1
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Bae S, Choi YJ, Park SE, Kim EJ, Lee MJ, Chung YB, Park SH, Min SG, Ku KM, Seo HY, Son HS. Effects of seasonal harvest of kimchi cabbage on microbial and metabolic profiles of kimchi. Food Res Int 2024; 188:114476. [PMID: 38823866 DOI: 10.1016/j.foodres.2024.114476] [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: 01/01/2024] [Revised: 03/28/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
Kimchi cabbage, the key ingredient in kimchi, is cultivated year-round to meet high production demands. This study aimed to examine the effects of seasonal harvesting (spring, summer, fall, and winter) on the microbial and metabolic profiles of kimchi during 30 days of fermentation. Lactic acid bacteria distribution is notably influenced by seasonal variations, with Latilactobacillus dominant in fall-harvested kimchi group and Weissella prevailing in spring, summer, and winter. The microbial communities of spring and fall group exhibited similar profiles before fermentation, whereas the microbial communities and metabolic profiles of spring and summer group were similar after 30 days of fermentation. Seasonal disparities in metabolite concentrations, including glutamic acid, serine, and cytosine, persist throughout fermentation. This study provides a comprehensive understanding of the substantial impact of seasonal harvesting of kimchi cabbage on the microbial and metabolic characteristics of kimchi, providing valuable insights into producing kimchi with diverse qualities.
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Affiliation(s)
- Soobin Bae
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea.
| | - Yun-Jeong Choi
- Kimchi Industry Promotion Division, World Institute of Kimchi, Gwangju 61755, Republic of Korea.
| | - Seong-Eun Park
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea.
| | - Eun-Ju Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea.
| | - Min Jung Lee
- Kimchi Industry Promotion Division, World Institute of Kimchi, Gwangju 61755, Republic of Korea.
| | - Young Bae Chung
- Kimchi Industry Promotion Division, World Institute of Kimchi, Gwangju 61755, Republic of Korea.
| | - Sung Hee Park
- Kimchi Industry Promotion Division, World Institute of Kimchi, Gwangju 61755, Republic of Korea.
| | - Sung Gi Min
- Kimchi Industry Promotion Division, World Institute of Kimchi, Gwangju 61755, Republic of Korea.
| | - Kang-Mo Ku
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea.
| | - Hye-Young Seo
- Kimchi Industry Promotion Division, World Institute of Kimchi, Gwangju 61755, Republic of Korea.
| | - Hong-Seok Son
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea.
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2
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Seo WH, You Y, Baek HH. Changes in volatile flavor compounds of Kimchi cabbage ( Brassica rapa subsp. pekinensis) during salting and fermentation. Food Sci Biotechnol 2024; 33:1623-1632. [PMID: 38623438 PMCID: PMC11016023 DOI: 10.1007/s10068-023-01469-w] [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: 07/13/2023] [Revised: 09/21/2023] [Accepted: 10/12/2023] [Indexed: 04/17/2024] Open
Abstract
A main ingredient of Kimchi is Kimchi cabbage, which is soaked in brine to reduce its crispness. Volatile profile of raw Kimchi cabbage (RC) is changed during salting; however, characteristic aroma-active compounds of salted Kimchi cabbage (SC) have not been investigated. The objective of this study was to evaluate changes in aroma characteristics of Kimchi cabbage during salting and fermentation. Sulfur-containing compounds, such as sulfides and isothiocyanates, increased markedly by salting. (Z)-3-Hexen-1-ol, (Z)-3-hexenal, and hexanal decreased by salting. Hexanal was the most intense in RC, followed by 3-(methylthio)butanal, (Z)-3-hexen-1-ol, and benzenepropanenitrile. Dimethyl trisulfide had the highest log3FD in SC. Methyl (methylthio)methyl disulfide, allyl methyl trisulfide, and dimethyl tetrasulfide were detected only in SC. Dimethyl trisulfide, dimethyl tetrasulfide, methyl (methylthio) methyl disulfide, and allyl methyl trisulfide, decreased greatly in SC during fermentation. Our results demonstrated that characteristic odor of Kimchi cabbage could be significantly changed by salting and fermentation.
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Affiliation(s)
- Won Ho Seo
- R&D Solution Center, OURHOME, 91 Magokjungang 10-Ro, Gangseo-Gu, Seoul, 07792 Republic of Korea
| | - Youngsang You
- Department of Food Engineering, Dankook University, 119 Dandae-Ro, Dongnam-Gu, Cheonan, Chungcheongnam-Do 31116 Republic of Korea
| | - Hyung Hee Baek
- Department of Food Engineering, Dankook University, 119 Dandae-Ro, Dongnam-Gu, Cheonan, Chungcheongnam-Do 31116 Republic of Korea
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3
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Kim SJ, Ha S, Dang YM, Chang JY, Mun SY, Ha JH. Combined Non-Thermal Microbial Inactivation Techniques to Enhance the Effectiveness of Starter Cultures for Kimchi Fermentation. J Microbiol Biotechnol 2024; 34:622-633. [PMID: 37997263 PMCID: PMC11016767 DOI: 10.4014/jmb.2310.10010] [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: 10/10/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023]
Abstract
For quality standardization, the application of functional lactic acid bacteria (LAB) as starter cultures for food fermentation is a well-known method in the fermented food industry. This study assessed the effect of adding a non-thermally microbial inactivated starter culture to kimchi, a traditional Korean food, in standardizing its quality. In this study, pretreatment based on sterilization processes, namely, slightly acidic electrolyzed water (SAEW) disinfection and ultraviolet C light-emitting diode (UVC-LED) of raw and subsidiary kimchi materials were used to reduce the initial microorganisms in them, thereby increasing the efficiency and value of the kimchi LAB starter during fermentation. Pretreatment sterilization effectively suppressed microorganisms that threatened the sanitary value and quality of kimchi. In addition, pretreatment based on sterilization effectively reduced the number of initial microbial colonies in kimchi, creating an environment in which kimchi LAB starters could settle or dominate, compared to non-sterilized kimchi. These differences in the initial microbial composition following the sterilization process and the addition of kimchi LAB starters led to differences in the metabolites that positively affect the taste and flavor of kimchi. The combined processing technology used in our study, that is, pre-sterilization and LAB addition, may be a powerful approach for kimchi quality standardization.
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Affiliation(s)
- Su-Ji Kim
- Hygienic Safety · Materials Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
- Department of Food Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Sanghyun Ha
- Hygienic Safety · Materials Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - Yun-Mi Dang
- Hygienic Safety · Materials Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - Ji Yoon Chang
- Fermentation Regulation Technology Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - So Yeong Mun
- Fermentation Regulation Technology Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - Ji-Hyoung Ha
- Hygienic Safety · Materials Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
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4
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White K, Eraclio G, McDonnell B, Bottacini F, Lugli GA, Ventura M, Volontè F, Dal Bello F, Mahony J, van Sinderen D. A multifaceted investigation of lactococcal strain diversity in undefined mesophilic starter cultures. Appl Environ Microbiol 2024; 90:e0215223. [PMID: 38334291 PMCID: PMC10952461 DOI: 10.1128/aem.02152-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 12/20/2023] [Indexed: 02/10/2024] Open
Abstract
The dairy fermentation industry relies on the activity of lactic acid bacteria in robust starter cultures to accomplish milk acidification. Maintenance of the composition of these starter cultures, whether defined or undefined, is essential to ensure consistent and high-quality fermentation end products. To date, limited information exists regarding the microbial composition of undefined starter culture systems. Here, we describe a culture-based analysis combined with a metagenomics approach to evaluate the composition of two undefined mesophilic starter cultures. In addition, we describe a qPCR-based genotype detection assay, which is capable of discerning nine distinct lactococcal genotypes to characterize these undefined starter cultures, and which can be applied to monitor compositional changes in an undefined starter culture during a fermentation. IMPORTANCE This study reports on the development of a combined culture-based analysis and metagenomics approach to evaluate the composition of two undefined mesophilic starter cultures. In addition, a novel qPCR-based genotype detection assay, capable of discerning nine distinct lactococcal genotypes (based on lactococcal cell wall polysaccharide biosynthesis gene clusters), was used to monitor compositional changes in an undefined starter culture following phage attack. These analytical approaches facilitate a multifaceted assessment of starter culture compositional stability during milk fermentation, which has become an important QC aspect due to the increasing demand for consistent and high-quality dairy products.
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Affiliation(s)
- Kelsey White
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Brian McDonnell
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Francesca Bottacini
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Gabriele Andrea Lugli
- Department of Chemistry, Life Sciences, and Environmental Sustainability, Laboratory of Probiogenomics,University of Parma, Parma, Italy
| | - Marco Ventura
- Department of Chemistry, Life Sciences, and Environmental Sustainability, Laboratory of Probiogenomics,University of Parma, Parma, Italy
| | | | | | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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5
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Xiang Y, Zhou B, Jiang C, Tang Z, Liu P, Ding W, Lin H, Tang J. Revealing the formation mechanisms of key flavors in fermented broad bean paste. Food Res Int 2024; 177:113880. [PMID: 38225117 DOI: 10.1016/j.foodres.2023.113880] [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: 06/11/2023] [Revised: 12/08/2023] [Accepted: 12/14/2023] [Indexed: 01/17/2024]
Abstract
Pixian Douban (PXDB) is a popular Chinese condiment for its distinctive flavor. Broad bean fermentation (Meju) is the most important process in the formation of flavor substances. Key flavors were analyzed qualitatively and quantitatively, and metagenomic technology was applied to study the microbial diversity during broad bean fermentation. In addition, the main metabolic pathways of key flavors were explored. Results indicated that Staphylococcus_gallinarum was the main microorganism in the microbial community, accounting for 39.13%, followed by Lactobacillus_agilis, accounting for 13.76%. Aspergillus_flavus was the fungus with the highest species abundance, accounting for 3.02%. The KEGG Pathway enrichment analysis showed that carbohydrate metabolism and amino acid metabolism were the main metabolic pathways. Glycoside hydrolase and glycosyltransferase genes were the most abundant, accounting for more than 70% of the total number of active enzyme genes. A total of 113 enzymes related to key flavors and 39 microorganisms corresponding to enzymes were annotated. And Staphylococcus_gallinarum, Lactobacillus_agilis, Weissella_confusa, Pediococcus_acidilactici, Staphylococcus_kloosii, Aspergillus_oryzae, and Aspergillus_flavus played a key role in the metabolic pathway. This study reveals the formation mechanism of key flavors in fermented broad bean, it is important for guiding the industrial production of PXDB and improving product quality.
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Affiliation(s)
- Yue Xiang
- School of Food and Bio-engineering, Xihua University, Chengdu 610039, China; Food Microbiology Key Laboratory of Sichuan Province, Chengdu 610039, China.
| | - Binbin Zhou
- School of Food and Bio-engineering, Xihua University, Chengdu 610039, China
| | - Chunyan Jiang
- School of Food and Bio-engineering, Xihua University, Chengdu 610039, China; Chongqing Key Laboratory of Specialty Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China
| | - Zhirui Tang
- School of Food and Bio-engineering, Xihua University, Chengdu 610039, China; Chongqing Key Laboratory of Specialty Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China
| | - Ping Liu
- School of Food and Bio-engineering, Xihua University, Chengdu 610039, China; Chongqing Key Laboratory of Specialty Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China
| | - Wenwu Ding
- School of Food and Bio-engineering, Xihua University, Chengdu 610039, China; Chongqing Key Laboratory of Specialty Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China
| | - Hongbin Lin
- School of Food and Bio-engineering, Xihua University, Chengdu 610039, China; Chongqing Key Laboratory of Specialty Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China.
| | - Jie Tang
- Food Microbiology Key Laboratory of Sichuan Province, Chengdu 610039, China.
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6
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Ma D, Liu S, Liu H, Zhang S, Xu Y, Mao J. Environmental factors drive microbial community succession in biofortified wheat Qu and its improvement on the quality of Chinese huangjiu. J Biosci Bioeng 2024; 137:124-133. [PMID: 38102024 DOI: 10.1016/j.jbiosc.2023.11.008] [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: 04/03/2023] [Revised: 11/04/2023] [Accepted: 11/19/2023] [Indexed: 12/17/2023]
Abstract
Wheat Qu plays the role of saccharification fermentation, providing microorganisms and flavor in the fermentation of huangjiu, and the use of functional microorganisms to fortify wheat Qu is becoming increasingly popular. Yet, the mechanisms promoting microbial successions of wheat Qu remain unclear. In this study, we first correlated microbial community succession with physicochemical factors (moisture, temperature, acidity, glucoamylase and amylase) in inoculated raw wheat Qu (IRWQ) with Saccharopolyspora rosea. The Mantel test was performed to investigate the significance and found that temperature (r = 0.759, P = 0.001), moisture (r = 0.732, P = 0.006), and acidity (r = 0.712, P = 0.017) correlated significantly with the bacterial community in phase 1 (0-40 h). Meanwhile, temperature correlated significantly with the fungal community in phases 1 and 2 (40-120 h). To confirm the effect of temperature on microbial communities, the artificial reduction of bio-heat (37°C) in IRWQ also reduced the relative abundance of heat-resistant microorganisms including Bacillus and Saccharopolyspora. A higher abundance of Saccharopolyspora (87%) in IRWQ was observed following biofortified inoculation of S. rosea, in which glucoamylase activity increased by 40% compared to non-inoculated raw wheat Qu (NIRWQ) (1086 U/g vs 776 U/g). Finally, the IRWQ was employed to mechanized huangjiu fermentation and it was found to reduce the bitter amino acid and higher alcohol content by 27% and 8%, respectively, improving the drinking comfort and quality of huangjiu.
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Affiliation(s)
- Donglin Ma
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang 524088, China
| | - Shuangping Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, Zhejiang 312000, China; National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing, Zhejiang 312000, China
| | - Haipo Liu
- China Alcoholic Drinks Association, Haidian, Beijing 100089, China
| | - Suyi Zhang
- Luzhou Laojiao Group Co. Ltd., Luzhou 646000, China
| | - Yuezheng Xu
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing, Zhejiang 312000, China
| | - Jian Mao
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, Zhejiang 312000, China; National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing, Zhejiang 312000, China.
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7
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Mun SY, Lee W, Lee SY, Chang JY, Chang HC. Pediococcus inopinatus with a well-developed CRISPR-Cas system dominates in long-term fermented kimchi, Mukeunji. Food Microbiol 2024; 117:104385. [PMID: 37919000 DOI: 10.1016/j.fm.2023.104385] [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: 06/26/2023] [Revised: 08/16/2023] [Accepted: 09/12/2023] [Indexed: 11/04/2023]
Abstract
Kimchi is produced through a low-temperature fermentation without pre-sterilization, resulting in a heterogeneous microbial community. As fermentation progresses, dominant lactic acid bacteria (LAB) species emerge and undergo a transition process. In this study, LAB were isolated from Mukeunji, a long-term fermented kimchi that is in the final stage of kimchi fermentation process. It was confirmed, through culture-dependent and independent analysis, as well as metagenome analysis, that Pediococcus inopinatus are generally dominant in long-term fermented kimchi. Comparative analysis of the de novo assembled whole genome of P. inopinatus with other kimchi LAB revealed that this species has a well-developed clustered regularly interspaced short palindromic repeats (CRISPR) system. The CRISPR system of P. inopinatus has an additional copy of the csa3 gene, a transcription factor for cas genes. Indeed, this species not only highly expresses cas1 and cas2, which induce spacer acquisition, but also has many diverse spacers that are actively expressed. These findings indicate that the well-developed CRISPR-Cas system is enabling P. inopinatus to dominate in long-fermented kimchi. Overall, this study revealed that LAB with a robust defense system dominate in the final stage of kimchi fermentation and presented a model for the succession mechanism of kimchi LAB.
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Affiliation(s)
- So Yeong Mun
- Research and Development Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju, 61755, South Korea; Department of Food and Nutrition, Chosun University, 309 Pilmun-daero, Dong-gu, Gwangju, 61452, South Korea
| | - Wooje Lee
- Research and Development Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju, 61755, South Korea
| | - Soo-Young Lee
- Department of Food and Nutrition, Chosun University, 309 Pilmun-daero, Dong-gu, Gwangju, 61452, South Korea
| | - Ji Yoon Chang
- Research and Development Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju, 61755, South Korea
| | - Hae Choon Chang
- Research and Development Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju, 61755, South Korea; Department of Food and Nutrition, Chosun University, 309 Pilmun-daero, Dong-gu, Gwangju, 61452, South Korea.
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8
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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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9
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Rizo J, Leyva CT, Sánchez S, Rodríguez-Sanoja R. Extraction of Proteins from Fermented Food. Methods Mol Biol 2024; 2820:21-28. [PMID: 38941011 DOI: 10.1007/978-1-0716-3910-8_3] [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: 06/29/2024]
Abstract
The metaproteomic approach allows a deep microbiome characterization in different complex systems. Based on metaproteome data, microbial communities' composition, succession, and functional role in different environmental conditions can be established.The main challenge in metaproteomic studies is protein extraction, and although many protocols have been developed, a few are focused on the protein extraction of fermented foods. In this chapter, a reproducible and efficient method for the extraction of proteins from a traditionally fermented starchy food is described. The method can be applied to any fermented food and aims to enrich the extraction of proteins from microorganisms for their subsequent characterization.
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Affiliation(s)
- Jocelin Rizo
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Cynthia T Leyva
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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10
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White K, Eraclio G, Lugli GA, Ventura M, Mahony J, Bello FD, van Sinderen D. A Metagenomics Approach to Enumerate Bacteriophages in a Food Niche. Methods Mol Biol 2024; 2738:185-199. [PMID: 37966600 DOI: 10.1007/978-1-0716-3549-0_12] [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: 11/16/2023]
Abstract
Dairy fermentation relies on the activity of starter cultures composed primarily of lactic acid bacteria such as Lactococcus and Streptococcus thermophilus strains to produce consistent, high-quality products. Bacteriophages are a constant threat to the industry, often causing slowed or failed fermentation resulting in significant economic losses. To ensure the continuation of reliable fermentation practices, it is important to detect and monitor the phage populations impacting different starter cultures. This has traditionally been done primarily through culture-dependent methods but has since expanded into viral metagenomics. Here we outline a protocol for a targeted virome extraction from a dairy whey sample, followed by subsequent sequencing and phageome analysis of the sample.
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Affiliation(s)
- Kelsey White
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland.
| | | | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland.
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11
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Fusco V, Chieffi D, Fanelli F, Montemurro M, Rizzello CG, Franz CMAP. The Weissella and Periweissella genera: up-to-date taxonomy, ecology, safety, biotechnological, and probiotic potential. Front Microbiol 2023; 14:1289937. [PMID: 38169702 PMCID: PMC10758620 DOI: 10.3389/fmicb.2023.1289937] [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: 09/06/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024] Open
Abstract
Bacteria belonging to the genera Weissella and Periweissella are lactic acid bacteria, which emerged in the last decades for their probiotic and biotechnological potential. In 2015, an article reviewing the scientific literature till that date on the taxonomy, ecology, and biotechnological potential of the Weissella genus was published. Since then, the number of studies on this genus has increased enormously, several novel species have been discovered, the taxonomy of the genus underwent changes and new insights into the safety, and biotechnological and probiotic potential of weissellas and periweissellas could be gained. Here, we provide an updated overview (from 2015 until today) of the taxonomy, ecology, safety, biotechnological, and probiotic potential of these lactic acid bacteria.
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Affiliation(s)
- Vincenzina Fusco
- National Research Council, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy
| | - Daniele Chieffi
- National Research Council, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy
| | - Francesca Fanelli
- National Research Council, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy
| | - Marco Montemurro
- National Research Council, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy
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12
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Walsh LH, Coakley M, Walsh AM, O'Toole PW, Cotter PD. Bioinformatic approaches for studying the microbiome of fermented food. Crit Rev Microbiol 2023; 49:693-725. [PMID: 36287644 DOI: 10.1080/1040841x.2022.2132850] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/11/2022] [Accepted: 09/28/2022] [Indexed: 11/03/2022]
Abstract
High-throughput DNA sequencing-based approaches continue to revolutionise our understanding of microbial ecosystems, including those associated with fermented foods. Metagenomic and metatranscriptomic approaches are state-of-the-art biological profiling methods and are employed to investigate a wide variety of characteristics of microbial communities, such as taxonomic membership, gene content and the range and level at which these genes are expressed. Individual groups and consortia of researchers are utilising these approaches to produce increasingly large and complex datasets, representing vast populations of microorganisms. There is a corresponding requirement for the development and application of appropriate bioinformatic tools and pipelines to interpret this data. This review critically analyses the tools and pipelines that have been used or that could be applied to the analysis of metagenomic and metatranscriptomic data from fermented foods. In addition, we critically analyse a number of studies of fermented foods in which these tools have previously been applied, to highlight the insights that these approaches can provide.
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Affiliation(s)
- Liam H Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- School of Microbiology, University College Cork, Ireland
| | - Mairéad Coakley
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Aaron M Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Paul W O'Toole
- School of Microbiology, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Ireland
- VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Cork, Ireland
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Yu HJ, Park SH, Kim EH, Choi YJ, Min SG. Effect of headspace gas composition in kimchi packaging on the quality characteristics of kimchi. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2023; 60:2695-2703. [PMID: 37599852 PMCID: PMC10439095 DOI: 10.1007/s13197-023-05795-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 01/19/2023] [Accepted: 06/13/2023] [Indexed: 08/22/2023]
Abstract
This study evaluated the effects of gas composition in kimchi packaging on kimchi quality. Completely sealed packaging without gas inflow/outflow during fermentation (S1), packaging allowing gas outflow (S2), and packaging allowing gas inflow and outflow (S3) were used. Microbial composition analysis, volatile compound content analysis, and sensory evaluation were performed to determine the differences in kimchi quality among samples. Metabolites were examined using principal component analysis. Gas composition analysis showed that the ratio of CO2 increased during the storage period in S1, the ratio of nitrogen and CO2 contents was constant in S2, and the ratio of oxygen was significantly higher in S3. No significant differences in the lactic acid bacteria number were observed. However, coliforms were only detected in S3, and yeast and mold proliferated faster in S3 than in S2 or S1. The main compounds detected in S1 and S2 were alcohols, whereas those in S3 were esters such as β-phenethyl acetate produced by yeast. Sensory evaluation showed that S3 had the lowest odor, taste, and overall scores, whereas S2 had the highest. In conclusion, the gas composition inside the kimchi package greatly affects the quality of kimchi. Our findings provide important data that can be useful in the manufacture of commercial kimchi. Supplementary Information The online version contains supplementary material available at 10.1007/s13197-023-05795-z.
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Affiliation(s)
- Hye Jin Yu
- Research and Development Division, World Institute of Kimchi, Nam-gu, Gwangju, 61755 Korea
| | - Sung Hee Park
- Research and Development Division, World Institute of Kimchi, Nam-gu, Gwangju, 61755 Korea
| | - Eun Hae Kim
- Research and Development Division, World Institute of Kimchi, Nam-gu, Gwangju, 61755 Korea
| | - Yun-Jeong Choi
- Research and Development Division, World Institute of Kimchi, Nam-gu, Gwangju, 61755 Korea
| | - Sung Gi Min
- Research and Development Division, World Institute of Kimchi, Nam-gu, Gwangju, 61755 Korea
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Lax S, Gore J. Strong ethanol- and frequency-dependent ecological interactions in a community of wine-fermenting yeasts. Commun Biol 2023; 6:939. [PMID: 37704781 PMCID: PMC10499898 DOI: 10.1038/s42003-023-05284-1] [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: 10/31/2022] [Accepted: 08/24/2023] [Indexed: 09/15/2023] Open
Abstract
Natural wine fermentation depends on a complex consortium of native microorganisms rather than inoculation of industrial yeast strains. While this diversity of yeasts can result in an increased repertoire of wine flavors and aromas, it can also result in the inhibition of Saccharomyces cerevisiae, which is uniquely able to complete fermentation. Understanding how yeast species interact with each other within the wine-fermenting community and disentangling ecological interactions from environmental impacts on growth rates, is key to developing synthetic communities that can provide the sensory benefits of natural fermentation while lowering the risk of stuck ferments. Here, we co-culture all pairwise combinations of five commonly isolated wine-fermenting yeasts and show that competitive outcomes are a strong function of ethanol concentration, with frequency-dependent bistable interactions common at low alcohol and an increasingly transitive competitive hierarchy developing as alcohol increases. We also show that pairwise outcomes are predictive of five-species community outcomes, and that frequency dependence in pairwise interactions propagates to alternative states in the full community, highlighting the importance of species abundance as well as composition. We also observe that monoculture growth rates are only weakly predictive of competitive success, highlighting the need to incorporate ecological interactions when designing synthetic fermenting communities.
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Affiliation(s)
- Simon Lax
- Physics of Living Systems, Department of Physics, MIT, 400 Technology Square, NE46-609, Cambridge, MA, 02139, USA.
| | - Jeff Gore
- Physics of Living Systems, Department of Physics, MIT, 400 Technology Square, NE46-609, Cambridge, MA, 02139, USA.
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15
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Page CA, Pérez-Díaz IM, Pan M, Barrangou R. Genome-Wide Comparative Analysis of Lactiplantibacillus pentosus Isolates Autochthonous to Cucumber Fermentation Reveals Subclades of Divergent Ancestry. Foods 2023; 12:2455. [PMID: 37444193 DOI: 10.3390/foods12132455] [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: 04/28/2023] [Revised: 06/07/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023] Open
Abstract
Lactiplantibacillus pentosus, commonly isolated from commercial cucumber fermentation, is a promising candidate for starter culture formulation due to its ability to achieve complete sugar utilization to an end pH of 3.3. In this study, we conducted a comparative genomic analysis encompassing 24 L. pentosus and 3 Lactiplantibacillus plantarum isolates autochthonous to commercial cucumber fermentation and 47 lactobacillales reference genomes to determine species specificity and provide insights into niche adaptation. Results showed that metrics such as average nucleotide identity score, emulated Rep-PCR-(GTG)5, computed multi-locus sequence typing (MLST), and multiple open reading frame (ORF)-based phylogenetic trees can robustly and consistently distinguish the two closely related species. Phylogenetic trees based on the alignment of 587 common ORFs separated the L. pentosus autochthonous cucumber isolates from olive fermentation isolates into clade A and B, respectively. The L. pentosus autochthonous clade partitions into subclades A.I, A.II, and A.III, suggesting substantial intraspecies diversity in the cucumber fermentation habitat. The hypervariable sequences within CRISPR arrays revealed recent evolutionary history, which aligns with the L. pentosus subclades identified in the phylogenetic trees constructed. While L. plantarum autochthonous to cucumber fermentation only encode for Type II-A CRISPR arrays, autochthonous L. pentosus clade B codes for Type I-E and L. pentosus clade A hosts both types of arrays. L. pentosus 7.8.2, for which phylogeny could not be defined using the varied methods employed, was found to uniquely encode for four distinct Type I-E CRISPR arrays and a Type II-A array. Prophage sequences in varied isolates evidence the presence of adaptive immunity in the candidate starter cultures isolated from vegetable fermentation as observed in dairy counterparts. This study provides insight into the genomic features of industrial Lactiplantibacillus species, the level of species differentiation in a vegetable fermentation habitat, and diversity profile of relevance in the selection of functional starter cultures.
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Affiliation(s)
- Clinton A Page
- United States Department of Agriculture, Agricultural Research Service, SEA Food Science and Market Quality and Handling Research Unit, 322 Schaub Hall, Box 7624, Raleigh, NC 27695-7624, USA
| | - Ilenys M Pérez-Díaz
- United States Department of Agriculture, Agricultural Research Service, SEA Food Science and Market Quality and Handling Research Unit, 322 Schaub Hall, Box 7624, Raleigh, NC 27695-7624, USA
| | - Meichen Pan
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, 322 Schaub Hall, Box 7624, Raleigh, NC 27695-7624, USA
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, 322 Schaub Hall, Box 7624, Raleigh, NC 27695-7624, USA
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16
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Nam NN, Do HDK, Loan Trinh KT, Lee NY. Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions. Foods 2023; 12:foods12112140. [PMID: 37297385 DOI: 10.3390/foods12112140] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.
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Affiliation(s)
- Nguyen Nhat Nam
- Biotechnology Center, School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh City 87000, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ward 13, District 04, Ho Chi Minh City 72820, Vietnam
| | - Kieu The Loan Trinh
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
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Walsh AM, Leech J, Huttenhower C, Delhomme-Nguyen H, Crispie F, Chervaux C, Cotter P. Integrated molecular approaches for fermented food microbiome research. FEMS Microbiol Rev 2023; 47:fuad001. [PMID: 36725208 PMCID: PMC10002906 DOI: 10.1093/femsre/fuad001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 12/28/2022] [Accepted: 01/09/2023] [Indexed: 02/03/2023] Open
Abstract
Molecular technologies, including high-throughput sequencing, have expanded our perception of the microbial world. Unprecedented insights into the composition and function of microbial communities have generated large interest, with numerous landmark studies published in recent years relating the important roles of microbiomes and the environment-especially diet and nutrition-in human, animal, and global health. As such, food microbiomes represent an important cross-over between the environment and host. This is especially true of fermented food microbiomes, which actively introduce microbial metabolites and, to a lesser extent, live microbes into the human gut. Here, we discuss the history of fermented foods, and examine how molecular approaches have advanced research of these fermented foods over the past decade. We highlight how various molecular approaches have helped us to understand the ways in which microbes shape the qualities of these products, and we summarize the impacts of consuming fermented foods on the gut. Finally, we explore how advances in bioinformatics could be leveraged to enhance our understanding of fermented foods. This review highlights how integrated molecular approaches are changing our understanding of the microbial communities associated with food fermentation, the creation of unique food products, and their influences on the human microbiome and health.
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Affiliation(s)
- Aaron M Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork and APC Microbiome Ireland, P61 C996, Ireland
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - John Leech
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork and APC Microbiome Ireland, P61 C996, Ireland
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork and APC Microbiome Ireland, P61 C996, Ireland
| | - Christian Chervaux
- Danone Nutricia Research, Centre Daniel Carasso, Palaiseau 91120, France
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork and APC Microbiome Ireland, P61 C996, Ireland
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18
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Kim SJ, Lee HW, Lee JY, Moon EW, Song H, Ha JH. Comparison of inactivation kinetics of Yersinia enterocolitica in vegan and non-vegan kimchi during fermentation. Heliyon 2023; 9:e15031. [PMID: 37095920 PMCID: PMC10121824 DOI: 10.1016/j.heliyon.2023.e15031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
Yersinia enterocolitica is occasionally detected in kimchi, a traditional food prepared from fermented vegetables. Changes in growth properties of Y. enterocolitica during kimchi fermentation are largely unknown. We investigated the viability of Y. enterocolitica during the fermentation of vegan and non-vegan kimchi at different temperatures. Changes in Y. enterocolitica population, pH, and titratable acidity were measured for 24 days. In a suspension test with kimchi juice, populations of three Y. enterocolitica strains were above 3.30 log10 CFU/mL at pH > 5 for 7 days. Yersinia enterocolitica counts in vegan kimchi were considerably reduced at 0 °C and 6 °C. During fermentation at 6 °C, Y. enterocolitica populations in non-vegan kimchi and vegan kimchi were not detected starting from days 14 and 10, respectively. In kimchi samples stored at 0 °C and 6 °C, Y. enterocolitica survival correlated with pH changes during fermentation; in samples stored for up to 24 days, Y. enterocolitica was not detected. According to the k max values from the "log-linear with shoulder and tail" model, Y. enterocolitica was more sensitive to vegan kimchi fermentation than to non-vegan kimchi fermentation. Our findings provide an important basis for ensuring the safe production of kimchi without Y. enterocolitica contamination. Further research is necessary to elucidate the mechanism of Y. enterocolitica inactivation and the major bacterial and physicochemical factors involved in kimchi fermentation.
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Chien HI, Yen YF, Lee YC, Wei PC, Huang CY, Tseng CH, Yen FL, Tsai YH. Determination of the Bacterial Community of Mustard Pickle Products and Their Microbial and Chemical Qualities. BIOLOGY 2023; 12:biology12020258. [PMID: 36829535 PMCID: PMC9953598 DOI: 10.3390/biology12020258] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 01/20/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023]
Abstract
We assessed the microbial and chemical qualities and microbiomes of 14 mustard pickle products coded sequentially from A to N and sold in traditional Taiwanese markets. The results showed that the aerobic plate count and lactic acid bacteria count of commercially available mustard pickle products were 2.18-4.01 and <1.0-3.77 log CFU/g, respectively. Moreover, no coliform bacteria, Escherichia coli, Staphylococcus aureus, Salmonella spp., or Listeria monocytogenes were detected in any of the samples. Analysis of the chemical quality showed that the sulfite content of all samples exceeded 30 ppm, which is the food additive limit in Taiwan. Furthermore, the mean contents of eight biogenic amines in the mustard pickle product samples were below 48.0 mg/kg. The results of high-throughput sequencing showed that the dominant bacterial genera in sample A were Proteus spp. (25%), Vibrio (25%), and Psychrobacter (10%), in sample C they were Weissella (62%) and Lactobacillus (15%), in sample E it was Lactobacillus (97%), and in sample J it was Companilactobacillus (57%). Mustard pickle product samples from different sources contained different microbiomes. The dominant bacterial family was Lactobacillaceae in all samples except for sample A. In contrast, the microbiome of sample A mainly consisted of Morganellaceae and Vibrionaceae, which may have resulted from environmental contamination during storage and sales. The result of this work suggests it may be necessary to monitor sulfite levels and potential sources of bacterial contamination in mustard pickle products, and to take appropriate measures to rule out any public health risks.
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Affiliation(s)
- Hung-I Chien
- Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung 811213, Taiwan
| | - Yu-Fan Yen
- Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung 811213, Taiwan
| | - Yi-Chen Lee
- Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung 811213, Taiwan
- Correspondence: (Y.-C.L.); (Y.-H.T.); Tel.: +886-7-3617141-23613 (Y.-C.L.); +886-7-3617141-23609 (Y.-H.T.); Fax: +886-7-3640634 (Y.-H.T.)
| | - Pi-Chen Wei
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan
| | - Chun-Yung Huang
- Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung 811213, Taiwan
| | - Chih-Hua Tseng
- Department of Fragrance and Cosmetic Science, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
| | - Feng-Lin Yen
- Department of Fragrance and Cosmetic Science, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
| | - Yung-Hsiang Tsai
- Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung 811213, Taiwan
- Correspondence: (Y.-C.L.); (Y.-H.T.); Tel.: +886-7-3617141-23613 (Y.-C.L.); +886-7-3617141-23609 (Y.-H.T.); Fax: +886-7-3640634 (Y.-H.T.)
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Opportunities and Challenges of Understanding Community Assembly in Spontaneous Food Fermentation. Foods 2023; 12:foods12030673. [PMID: 36766201 PMCID: PMC9914028 DOI: 10.3390/foods12030673] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Spontaneous fermentations that do not rely on backslopping or industrial starter cultures were especially important to the early development of society and are still practiced around the world today. While current literature on spontaneous fermentations is observational and descriptive, it is important to understand the underlying mechanism of microbial community assembly and how this correlates with changes observed in microbial succession, composition, interaction, and metabolite production. Spontaneous food and beverage fermentations are home to autochthonous bacteria and fungi that are naturally inoculated from raw materials, environment, and equipment. This review discusses the factors that play an important role in microbial community assembly, particularly focusing on commonly reported yeasts and bacteria isolated from spontaneously fermenting food and beverages, and how this affects the fermentation dynamics. A wide range of studies have been conducted in spontaneously fermented foods that highlight some of the mechanisms that are involved in microbial interactions, niche adaptation, and lifestyle of these microorganisms. Moreover, we will also highlight how controlled culture experiments provide greater insight into understanding microbial interactions, a modest attempt in decoding the complexity of spontaneous fermentations. Further research using specific in vitro microbial models to understand the role of core microbiota are needed to fill the knowledge gap that currently exists in understanding how the phenotypic and genotypic expression of these microorganisms aid in their successful adaptation and shape fermentation outcomes. Furthermore, there is still a vast opportunity to understand strain level implications on community assembly. Translating these findings will also help in improving other fermentation systems to help gain more control over the fermentation process and maintain consistent and superior product quality.
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Moon HJ, Oh SH, Park KB, Cha YS. Kimchi and Leuconostoc mesenteroides DRC 1506 Alleviate Dextran Sulfate Sodium (DSS)-Induced Colitis via Attenuating Inflammatory Responses. Foods 2023; 12:foods12030584. [PMID: 36766113 PMCID: PMC9914003 DOI: 10.3390/foods12030584] [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: 01/06/2023] [Revised: 01/18/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Ulcerative colitis (UC) is caused by inflammation only in the mucosa of the colon, and its incidence is increasing worldwide. The intake of probiotics is known to have a beneficial effect on the development of UC. In this study, we investigated the alleviating effects of kimchi (KC), a fermented food rich in probiotics, and Leuconostoc mesenteroides DRC 1506 (DRC) isolated from kimchi on UC. A freeze-dried kimchi suspension and DRC were orally given to mice at a dose of 1 × 109 CFU/day for 3 weeks. Furthermore, 3% dextran sulfate sodium (DSS) in drinking water was given to induce UC. The KC and DRC groups reduced symptoms of colitis, such as disease activity index, decrease in colon length, colon weight-to-length ratio, and pathological damage to the colon caused by DSS treatment. The KC and DRC groups decreased the levels of pro-inflammatory cytokine (TNF-α) and increased anti-inflammatory cytokine (IL-10) in the colon tissues. At the mRNA and protein expression levels in the colon tissue, KC and DRC groups downregulated inflammatory factors and upregulated tight junction-related factors. Therefore, DRC, as well as KC supplementation, are potent in alleviating UC by improving the inflammatory response and mucosal barrier function in the colon.
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Affiliation(s)
- Hye-Jung Moon
- Department of Food Science and Human Nutrition, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Suk-Heung Oh
- Department of Food & Biotechnology & Woosuk Institute of Smart Convergence Life Care, Woosuk University, Wanju 55338, Republic of Korea
| | - Ki-Bum Park
- Institute of Kimchi Technology, Daesang Co., Icheon 17384, Republic of Korea
| | - Youn-Soo Cha
- Department of Food Science and Human Nutrition, Jeonbuk National University, Jeonju 54896, Republic of Korea
- K-Food Research Center, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Correspondence: ; Tel.: +82-63-270-3822
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22
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Chien HI, Lee YC, Yen YF, Wei PC, Hwang CC, Kuo CH, Yen FL, Tsai YH. Replacing the Addition of Sulfite in Mustard Pickle Products by High-Hydrostatic-Pressure Processing to Delay Quality Deterioration during Storage. Foods 2023; 12:foods12020317. [PMID: 36673409 PMCID: PMC9858118 DOI: 10.3390/foods12020317] [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: 11/26/2022] [Revised: 12/23/2022] [Accepted: 12/28/2022] [Indexed: 01/11/2023] Open
Abstract
This study aimed to assess the use of the high-hydrostatic-pressure (HHP) method (200-600 MPa, 5 min) for bleaching mustard pickle products as an alternative to the conventional method of sulfite addition. The aerobic plate count (APC) and lactic acid bacteria count (LAB) of the samples decreased with the increase in pressure, and the yeast count decreased to no detectable levels. Next, compared with the control group (no high-pressure treatment) the L* (lightness), W (whiteness), ΔE (color difference), and texture (hardness and chewiness) of the HHP-processed samples, which increased significantly with increasing pressure, while the a* (redness) and b* (yellowness) values decreased slightly. This indicates that HHP processing gave the mustard pickle a harder texture and a brighter white color and appearance. Furthermore, when the mustard pickle was treated with HHP 400 and 600 MPa for 5 min and stored at 25 °C for 60 days, it was found that the APC and LAB counts in the HHP-processed group recovered rapidly and did not differ from those in the control group (the non-HHP treated group) but significantly delayed the growth of yeast, the increase in pH value, and total volatile basic nitrogen (TVBN). The high-throughput sequencing (HTS) analysis revealed that the predominant bacterial genera in the non-HHP-treated mustard pickle were Lactiplantibacillus (74%), Lactilactobacillus (12%), and Levilactobacillus (6%); after 60 days of storage, Companilactobacillus (80%) became dominant. However, after 60 days of storage, Lactiplantibacillus (92%) became dominant in the samples processed at 400 MPa, while Levilactobacillus (52%), Pediococcus (17%), and Lactiplantibacillus (17%) became dominant in the samples processed at 600 MPa. This indicated that the HHP treatment changed the lactic acid bacterial flora of the mustard pickle during the storage period. Overall, it is recommended to treat the mustard pickle with HHP above 400 MPa for 5 min to improve its texture and color and delay the deterioration of quality during storage. Therefore, HHP technology has the potential to be developed as a treatment technique to replace the addition of sulfite.
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Affiliation(s)
- Hung-I Chien
- Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung 811213, Taiwan
| | - Yi-Chen Lee
- Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung 811213, Taiwan
| | - Yu-Fan Yen
- Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung 811213, Taiwan
| | - Pi-Chen Wei
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan
| | - Chiu-Chu Hwang
- Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung 811213, Taiwan
| | - Chia-Hung Kuo
- Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung 811213, Taiwan
| | - Feng-Lin Yen
- Department of Fragrance and Cosmetic Science, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
| | - Yung-Hsiang Tsai
- Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung 811213, Taiwan
- Correspondence: ; Tel.: +886-7-3617141-23609; Fax: +886-7-3640634
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23
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Han J, Kong T, Jiang J, Zhao X, Zhao X, Li P, Gu Q. Characteristic flavor metabolic network of fish sauce microbiota with different fermentation processes based on metagenomics. Front Nutr 2023; 10:1121310. [PMID: 36950329 PMCID: PMC10025566 DOI: 10.3389/fnut.2023.1121310] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/08/2023] [Indexed: 03/08/2023] Open
Abstract
This article purposed to discuss the connection between microbiota and characteristic flavor of different fish sauces (Natural fermentation (WQ), koji outdoor fermentation (YQ), heat preservation with enzyme (BWE), and heat preservation with koji (BWQ)) at the early (3 months) and late stage (7 months). A total of 117 flavor compounds were determined according to SPME-GC-MS analysis. O2PLS-DA and VIP values were used to reveal 15 and 28 flavor markers of different fish sauces at 3 and 7 M of fermentation. Further, the possible flavor formation pathways were analyzed using metagenomic sequencing, and the key microbes associated with flavor formation were identified at the genetic level. The top 10 genera related to flavor generation, such as Lactobacillus, Staphylococcus, Enterobacter, etc., appeared to play a prominent part in the flavor formation of fish sauce. The difference was that only BWQ and BWE groups could produce ethyl-alcohol through amino acid metabolism, while YQ, BWE and BWQ groups could generate phenylacetaldehyde through the transformation of Phe by α-ketoacid decarboxylase and aromatic amino acid transferase. Our research contributes to clarifying the various metabolic roles of microorganisms in the flavor generation of fish sauce.
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Lee HG, Jeong S, Yoo S. Development of a calcium hydroxide–dye kimchi ripening indicator and its application in kimchi packaging. Food Chem 2023; 400:134039. [DOI: 10.1016/j.foodchem.2022.134039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 11/15/2022]
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25
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Effects of the addition of starches with different amylose contents on kimchi microbiota and metabolites. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Ma D, Liu S, Liu H, Nan M, Xu Y, Han X, Mao J. Developing an innovative raw wheat Qu inoculated with Saccharopolyspora and its application in Huangjiu. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:7301-7312. [PMID: 35757866 DOI: 10.1002/jsfa.12096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/15/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Mechanized Huangjiu is a stable product, is not subject to seasonal production restrictions, and markedly reduces labor intensity compared to traditional manual Huangjiu. However, the bitterness of mechanized Huangjiu impedes its further development. RESULTS Based on process optimization, when the fermentation temperature was 45 °C and the fermentation time was 122 h, the inoculation amount of Saccharopolyspora was 5%, the amount of added water was 26%, and the glucoamylase and amylase activities of wheat Qu increased by 27% and 40% respectively, compared with those before optimization. Huangjiu fermented by raw wheat Qu inoculated with Saccharopolyspora rosea F2014 showed a significant (P < 0.05) decrease in bitter amino acid content (1.24 vs. 2.86 g L-1 , a decrease of 56%), which attenuated its bitterness. CONCLUSION An innovative fermentation process of inoculating Saccharopolyspora into raw wheat Qu was developed for the first time. Such a process could be used to control bitterness based on raw wheat Qu inoculated with Saccharopolyspora rosea F2014, instead of traditional wheat Qu in Huangjiu fermentation. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Donglin Ma
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Shuangping Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
- Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Zhejiang, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co. Ltd, Zhejiang, China
| | - Haipo Liu
- Famous Wine Collection Committee, China Alcoholic Drinks Association, Beijing, China
| | - Mujia Nan
- Basic Department, University of Tibetan Medicine, Lhasa, China
| | - Yuezheng Xu
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co. Ltd, Zhejiang, China
| | - Xiao Han
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
- Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Zhejiang, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co. Ltd, Zhejiang, China
| | - Jian Mao
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
- Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Zhejiang, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co. Ltd, Zhejiang, China
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Effects of glutinous rice paste and fish sauce on kimchi fermentation. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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Maske BL, De Carvalho Neto DP, da Silva GB, De Dea Lindner J, Soccol CR, de Melo Pereira GV. Yeast viruses and their implications in fermented foods and beverages. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Jia Z, Zhang B, Sharma A, Kim NS, Purohit SM, Green MM, Roche MR, Holliday E, Chen H. Revelation of the sciences of traditional foods. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zhai Y, Wei C. Open pangenome of Lactococcus lactis generated by a combination of metagenome-assembled genomes and isolate genomes. Front Microbiol 2022; 13:948138. [PMID: 36081802 PMCID: PMC9445621 DOI: 10.3389/fmicb.2022.948138] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022] Open
Abstract
Lactococcus lactis (L. lactis) is a well isolated and cultured lactic acid bacterium, but if utilizing the isolate genomes alone, the genome-based analysis of this taxon would be incomplete, because there are still uncultured strains in some ecological niches. In this study, we recovered 93 high-quality metagenome-assembled genomes (MAGs) of L. lactis from food and human gut metagenomes with a culture-independent method. We then constructed a unified genome catalog of L. lactis by integrating these MAGs with 70 publicly available isolated genomes. Having this comprehensive resource, we assessed the genomic diversity and phylogenetic relationships to further explore the genetic and functional properties of L. lactis. An open pangenome of L. lactis was generated using our genome catalog, consisting of 13,066 genes in total, from which 5,448 genes were not identified in the isolate genomes. The core genome-based phylogenetic analysis showed that L. lactis strains we collected were separated into two main subclades corresponding to two subspecies, with some uncultured phylogenetic lineages discovered. The species disparity was also indicated in PCA analysis based on accessory genes of our pangenome. These various analyzes shed further light on unexpectedly high diversity within the taxon at both genome and gene levels and gave clues about its population structure and evolution. Lactococcus lactis has a long history of safe use in food fermentations and is considered as one of the important probiotic microorganisms. Obtaining the complete genetic information of L. lactis is important to the food and health industry. However, it can naturally inhabit many environments other than dairy products, including drain water and human gut samples. Here we presented an open pan-genome of L. lactis constructed from 163 high-quality genomes obtained from various environments, including MAGs recovered from environmental metagenomes and isolate genomes. This study expanded the genetic information of L. lactis about one third, including more than 5,000 novel genes found in uncultured strains. This more complete gene repertoire of L. lactis is crucial to further understanding the genetic and functional properties. These properties may be harnessed to impart additional value to dairy fermentation or other industries.
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Kim J, Ahn SW, Kim JY, Whon TW, Lim SK, Ryu BH, Han NS, Choi HJ, Roh SW, Lee SH. Probiotic Lactobacilli ameliorate alcohol-induced hepatic damage via gut microbial alteration. Front Microbiol 2022; 13:869250. [PMID: 36081800 PMCID: PMC9446534 DOI: 10.3389/fmicb.2022.869250] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Alcoholic liver disease (ALD), which includes fatty liver, cirrhosis, steatosis, fibrosis, and hepatocellular carcinoma, is a global health problem. The probiotic effects of lactic acid bacteria (LAB) are well-known; however, their protective effect against ALD remains unclear. Therefore, in this study, our objective was to assess the protective effects of LAB on ALD. To this end, mice were fed either a normal diet or an alcohol diet for 10 days (to induce ALD) accompanied by vehicle treatment (the NC and AC groups) or kimchi-derived LAB (Lactiplantibacillus plantarum DSR J266 and Levilactobacillus brevis DSR J301, the AL group; or Lacticaseibacillus rhamnosus GG, the AG group). Our results showed that mice in the AC group showed significantly higher serum aspartate aminotransferase and alanine aminotransferase levels than those in the normal diet groups; however, their levels in the AL and AG groups were relatively lower. We also observed that the AL and AG groups showed relatively lower interleukin-6 levels than the AC group. Additionally, AC group showed the accumulation of several fat vesicles in the liver, while the AL and AG groups showed remarkably lower numbers of fat vesicles. The relative abundance of Enterococcus feacalis, which showed association with liver injury, significantly increased in the AC group compared with its levels in the normal diet groups. However, the AG group showed a decreased relative abundance in this regard, confirming that LAB exerted an improvement effect on gut microbial community. These findings suggested that via gut microbiota alteration, the ingestion of LAB can alleviate the ill effects of alcohol consumption, including inflammation, liver damage, gut dysbiosis, and abnormal intestinal nutrient metabolism.
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Affiliation(s)
- Juseok Kim
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, South Korea
- Microbiome Research Team, LISCure Biosciences Inc., Seongnam, South Korea
| | - Seong Woo Ahn
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, South Korea
- Microbiome Research Team, LISCure Biosciences Inc., Seongnam, South Korea
| | - Joon Yong Kim
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, South Korea
- Microbiome Research Team, LISCure Biosciences Inc., Seongnam, South Korea
| | - Tae Woong Whon
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, South Korea
| | - Seul Ki Lim
- Fermentation Regulation Technology Research Group, World Institute of Kimchi, Gwangju, South Korea
| | - Byung Hee Ryu
- Food Research Division, Food BU, Daesang Corporation Research Institute, Icheon, South Korea
| | - Nam Soo Han
- Department of Food Science and Biotechnology, Brain Korea 21 Center for Bio-Health Industry, Chungbuk National University, Cheongju, South Korea
| | - Hak-Jong Choi
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, South Korea
| | - Seong Woon Roh
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, South Korea
- Microbiome Research Team, LISCure Biosciences Inc., Seongnam, South Korea
| | - Se Hee Lee
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, South Korea
- *Correspondence: Se Hee Lee,
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Guan Q, Huang T, Peng F, Huang J, Liu Z, Peng Z, Xie M, Xiong T. The microbial succession and their correlation with the dynamics of flavor compounds involved in the natural fermentation of suansun, a traditional Chinese fermented bamboo shoots. Food Res Int 2022; 157:111216. [DOI: 10.1016/j.foodres.2022.111216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 04/01/2022] [Accepted: 04/02/2022] [Indexed: 01/20/2023]
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Yasir M, Al-Zahrani IA, Bibi F, Abd El Ghany M, Azhar EI. New insights of bacterial communities in fermented vegetables from shotgun metagenomics and identification of antibiotic resistance genes and probiotic bacteria. Food Res Int 2022; 157:111190. [DOI: 10.1016/j.foodres.2022.111190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 11/04/2022]
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Kim HY, Park ES, Choi YS, Park SJ, Kim JH, Chang HK, Park KY. Kimchi improves irritable bowel syndrome: results of a randomized, double-blind placebo-controlled study. Food Nutr Res 2022; 66:8268. [PMID: 35721806 PMCID: PMC9180131 DOI: 10.29219/fnr.v66.8268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 12/12/2022] Open
Abstract
Background Irritable bowel syndrome (IBS) can be caused by abnormal bowel movements, altered brain-gut axis, gut microbiota change, and low levels of inflammation or immune activation. The intake of food containing much fiber and lactic acid bacteria (LABs) can alleviate IBS. Objective This study was undertaken to confirm the alleviative effect of kimchi on symptoms of IBS. Design Three types of kimchi (standard kimchi, SK; dead nano-sized Lactobacillus plantarum nF1 (nLp) added to standard kimchi, nLpSK; or functional kimchi, FK) were given to 30 individuals in each of three groups, that is, the SK group (n = 30), the nLpSK group (n = 30), or the FK group (n = 30) at 210 g a day for 12 weeks. Food intake records, serum levels of inflammatory factors, fecal levels of harmful enzymes, and microbiome changes were investigated over the 12-week study period. Results After intervention, dietary fiber intake was increased in all groups. Typical IBS symptoms (abdominal pain or inconvenience, desperation, incomplete evacuation, and bloating), defecation time, and stool type were also improved. In serum, all groups showed reductions in tumor necrosis factor (TNF)-α (P < 0.001) levels. In addition, serum IL-4 (P < 0.001), IL-10 (P < 0.001), and IL-12 (P < 0.01) were significantly reduced in the nLpSK and FK groups, and serum monocyte chemotactic protein (MCP)-1 (P < 0.05) was significantly reduced in the nLpSK group. Furthermore, activities of fecal β-glucosidase and β-glucuronidase were significantly decreased in all three groups, and these reductions were greatest in the nLpSK group. Gut microbiome analysis showed that kimchi consumption increased Firmicutes populations at the expense of Bacteroidetes and Tenericutes populations. In addition, the Bifidobacterium adolescentis population increased significantly in the FK group (P = 0.026). Conclusion Kimchi intake helps alleviate IBS by increasing dietary fiber intake and reducing serum inflammatory cytokine levels and harmful fecal enzyme activities. Notably, nLp improved the immune system, and several functional ingredients in FK promoted the growth of Bifidobacterium adolescentis in gut.
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Affiliation(s)
- Hee-Young Kim
- Korean Medicine Research Center for Healthy Aging, Pusan National University, Yangsan, Gyeongsangnam-do, Republic of Korea
| | - Eui-Seong Park
- Yuhan Care R&D Center, Yongin, Gyeonggi-do, Republic of Korea
| | - Young Sik Choi
- Department of Internal Medicine, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Republic of Korea
| | - Seun Ja Park
- Department of Internal Medicine, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Republic of Korea
| | - Jae Hyun Kim
- Department of Internal Medicine, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Republic of Korea
| | - Hee Kyung Chang
- Department of Pathology, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Republic of Korea
| | - Kun-Young Park
- Department of Food Science and Biotechnology, Cha University, Seongnam, Gyeonggi-do, Republic of Korea.,Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing, China
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Zheng S, Wu W, Zhang Y, Hu P, Li J, Jiang J. Improvement of tomato sour soup fermentation by
Lacticaseibacillus casei
H1
addition. J FOOD PROCESS PRES 2022. [DOI: 10.1111/jfpp.16806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shasha Zheng
- College of Brewing and Food Engineering Guizhou University Guiyang China
| | - Wenyan Wu
- College of Brewing and Food Engineering Guizhou University Guiyang China
| | - Yulong Zhang
- College of Brewing and Food Engineering Guizhou University Guiyang China
| | - Ping Hu
- College of Brewing and Food Engineering Guizhou University Guiyang China
| | - Juan Li
- College of Brewing and Food Engineering Guizhou University Guiyang China
| | - Jingzhu Jiang
- College of Brewing and Food Engineering Guizhou University Guiyang China
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Zhou Y, Ren M, Zhang P, Jiang D, Yao X, Luo Y, Yang Z, Wang Y. Application of Nanopore Sequencing in the Detection of Foodborne Microorganisms. NANOMATERIALS 2022; 12:nano12091534. [PMID: 35564242 PMCID: PMC9100974 DOI: 10.3390/nano12091534] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 12/21/2022]
Abstract
Foodborne pathogens have become the subject of intense interest because of their high incidence and mortality worldwide. In the past few decades, people have developed many methods to solve this challenge. At present, methods such as traditional microbial culture methods, nucleic acid or protein-based pathogen detection methods, and whole-genome analysis are widely used in the detection of pathogenic microorganisms in food. However, these methods are limited by time-consuming, cumbersome operations or high costs. The development of nanopore sequencing technology offers the possibility to address these shortcomings. Nanopore sequencing, a third-generation technology, has the advantages of simple operation, high sensitivity, real-time sequencing, and low turnaround time. It can be widely used in the rapid detection and serotyping of foodborne pathogens. This review article discusses foodborne diseases, the principle of nanopore sequencing technology, the application of nanopore sequencing technology in foodborne pathogens detection, as well as its development prospects.
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Ameur H, Cantatore V, Filannino P, Cavoski I, Nikoloudaki O, Gobbetti M, Di Cagno R. Date Seeds Flour Used as Value-Added Ingredient for Wheat Sourdough Bread: An Example of Sustainable Bio-Recycling. Front Microbiol 2022; 13:873432. [PMID: 35516437 PMCID: PMC9062590 DOI: 10.3389/fmicb.2022.873432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/16/2022] [Indexed: 11/13/2022] Open
Abstract
Our study proposed date seeds flour (DSF) as an innovative ingredient for sourdough bread production through sustainable bio-recycling. We isolated autochthonous lactic acid bacteria and yeasts from DSF and DSF-derived doughs to build up a reservoir of strains from which to select starters ensuring rapid adaptation and high ecological fitness. The screening based on pro-technological criteria led to the formulation of a mixed starter consisting of Leuconostoc mesenteroides, Lactiplantibacillus plantarum, and Saccharomyces cerevisiae strains, which allowed obtaining a mature type I sourdough after consecutive refreshments, in which an aliquot of the durum wheat flour (DWF) was replaced by DSF. The resulting DSF sourdough and bread underwent an integrated characterization. Sourdough biotechnology was confirmed as a suitable procedure to improve some functional and sensory properties of DWF/DSF mixture formulation. The radical scavenging activity increased due to the consistent release of free phenolics. Perceived bitterness and astringency were considerably diminished, likely because of tannin degradation.
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Affiliation(s)
- Hana Ameur
- Faculty of Science and Technology, Libera Università di Bolzano, Bolzano, Italy
| | - Vincenzo Cantatore
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Pasquale Filannino
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
- *Correspondence: Pasquale Filannino,
| | - Ivana Cavoski
- CIHEAM-MAIB, Mediterranean Agronomic Institute of Bari, Valenzano, Bari, Italy
| | - Olga Nikoloudaki
- Faculty of Science and Technology, Libera Università di Bolzano, Bolzano, Italy
| | - Marco Gobbetti
- Faculty of Science and Technology, Libera Università di Bolzano, Bolzano, Italy
| | - Raffaella Di Cagno
- Faculty of Science and Technology, Libera Università di Bolzano, Bolzano, Italy
- Raffaella Di Cagno,
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Kim SH, Park JH. Characterization of Prophages in Leuconostoc Derived from Kimchi and Genomic Analysis of the Induced Prophage in Leuconostoc lactis. J Microbiol Biotechnol 2022; 32:333-340. [PMID: 34949750 PMCID: PMC9628853 DOI: 10.4014/jmb.2110.10046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 12/15/2022]
Abstract
Leuconostoc has been used as a principal starter in natural kimchi fermentation, but limited research has been conducted on its phages. In this study, prophage distribution and characterization in kimchi-derived Leuconostoc strains were investigated, and phage induction was performed. Except for one strain, 16 Leuconostoc strains had at least one prophage region with questionable and incomplete regions, which comprised 0.5-6.0% of the bacterial genome. Based on major capsid protein analysis, ten intact prophages and an induced incomplete prophage of Leu. lactis CBA3626 belonged to the Siphoviridae family and were similar to Lc-Nu-like, sha1-like, phiMH1-like, and TPA_asm groups. Bacterial immunology genes, such as superinfection exclusion proteins and methylase, were found on several prophages. One prophage of Leu. lactis CBA3626 was induced using mitomycin C and was confirmed as belonging to the Siphoviridae family. Homology of the induced prophage with 21 reported prophages was not high (< 4%), and 47% identity was confirmed only with TPA_asm from Siphoviridae sp. isolate ct3pk4. Therefore, it is suggested that Leuconostoc from kimchi had diverse prophages with less than 6% genome proportion and some immunological genes. Interestingly, the induced prophage was very different from the reported prophages of other Leuconostoc species.
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Affiliation(s)
- Song-Hee Kim
- Department of Food Science and Biotechnology, College of BioNano Technology, Gachon University, Seongnam 13120, Republic of Korea
| | - Jong-Hyun Park
- Department of Food Science and Biotechnology, College of BioNano Technology, Gachon University, Seongnam 13120, Republic of Korea,Corresponding author J.H. Park Phone: +82-31-750-5523 Fax: +82-31-750-5283 E-mail:
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Abstract
The interest in fermented food products has been increasing in recent years. Details about their microbial composition and the effects of their consumption on the human gut microbiome are of particular interest. However, evidence regarding their potential to increase gut microbial diversity, a measure likely associated with health, is lacking. To address this, we analyzed the microbial composition of commercially available fermented vegetables using 16S rRNA sequencing. We also conducted a pilot study to assess the feasibility of studying the effects of regular consumption of fermented vegetables on the gut microbiome. Six healthy male volunteers participated in a randomized crossover trial, with two two-week intervention phases. Volunteers consumed 150 g/d of either sauerkraut or a variety of six different commercially available fermented vegetables. This study is registered at the German Clinical Trials Register (DRKS-ID: DRKS00014840). Lactobacillales was the dominant family in all fermented vegetables studied. However, the alpha diversity, richness and evenness of the microbiota differed substantially among the different products. The number of species per product varied between 20 and 95. After consumption of both sauerkraut and the selection of fermented vegetables, we observed a slight increase in alpha diversity. Specifically, the amount of the genus Prevotella decreased while the amount of Bacteroides increased after both interventions. However, these initial observations need to be confirmed in larger studies. This pilot study demonstrates the feasibility of this type of research.
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Identification of characteristic flavor and microorganisms related to flavor formation in fermented common carp (Cyprinus carpio L.). Food Res Int 2022; 155:111128. [DOI: 10.1016/j.foodres.2022.111128] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 01/20/2023]
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Dreier M, Meola M, Berthoud H, Shani N, Wechsler D, Junier P. High-throughput qPCR and 16S rRNA gene amplicon sequencing as complementary methods for the investigation of the cheese microbiota. BMC Microbiol 2022; 22:48. [PMID: 35130830 PMCID: PMC8819918 DOI: 10.1186/s12866-022-02451-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/17/2022] [Indexed: 12/31/2022] Open
Abstract
Background Next-generation sequencing (NGS) methods and especially 16S rRNA gene amplicon sequencing have become indispensable tools in microbial ecology. While they have opened up new possibilities for studying microbial communities, they also have one drawback, namely providing only relative abundances and thus compositional data. Quantitative PCR (qPCR) has been used for years for the quantification of bacteria. However, this method requires the development of specific primers and has a low throughput. The constraint of low throughput has recently been overcome by the development of high-throughput qPCR (HT-qPCR), which allows for the simultaneous detection of the most prevalent bacteria in moderately complex systems, such as cheese and other fermented dairy foods. In the present study, the performance of the two approaches, NGS and HT-qPCR, was compared by analyzing the same DNA samples from 21 Raclette du Valais protected designation of origin (PDO) cheeses. Based on the results obtained, the differences, accuracy, and usefulness of the two approaches were studied in detail. Results The results obtained using NGS (non-targeted) and HT-qPCR (targeted) show considerable agreement in determining the microbial composition of the cheese DNA samples studied, albeit the fundamentally different nature of these two approaches. A few inconsistencies in species detection were observed, particularly for less abundant ones. The detailed comparison of the results for 15 bacterial species/groups measured by both methods revealed a considerable bias for certain bacterial species in the measurements of the amplicon sequencing approach. We identified as probable origin to this PCR bias due to primer mismatches, variations in the number of copies for the 16S rRNA gene, and bias introduced in the bioinformatics analysis. Conclusion As the normalized microbial composition results of NGS and HT-qPCR agreed for most of the 21 cheese samples analyzed, both methods can be considered as complementary and reliable for studying the microbial composition of cheese. Their combined application proved to be very helpful in identifying potential biases and overcoming methodological limitations in the quantitative analysis of the cheese microbiota. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02451-y.
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Affiliation(s)
- Matthias Dreier
- Agroscope, Schwarzenburgstrasse 161, CH-3003, Bern, Switzerland. .,Laboratory of Microbiology, University of Neuchâtel, Emile-Argand 11, CH-2000, Neuchâtel, Switzerland.
| | - Marco Meola
- Agroscope, Schwarzenburgstrasse 161, CH-3003, Bern, Switzerland.,Department of Biomedicine, Applied Microbiology Research, University of Basel, Basel, Switzerland.,Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Swiss Institute for Bioinformatics, Basel, Switzerland
| | - Hélène Berthoud
- Agroscope, Schwarzenburgstrasse 161, CH-3003, Bern, Switzerland
| | - Noam Shani
- Agroscope, Schwarzenburgstrasse 161, CH-3003, Bern, Switzerland
| | - Daniel Wechsler
- Agroscope, Schwarzenburgstrasse 161, CH-3003, Bern, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Emile-Argand 11, CH-2000, Neuchâtel, Switzerland
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42
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White K, Yu JH, Eraclio G, Dal Bello F, Nauta A, Mahony J, van Sinderen D. Bacteriophage-host interactions as a platform to establish the role of phages in modulating the microbial composition of fermented foods. MICROBIOME RESEARCH REPORTS 2022; 1:3. [PMID: 38089066 PMCID: PMC10714293 DOI: 10.20517/mrr.2021.04] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/23/2021] [Accepted: 12/31/2021] [Indexed: 02/19/2024]
Abstract
Food fermentation relies on the activity of robust starter cultures, which are commonly comprised of lactic acid bacteria such as Lactococcus and Streptococcus thermophilus. While bacteriophage infection represents a persistent threat that may cause slowed or failed fermentations, their beneficial role in fermentations is also being appreciated. In order to develop robust starter cultures, it is important to understand how phages interact with and modulate the compositional landscape of these complex microbial communities. Both culture-dependent and -independent methods have been instrumental in defining individual phage-host interactions of many lactic acid bacteria (LAB). This knowledge needs to be integrated and expanded to obtain a full understanding of the overall complexity of such interactions pertinent to fermented foods through a combination of culturomics, metagenomics, and phageomics. With such knowledge, it is believed that factory-specific detection and monitoring systems may be developed to ensure robust and reliable fermentation practices. In this review, we explore/discuss phage-host interactions of LAB, the role of both virulent and temperate phages on the microbial composition, and the current knowledge of phageomes of fermented foods.
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Affiliation(s)
- Kelsey White
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
- Authors contributed equally
| | - Jun-Hyeok Yu
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
- Authors contributed equally
| | | | | | - Arjen Nauta
- FrieslandCampina, Amersfoort 3800 BN, The Netherlands
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
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43
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Tian S, Zeng W, Fang F, Zhou J, Du G. The microbiome of Chinese rice wine (Huangjiu). Curr Res Food Sci 2022; 5:325-335. [PMID: 35198991 PMCID: PMC8844729 DOI: 10.1016/j.crfs.2022.01.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/30/2021] [Accepted: 01/09/2022] [Indexed: 12/30/2022] Open
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44
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Ilango S, Antony U. Probiotic microorganisms from non-dairy traditional fermented foods. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.05.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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45
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Lee W, Choi HJ, Zin H, Kim E, Yang SM, Hwang J, Kwak HS, Kim SH, Kim HY. Effect of Enterotoxigenic Escherichia coli on Microbial Communities during Kimchi Fermentation. J Microbiol Biotechnol 2021; 31:1552-1558. [PMID: 34489379 PMCID: PMC9705866 DOI: 10.4014/jmb.2108.08038] [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: 08/30/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 12/15/2022]
Abstract
The diverse microbial communities in kimchi are dependent on fermentation period and temperature. Here, we investigated the effect of enterotoxigenic Escherichia coli (ETEC) during the fermentation of kimchi at two temperatures using high-throughput sequencing. There were no differences in pH between the control group, samples not inoculated with ETEC, and the ETEC group, samples inoculated with ETEC MFDS 1009477. The pH of the two groups, which were fermented at 10 and 25°C, decreased rapidly at the beginning of fermentation and then reached pH 3.96 and pH 3.62. In both groups, the genera Lactobacillus, Leuconostoc, and Weissella were predominant. Our result suggests that microbial communities during kimchi fermentation may be affected by the fermentation parameters, such as temperature and period, and not enterotoxigenic E. coli (ETEC).
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Affiliation(s)
- Woojung Lee
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea,Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Hyo Ju Choi
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Hyunwoo Zin
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Eiseul Kim
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Seung-Min Yang
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Jinhee Hwang
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Hyo-Sun Kwak
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea,Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Soon Han Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea,Corresponding authors S.H. Kim E-mail:
| | - Hae-Yeong Kim
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea,
H.Y. Kim Phone: +82-31-201-2123 Fax: +82-31-204-8116 E-mail:
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Distribution and characterization of prophages in Lactobacillus plantarum derived from kimchi. Food Microbiol 2021; 102:103913. [PMID: 34809939 DOI: 10.1016/j.fm.2021.103913] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 08/28/2021] [Accepted: 09/21/2021] [Indexed: 12/11/2022]
Abstract
Prophage distribution and phage characteristics based on the genome of Lactobacillus plantarum derived from kimchi were investigated. Prophage genomes retrieved from a database were analyzed in silico with prophage inducibility. Twenty-one kimchi-derived L. plantarum had at least one intact prophage, including a putative cryptic state on the chromosome. They were all confirmed to belong to the Siphoviridae family. Intact prophages can be classified into three different groups: PM411-like, Sha1-like, and unclassified phage groups. Some prophage regions were encoded with superinfection exclusion proteins and orphan methylases, suggesting that the phages co-evolved with their hosts. Interestingly, prophage inducibility showed that only DNA damage could induce prophages and that pH stresses by organic acids could not. Therefore, the prophage of L. plantarum did not affect the host unless DNA was damaged, and it would hardly affect the viability of the host through phage induction during kimchi fermentation. Our results might provide insights into the distribution and non-inducibility of prophages, existence of phage-immunity genes, and role of plant-derived L. plantarum prophages in host survival during late acidic kimchi fermentation.
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Mannaa M, Han G, Seo YS, Park I. Evolution of Food Fermentation Processes and the Use of Multi-Omics in Deciphering the Roles of the Microbiota. Foods 2021; 10:2861. [PMID: 34829140 PMCID: PMC8618017 DOI: 10.3390/foods10112861] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/11/2021] [Accepted: 11/17/2021] [Indexed: 12/22/2022] Open
Abstract
Food fermentation has been practised since ancient times to improve sensory properties and food preservation. This review discusses the process of fermentation, which has undergone remarkable improvement over the years, from relying on natural microbes and spontaneous fermentation to back-slopping and the use of starter cultures. Modern biotechnological approaches, including genome editing using CRISPR/Cas9, have been investigated and hold promise for improving the fermentation process. The invention of next-generation sequencing techniques and the rise of meta-omics tools have advanced our knowledge on the characterisation of microbiomes involved in food fermentation and their functional roles. The contribution and potential advantages of meta-omics technologies in understanding the process of fermentation and examples of recent studies utilising multi-omics approaches for studying food-fermentation microbiomes are reviewed. Recent technological advances in studying food fermentation have provided insights into the ancient wisdom in the practice of food fermentation, such as the choice of substrates and fermentation conditions leading to desirable properties. This review aims to stimulate research on the process of fermentation and the associated microbiomes to produce fermented food efficiently and sustainably. Prospects and the usefulness of recent advances in molecular tools and integrated multi-omics approaches are highlighted.
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Affiliation(s)
- Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (M.M.); (G.H.)
- Department of Plant Pathology, Cairo University, Giza 12613, Egypt
| | - Gil Han
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (M.M.); (G.H.)
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (M.M.); (G.H.)
| | - Inmyoung Park
- School of Culinary Arts, Youngsan University, Busan 48015, Korea
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Effects of the main ingredients of the fermented food, kimchi, on bacterial composition and metabolite profile. Food Res Int 2021; 149:110668. [PMID: 34600670 DOI: 10.1016/j.foodres.2021.110668] [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: 03/31/2021] [Revised: 08/05/2021] [Accepted: 08/24/2021] [Indexed: 12/26/2022]
Abstract
Kimchi is a fermented food prepared via spontaneous fermentation by lactic acid bacteria originating from raw ingredients. To investigate the effect of these ingredients on food fermentation, four types of food that differed only in their main raw ingredients (kimchi cabbage, green onion, leaf mustard, and young radish) were evaluated. The major microorganisms were Leuconostoc gelidum, Weissella kandleri, and Lactobacillus sakei groups. The distribution of these species depended on the sample type. All three species were primarily distributed in the food prepared from kimchi cabbage and young radish; however, the Lac. sakei group was hardly found in the food prepared using green onion and leaf mustard. Metabolite analysis results showed that the free sugar, organic acid, ethanol, and amino acid profiles differed with the sample type. This study indicates that the main ingredients could be an important factor in determining the composition of the microbial community and the metabolite composition.
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49
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Alekseeva AY, Groenenboom AE, Smid EJ, Schoustra SE. Eco-Evolutionary Dynamics in Microbial Communities from Spontaneous Fermented Foods. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph181910093. [PMID: 34639397 PMCID: PMC8508538 DOI: 10.3390/ijerph181910093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/15/2021] [Accepted: 09/20/2021] [Indexed: 01/02/2023]
Abstract
Eco-evolutionary forces are the key drivers of ecosystem biodiversity dynamics. This resulted in a large body of theory, which has partially been experimentally tested by mimicking evolutionary processes in the laboratory. In the first part of this perspective, we outline what model systems are used for experimental testing of eco-evolutionary processes, ranging from simple microbial combinations and, more recently, to complex natural communities. Microbial communities of spontaneous fermented foods are a promising model system to study eco-evolutionary dynamics. They combine the complexity of a natural community with extensive knowledge about community members and the ease of manipulating the system in a laboratory setup. Due to rapidly developing sequencing techniques and meta-omics approaches incorporating data in building ecosystem models, the diversity in these communities can be analysed with relative ease while hypotheses developed in simple systems can be tested. Here, we highlight several eco-evolutionary questions that are addressed using microbial communities from fermented foods. These questions relate to analysing species frequencies in space and time, the diversity-stability relationship, niche space and community coalescence. We provide several hypotheses of the influence of these factors on community evolution specifying the experimental setup of studies where microbial communities of spontaneous fermented food are used.
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Affiliation(s)
- Anna Y. Alekseeva
- Laboratory of Genetics, Wageningen University and Research, 6700 HB Wageningen, The Netherlands; (A.E.G.); (S.E.S.)
- Correspondence:
| | - Anneloes E. Groenenboom
- Laboratory of Genetics, Wageningen University and Research, 6700 HB Wageningen, The Netherlands; (A.E.G.); (S.E.S.)
- Laboratory of Food Microbiology, Wageningen University and Research, 6700 HB Wageningen, The Netherlands;
| | - Eddy J. Smid
- Laboratory of Food Microbiology, Wageningen University and Research, 6700 HB Wageningen, The Netherlands;
| | - Sijmen E. Schoustra
- Laboratory of Genetics, Wageningen University and Research, 6700 HB Wageningen, The Netherlands; (A.E.G.); (S.E.S.)
- Department of Food Science and Nutrition, School of Agricultural Sciences, University of Zambia, Lusaka 10101, Zambia
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Metagenomic Analysis of Suansun, a Traditional Chinese Unsalted Fermented Food. Processes (Basel) 2021. [DOI: 10.3390/pr9091669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Suansun, made from fresh bamboo shoots fermented without salt, is a traditional food in China’s southern region and is popular for its nutritious and unique flavor. To comprehensively understand the microbial species and characteristics of suansun, Illumina HiSeq metagenomic sequencing technology was used to sequence suansun’s fermentation broth obtained from six traditional producing areas in southern China, and the microbial community structure, diversity, and functional genes were analyzed. A total of 8 phyla, 16 classes, 30 orders, 63 families, 92 genera, and 156 species of microorganisms were identified in the suansun samples, with Lactiplantibacillus predominating, accounting for up to 81% of the species, among which 12 species, including Lactiplantibacillus plantarum, were the main species. A total of 12,751 unigenes were annotated to 385 metabolic pathway classes, of which 2927 unigenes were involved in carbohydrate metabolism. Lactiplantibacillus fermentum, Lactiplantibacillus plantarum, and Lactiplantibacillus brucei were involved in the metabolism of most nutrients and flavor substances in suansun. Overall, these results provide insights into the suansun microbiota and shed light on the fermentation processes carried out by complex microbial communities.
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