douchi is a type of Chinese traditional fermented food that is an important source of protein and is used in flavouring ingredients. The end product is affected by the microbial community present during fermentation, but exactly how microbes influence the fermentation process remains poorly understood. We used an Illumina MiSeq approach to investigate bacterial and fungal community diversity during both douchi-koji making and fermentation. A total of 181,443 high quality bacterial 16S rRNA sequences and 221,059 high quality fungal internal transcribed spacer reads were used for taxonomic classification, revealing eight bacterial and three fungal phyla. Firmicutes, Actinobacteria and Proteobacteria were the dominant bacterial phyla, while Ascomycota and Zygomycota were the dominant fungal phyla. At the genus level, Staphylococcus and Weissella were the dominant bacteria, while Aspergillus and Lichtheimia were the dominant fungi. Principal coordinate analysis showed structural separation between the composition of bacteria in koji making and fermentation. However, multivariate analysis of variance based on unweighted UniFrac distances did identify distinct differences (p <0.05), and redundancy analysis identified two key genera that are largely responsible for the differences in bacterial composition between the two steps. Staphylococcus was enriched in koji making, while Corynebacterium was enriched in fermentation. This is the first investigation to integrate douchi fermentation and koji making and fermentation processes through this technological approach. The results provide insight into the microbiome of the douchi fermentation process, and reveal a structural separation that may be stratified by the environment during the production of this traditional fermented food.
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Affiliation(s)
- Lin Yang
- Key Lab of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, China
| | - Hui-lin Yang
- Key Lab of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, China
| | - Zong-cai Tu
- Key Lab of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, China
| | - Xiao-lan Wang
- Key Lab of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, China
- * E-mail:
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15
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Miguel MGCP, Collela CF, de Almeida EG, Dias DR, Schwan RF. Physicochemical and microbiological description ofCaxiri -a cassava and corn alcoholic beverage. Int J Food Sci Technol 2015. [DOI: 10.1111/ijfs.12921] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
| | | | | | - Disney R. Dias
- Biology Department; Federal University of Lavras; Lavras 37200-000 Brazil
| | - Rosane F. Schwan
- Biology Department; Federal University of Lavras; Lavras 37200-000 Brazil
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16
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Sulaiman J, Gan HM, Yin WF, Chan KG. Microbial succession and the functional potential during the fermentation of Chinese soy sauce brine. Front Microbiol 2014; 5:556. [PMID: 25400624 PMCID: PMC4215829 DOI: 10.3389/fmicb.2014.00556] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 10/05/2014] [Indexed: 12/05/2022] Open
Abstract
The quality of traditional Chinese soy sauce is determined by microbial communities and their inter-related metabolic roles in the fermentation tank. In this study, traditional Chinese soy sauce brine samples were obtained periodically to monitor the transitions of the microbial population and functional properties during the 6 months of fermentation process. Whole genome shotgun method revealed that the fermentation brine was dominated by the bacterial genus Weissella and later dominated by the fungal genus Candida. Metabolic reconstruction of the metagenome sequences demonstrated a characteristic profile of heterotrophic fermentation of proteins and carbohydrates. This was supported by the detection of ethanol with stable decrease of pH values. To the best of our knowledge, this is the first study that explores the temporal changes in microbial successions over a period of 6 months, through metagenome shotgun sequencing in traditional Chinese soy sauce fermentation and the biological processes therein.
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Affiliation(s)
- Joanita Sulaiman
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of MalayaKuala Lumpur, Malaysia
| | - Han Ming Gan
- School of Science, Monash University MalaysiaPetaling Jaya, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of MalayaKuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of MalayaKuala Lumpur, Malaysia
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17
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Wang P, Mao J, Meng X, Li X, Liu Y, Feng H. Changes in flavour characteristics and bacterial diversity during the traditional fermentation of Chinese rice wines from Shaoxing region. Food Control 2014. [DOI: 10.1016/j.foodcont.2014.03.018] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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18
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Evaluation of the aroma quality of Chinese traditional soy paste during storage based on principal component analysis. Food Chem 2014; 151:532-8. [DOI: 10.1016/j.foodchem.2013.11.095] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 10/08/2013] [Accepted: 11/18/2013] [Indexed: 11/20/2022]
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19
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Chen T, Wang M, Li S, Wu Q, Wei H. Molecular identification of microbial community in surface and undersurface douchi during postfermentation. J Food Sci 2014; 79:M653-8. [PMID: 24621312 DOI: 10.1111/1750-3841.12417] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 10/23/2013] [Indexed: 12/01/2022]
Abstract
To find the reason for fermentation failure of surface Douchi during postfermentation, the microbial communities in undersurface and surface samples were investigated using cell counting method and denaturing gradient gel electrophoresis (DGGE). The results showed that the microbial biomass in surface Douchi was obviously different from that in undersurface Douchi even sampled from the same fermentation tanks, and a 10- to 100-fold reduction of microbial cell counts in undersurface had been observed. The bacterial DGGE profile and principal component analysis (PCA) results indicated that only Lactococcus lacts subsp. lactis and Bacillus thermoamylovorans were detected from surface Douchi, while Lactococcus lacts subsp. lactis, Staphylococcus lentus and 2 uncultured strains occupied the dominant positions in undersurface Douchi; when amplified using Bacillus-specific primers, Bacillus thermoamylovorans, Bacillus subtilis, and Enterobacter sp. were found in undersurface Douchi, while only Bacillus thermoamylovorans were detected from surface Douchi; compared to the bacteria and Bacillus, the DGGE profiles and PCA plot of fungi indicated that the fungal community between surface and undersurface Douchi was similar and mainly composed by yeasts. In this study, we detected the microbial biomass and species in postfermentation stage of Douchi, and the various microbial diversity in undersurface and surface samples might be the cause of the fermentation failure in surface fermentation tanks.
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Affiliation(s)
- Tingtao Chen
- State Key Laboratory of Food Science and Technology, Nanchang, Jiangxi, 330047, China; Inst. of Translational Medicine, Nanchang Univ, Nanchang, Jiangxi, 332000, PR China
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20
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Wu JR, Zhang JC, Shi P, Wu R, Yue XQ, Zhang HP. Bacterial community involved in traditional fermented soybean paste dajiang made in northeast China. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0604-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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21
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Chen T, Jiang S, Xiong S, Wang M, Zhu D, Wei H. Application of denaturing gradient gel electrophoresis to microbial diversity analysis in Chinese Douchi. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2012; 92:2171-2176. [PMID: 22318896 DOI: 10.1002/jsfa.5604] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2011] [Revised: 12/04/2011] [Accepted: 12/25/2011] [Indexed: 05/31/2023]
Abstract
BACKGROUND Douchi is a traditional Chinese soybean food which has been consumed for thousands years as an important protein source and flavouring ingredient. Studies have rarely been carried out to investigate its microbial composition and these are urgently required for the commercial labels and safety considerations. RESULTS Microbial counts were statistically significant different among Douchi samples. Although the maximum diversity indexes of bacterial, bacillus and fungal polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) patterns were only 79%, 70% and 64%, some microorganisms, e.g. Bacillus subtilis, Bacillus amyloliquefaciens, Pseudomonas sp., Saccharomyces cerevisiae and Pichia farinose, were found to share dominant positions in most Douchi samples. In addition, some pathogens, e.g. Staphylococcus saprophyticus, Pantoea sp., Staphylococcus sciuri, Enterobacter sp. and Staphylococcus sp., were also identified. CONCLUSION The PCR-DGGE technique was used for the first time as an effective method to assess the microbial communities in different Chinese Douchi samples. This information may be useful in improving the product quality, reformatting production methods, extending shelf life and scaling up the fermentation process.
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Affiliation(s)
- Tingtao Chen
- State Key Laboratory of Food Science and Technology, Nanchang University, Jiangxi 330047, China
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22
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Hu H, Hao J, Cheng Y, Yin L, Ma Y, Yu Z, Li L. Effect of fermented rice culture on the microbiological, biochemical and sensory characteristics of low-salt douchi, a traditional Chinese fermented soybean condiment. Int J Food Sci Technol 2012. [DOI: 10.1111/j.1365-2621.2011.02894.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Nam YD, Lee SY, Lim SI. Microbial community analysis of Korean soybean pastes by next-generation sequencing. Int J Food Microbiol 2012; 155:36-42. [PMID: 22305887 DOI: 10.1016/j.ijfoodmicro.2012.01.013] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 01/16/2012] [Accepted: 01/16/2012] [Indexed: 11/18/2022]
Abstract
Soybean pastes, doenjang, have long been consumed as a fortified protein source in Korea. The quality of doenjang is determined by fermentation and Bacillus subtilis is suspected to be the main microorganism responsible. In the current culture-independent analysis, 17,675 bacterial sequences were derived from nine local and two commercial brands of doenjang samples by a barcoded pyrosequencing method targeting the hyper-variable regions V1/V2 of the 16S rRNA gene. In contrast to what has previously been found using plating or conventional molecular biology based methods, doenjang contains a diversity of bacterial species (total 208 species) and each doenjang reflects a region-specific bacterial community. While the Bacillus species was thought to be dominant in soybean pastes, we found that they were in high abundance (58.3-91.6%) only in samples from the central region of Korea, whereas lactic acid bacteria (LAB) (39.8-77.7%) were the dominant bacterial members of other doenjang samples. Compared to local brands of doenjang, commercial brands contain simple microbial communities dominated by Tetragenococcus and Staphylococcus that resemble the microbial communities of Japanese miso; this suggests that artificial inoculation was used for the quality control and standardization of doenjang. In this study, a massive sequencing approach was applied for the first time to analyze the microbial communities of different doenjang samples. Thus, we have determined that massive sequencing is a valid approach for assessing the overall microbial community of Korean fermented soybean pastes.
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Affiliation(s)
- Young-Do Nam
- Fermentation and Functionality Research Group, Korea Food Research Institute, Sungnam, Republic of Korea
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24
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Chen T, Xiong S, Jiang S, Wang M, Wu Q, Wei H. Molecular identification of microbial community in Chinese douchi during post-fermentation process. Food Sci Biotechnol 2011. [DOI: 10.1007/s10068-011-0225-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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25
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Chen T, Wang M, Jiang S, Xiong S, Zhu D, Wei H. Investigation of the microbial changes during koji-making process of Douchi by culture-dependent techniques and PCR-DGGE. Int J Food Sci Technol 2011. [DOI: 10.1111/j.1365-2621.2011.02696.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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26
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Wang HY, Gao YB, Fan QW, Xu Y. Characterization and comparison of microbial community of different typical Chinese liquor Daqus by PCR-DGGE. Lett Appl Microbiol 2011; 53:134-40. [PMID: 21554340 DOI: 10.1111/j.1472-765x.2011.03076.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To identify and compare microbiota in Chinese liquor Daqu, which were produced in the different regions using different production process. METHODS AND RESULTS The DNA exacted from Daqu samples was used as a template for PCR with universal primers of 16S rRNA, 26S rRNA and 18S rRNA, respectively. The amplicons were analysed using denaturing gradient gel electrophoresis (DGGE). It was observed that the bacterial DGGE profile indicated high diversity and predominance of lactic acid bacteria. The results showed that Saccharomycopsis fibuligera and Pichia anomal were dominant yeast species and that several non-Saccharomyces yeasts including Hanseniaspora guilliermondii, Debaryomyces hansenii, Issatchenkia orientalis and Trichosporon asahii were also detected. As for fungal DGGE, Aspergillus oryzae and Absidia blakesleeana were the most common species amongst different samples. Based on the DGGE analysis, a few differences in community structure were found between Daqu samples. CONCLUSIONS A variety of bacteria, yeast and moulds were identified in Daqu samples, in addition to the present knowledge obtained mainly through the traditional culture-dependent methods. Moreover, production temperature played a more decisive role on the formation of micro-organism composition in Daqu than geographical region. SIGNIFICANCE AND IMPACT OF THE STUDY PCR-DGGE technique was used in this study to fully observe and asses all microbial community (including bacteria, yeast and mould) in Chinese liquor Daqu for the first time and proved to be effective in profiling Daqu microbial diversity.
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Affiliation(s)
- H-Y Wang
- State Key Laboratory of Food Science and Technology, Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Jiangsu, China
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