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Belleggia L, Osimani A. Fermented fish and fermented fish-based products, an ever-growing source of microbial diversity: A literature review. Food Res Int 2023; 172:113112. [PMID: 37689879 DOI: 10.1016/j.foodres.2023.113112] [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: 03/30/2023] [Revised: 06/04/2023] [Accepted: 06/09/2023] [Indexed: 09/11/2023]
Abstract
Fermented fish and fermented fish-based products are part of the diet of many countries all over the world. Their popularity is not only due to the unique flavor, the distinct texture, and the good nutritional quality, but also to the easiness of the production process, that is commonly based on empirical traditional methods. Fish fermentation techniques ususally rely on the combination of some key steps, including salting, addition of spices or additives, and maintenance of anaerobic conditions, thus selecting for the multiplication of some pro-technological microorganisms. The objective of the present review was to provide an overview of the current knowledge of the microbial communities occurring in fermented fish and fish-based products. Specific information was collected from scientific publications published from 2000 to 2022 with the aim of generating a comprehensive database. The production of fermented fish and fish-based foods was mostly localized in West African countries, Northern European countries, and Southeast Asian countries. Based on the available literature, the microbial composition of fermented fish and fish-based products was delineated by using viable counting combined with identification of isolates, and culture-independent techniques. The data obtained from viable counting highlighted the occurrence of microbial groups usually associated with food fermentation, namely lactic acid bacteria, staphylococci, Bacillus spp., and yeasts. The identification of isolates combined with culture-independent methods showed that the fermentative process of fish-based products was generally guided by lactobacilli (Lactiplantibacillus plantarum, Latilactobacillus sakei, and Latilactobacillus curvatus) or Tetragenococcus spp. depending on the salt concentration. Among lactic acid bacteria populations, Lactococcus spp., Pediococcus spp., Leuconostoc spp., Weissella spp., Enterococcus spp., Streptococcus spp., and Vagococcus spp. were frequently identified. Staphylococcus spp. and Bacillus spp. confirmed a great adaptation to fermented fish-based products. Other noteworthy bacterial taxa included Micrococcus spp., Pseudomonas spp., Psychrobacter spp., Halanaerobium spp., and Halomonas spp. Among human pathogenic bacteria, the occurrence of Clostridium spp. and Vibrio spp. was documented. As for yeast populations, the predominance of Candida spp., Debaryomyces spp., and Saccharomyces spp. was evidenced. The present literature review could serve as comprehensive database for the scientific community, and as a reference for the food industry in order to formulate tailored starter or adjunctive cultures for product improvement.
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Affiliation(s)
- Luca Belleggia
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, Ancona, Italy
| | - Andrea Osimani
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, Ancona, Italy.
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Hori M, Kawai Y, Nakamura K, Shimada M, Iwahashi H, Nakagawa T. Characterization of the bacterial community structure in traditional Gifu ayu-narezushi (fermented sweetfish). J Biosci Bioeng 2022; 134:331-337. [PMID: 36030194 DOI: 10.1016/j.jbiosc.2022.07.012] [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: 05/11/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 11/30/2022]
Abstract
In this study, we aimed to elucidate the bacterial biota of ayu-nazushi, which is a fermented salted fish dish made in Gifu City, Japan. In traditional Gifu ayu-nazushi, Lactobacillaceae (mainly Latilactobacillus sakei) was the most dominant family, followed by Enterobacteriaceae. Moreover, fermentation bacteria in ayu-nazushi came from the salted fish, and the bacterial biota in the ayu-nazushi transferred as the fermentation process progressed. In the early stage of fermentation, Leuconostoc mesenteroides was main species, and then in the late stage, L. sakei became predominant. We also observed that when non-salted fish was used for the manufacture of ayu-nazushi, Aeromonas veronii, which is a pathogen for humans, was observed in significant quantities. These results indicate that L. sakei and L. mesenteroides were influential lactic acid bacteria for the fermentation of Gifu ayu-narezushi, and that salting treatment of the fish is an indispensable step in the manufacturing process in order to suppress the growth of Aeromonas species.
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Affiliation(s)
- Mitsuyo Hori
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Department of Food and Nutrition, Gifu City Women's College, 7-1 Hitoichiba Kitamachi, Gifu 501-0192, Japan
| | - Yusuke Kawai
- Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Kohei Nakamura
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Masaya Shimada
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Hitoshi Iwahashi
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Tomoyuki Nakagawa
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
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Transition and regulation mechanism of bacterial biota in Kishu saba-narezushi (mackerel narezushi) during its fermentation step. J Biosci Bioeng 2021; 132:606-612. [PMID: 34563462 DOI: 10.1016/j.jbiosc.2021.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 11/24/2022]
Abstract
The transition of the bacterial biota of Kishu saba-narezushi (mackerel-narezushi) in the Hidaka region of Wakayama prefecture, Japan, was analyzed using amplicon sequencing based on the V3-V4 variable region of the 16S rRNA gene. In the non-fermented sample (0 day), the major genus with the highest abundance ratio was Staphylococcus. In the early stage (fermentation for 2 days), however, the genus Lactococcus became a dominant species, and in the later stage (fermentation for 5 days), the abundance ratio of the genus Lactobacillus increased significantly. Lactococcus lactis strains isolated from the narezushi samples had the ability to suppress the growth of not only Staphylococcus genera but also Lactobacillus. Moreover, the isolates produced a bacteriocin, which was identified as nisin Z. On the basis of these results, it is concluded that L. lactis plays an important role in preparing the fermentation conditions of Kishu saba-narezushi in the early stage by suppressing unwanted microorganisms using lactic acid and nisin Z.
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Nagano H, Izumi Z, Uehara A, Hend A, Isobe Y, Yanase E, Nomura I, Suzuki T. Chemical Characteristics and Microbial Diversity of Ayu-narezushi from Gifu. J JPN SOC FOOD SCI 2020. [DOI: 10.3136/nskkk.67.101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Hiroko Nagano
- Faculty of Applied Biological Sciences, Gifu University
| | | | - Aoi Uehara
- Organization for Research and Community Development, Gifu University
| | - Altaib Hend
- The United Graduate School of Agricultural Science, Gifu University
| | | | - Emiko Yanase
- Faculty of Applied Biological Sciences, Gifu University
| | - Izumi Nomura
- Faculty of Applied Biological Sciences, Gifu University
| | - Tohru Suzuki
- Faculty of Applied Biological Sciences, Gifu University
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Xiang H, Sun-Waterhouse D, Waterhouse GI, Cui C, Ruan Z. Fermentation-enabled wellness foods: A fresh perspective. FOOD SCIENCE AND HUMAN WELLNESS 2019. [DOI: 10.1016/j.fshw.2019.08.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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6
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Bacterial and fungal microbiota in traditional Bangladeshi fermented milk products analysed by culture-dependent and culture-independent methods. Food Res Int 2018; 111:431-437. [DOI: 10.1016/j.foodres.2018.05.048] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/10/2018] [Accepted: 05/19/2018] [Indexed: 01/22/2023]
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7
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Bacterial and fungal microbiota of spontaneously fermented Chinese products, Rubing milk cake and Yan-cai vegetable pickles. Food Microbiol 2018; 72:106-111. [DOI: 10.1016/j.fm.2017.11.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/09/2017] [Accepted: 11/24/2017] [Indexed: 01/31/2023]
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Nakano M. 16S rRNA Gene Primer Validation for Bacterial Diversity Analysis of Vegetable Products. J Food Prot 2018; 81:848-859. [PMID: 29664320 DOI: 10.4315/0362-028x.jfp-17-346] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
High-throughput sequencing of the 16S rRNA gene enhances understanding of microbial diversity from complex environmental samples. The 16S rRNA gene is currently the most important target in bacterial evolution and ecology studies, particularly for determination of phylogenetic relationships among taxa, exploration of bacterial diversity in a given environment, and quantification of the relative abundance of taxa at various levels. However, some parts of the conserved region of the bacterial 16S rRNA gene are similar to the conserved regions of plant chloroplasts and eukaryotic mitochondria. Therefore, if DNA contains a large amount of nontarget DNA, this nontarget DNA can be coamplified and consequently produce useless sequence reads. We experimentally assessed the primer pair 335f/769r and the widely used bacterial primer pair SD (S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21). The primer pair 335f/769r was examined for its ability to amplify bacterial DNA in plant and animal feed samples by using the single-strand confirmation polymorphism method. In our present study, these primer pairs were validated for microbial community structure analysis with complex food matrices by using next-generation sequencing. The sequencing results revealed that the primer pair 335f/769r successfully resulted in fewer chloroplast and mitochondrial sequence reads than generated by the universal primer pair SD and therefore is comparatively suitable for metagenomic analyses of complex food matrices, particularly those that are rich in plant DNA. Additionally, some taxonomic groups were missed entirely when only the SD primer pair was used.
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Affiliation(s)
- Miyo Nakano
- Division of Food Science, Toyo Institute of Food Technology, 23-2, 4-chome, Minami-hanayashiki, Kawanishi-shi, Hyogo, 666-0026 Japan
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9
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Effect of the environment microbiota on the flavour of light-flavour Baijiu during spontaneous fermentation. Sci Rep 2018; 8:3396. [PMID: 29467508 PMCID: PMC5821866 DOI: 10.1038/s41598-018-21814-y] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 02/12/2018] [Indexed: 12/04/2022] Open
Abstract
Light-flavour Baijiu is a type of Chinese liquor with a pure and mild flavour produced by traditional spontaneous solid-state fermentation. The flavour of this liquor has been found to vary in the different periods of annual production. To explore the factors affecting flavour, the microbiota of the surrounding environment, starter and fermentation process in different periods were investigated. Results showed that the ester content and acidity of light-flavour Baijiu were significantly lower when annual production was resumed after a summer break. HCA plot of volatile flavour profile and bacterial PCoA results indicated that the differences occurred at later stages, mainly due to different structures of Lactobacillus. Correlation analysis by O2PLS indicated that Lactobacillus positively correlated with esters. Species-level analysis showed that the lack of L. acetotolerans on the surface of the jar might cause a lag in fermentation and lower ester content. Thereafter, L. acetotolerans was revived during fermentation and enriched on the surface of the jar, which promoted ester formation. As important sources of L. acetotolerans, the air and fermentation jars played a critical role during fermentation. Therefore, this systematic study on environmental microbial ecology is valuable for quality control and to explore environmental microbiota functions during spontaneous fermentation.
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Fujii T, Kyoui D, Takahashi H, Kuda T, Kimura B, Washizu Y, Emoto E, Hiramoto T. Pyrosequencing analysis of the microbiota of kusaya gravy obtained from Izu Islands. Int J Food Microbiol 2016; 238:320-325. [DOI: 10.1016/j.ijfoodmicro.2016.09.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 09/27/2016] [Accepted: 09/28/2016] [Indexed: 10/20/2022]
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11
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De Filippis F, Parente E, Ercolini D. Metagenomics insights into food fermentations. Microb Biotechnol 2016; 10:91-102. [PMID: 27709807 PMCID: PMC5270737 DOI: 10.1111/1751-7915.12421] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/12/2016] [Accepted: 09/15/2016] [Indexed: 11/26/2022] Open
Abstract
This review describes the recent advances in the study of food microbial ecology, with a focus on food fermentations. High‐throughput sequencing (HTS) technologies have been widely applied to the study of food microbial consortia and the different applications of HTS technologies were exploited in order to monitor microbial dynamics in food fermentative processes. Phylobiomics was the most explored application in the past decade. Metagenomics and metatranscriptomics, although still underexploited, promise to uncover the functionality of complex microbial consortia. The new knowledge acquired will help to understand how to make a profitable use of microbial genetic resources and modulate key activities of beneficial microbes in order to ensure process efficiency, product quality and safety.
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Affiliation(s)
- Francesca De Filippis
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Eugenio Parente
- Dipartimento di Scienze, Università degli Studi della Basilicata, Potenza, Italy
| | - Danilo Ercolini
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
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12
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Tian X, Wu W, Yu Q, Hou M, Gao F, Li X, Dai R. Bacterial diversity analysis of pork longissimus lumborum following long term ohmic cooking and water bath cooking by amplicon sequencing of 16S rRNA gene. Meat Sci 2016; 123:97-104. [PMID: 27665069 DOI: 10.1016/j.meatsci.2016.09.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/08/2016] [Accepted: 09/12/2016] [Indexed: 12/17/2022]
Abstract
The bacterial ecology of long term ohmic- (LTOH) and water bath- (WB) cooked pork longissimus lumborum during refrigerated storage was investigated by culture-dependent and amplicon sequencing of 16S rRNA gene. High bacterial diversity was observed in both LTOH- and WB-cooked meat, and the diversity decreased with prolonged storage, however, it was more complex in LTOH-cooked meat compared with WB treated ones. Bacillus, Pseudomonas, Enterococcus and Lactococcus were the most prevalent genera in the first two weeks and were replaced by Carnobacterium by the end of storage. Brevundimonas, Bacteroidaceae, Lactobacillaceae, uncultured Clostridiales Family_XIII, Alcaligenaceae and Micrococcales were more abundant in LTOH-cooked meat, while only Moraxellaceae were more abundant in WB-cooked samples. The different abundances may have resulted from the reaction of bacteria to different heating mechanisms. Overall, LTOH-cooked meat has a similar shelf-life with shorter processing time compared to WB treated ones.
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Affiliation(s)
- Xiaojing Tian
- College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China; Beijing Higher Institution Engineering Research Center of Animal Product, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China
| | - Wei Wu
- College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China; Beijing Higher Institution Engineering Research Center of Animal Product, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China
| | - Qianqian Yu
- College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China; Beijing Higher Institution Engineering Research Center of Animal Product, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China
| | - Man Hou
- College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China; Beijing Higher Institution Engineering Research Center of Animal Product, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China
| | - Fang Gao
- College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China; Beijing Higher Institution Engineering Research Center of Animal Product, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China
| | - Xingmin Li
- College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China; Beijing Higher Institution Engineering Research Center of Animal Product, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China
| | - Ruitong Dai
- College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China; Beijing Higher Institution Engineering Research Center of Animal Product, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China.
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Detection and genomic characterization of motility in Lactobacillus curvatus: confirmation of motility in a species outside the Lactobacillus salivarius clade. Appl Environ Microbiol 2016; 81:1297-1308. [PMID: 25501479 DOI: 10.1128/aem.03594-14] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Lactobacillus is the largest genus within the lactic acid bacteria (LAB), with almost 180 species currently identified. Motility has been reported for at least 13 Lactobacillus species, all belonging to the Lactobacillus salivarius clade. Motility in lactobacilli is poorly characterized. It probably confers competitive advantages, such as superior nutrient acquisition and niche colonization, but it could also play an important role in innate immune system activation through flagellin–Toll-like receptor 5 (TLR5) interaction. We now report strong evidence of motility in a species outside the L. salivarius clade, Lactobacillus curvatus (strain NRIC0822). The motility of L. curvatus NRIC 0822 was revealed by phase-contrast microscopy and soft-agar motility assays. Strain NRIC 0822 was motile at temperatures between 15 °C and 37 °C, with a range of different carbohydrates, and under varying atmospheric conditions. We sequenced the L. curvatus NRIC 0822 genome, which revealed that the motility genes are organized in a single operon and that the products are very similar (>98.5% amino acid similarity over >11,000 amino acids) to those encoded by the motility operon of Lactobacillus acidipiscis KCTC 13900 (shown for the first time to be motile also). Moreover, the presence of a large number of mobile genetic elements within and flanking the motility operon of L. curvatus suggests recent horizontal transfer between members of two distinct Lactobacillus clades: L. acidipiscis in the L. salivarius clade and L. curvatus inthe L. sakei clade. This study provides novel phenotypic, genetic, and phylogenetic insights into flagellum-mediated motility in lactobacilli.
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Bassi D, Puglisi E, Cocconcelli PS. Understanding the bacterial communities of hard cheese with blowing defect. Food Microbiol 2015; 52:106-18. [DOI: 10.1016/j.fm.2015.07.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/19/2015] [Accepted: 07/03/2015] [Indexed: 11/17/2022]
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Kergourlay G, Taminiau B, Daube G, Champomier Vergès MC. Metagenomic insights into the dynamics of microbial communities in food. Int J Food Microbiol 2015; 213:31-9. [DOI: 10.1016/j.ijfoodmicro.2015.09.010] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 09/04/2015] [Accepted: 09/13/2015] [Indexed: 02/06/2023]
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Połka J, Rebecchi A, Pisacane V, Morelli L, Puglisi E. Bacterial diversity in typical Italian salami at different ripening stages as revealed by high-throughput sequencing of 16S rRNA amplicons. Food Microbiol 2015; 46:342-356. [DOI: 10.1016/j.fm.2014.08.023] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 07/26/2014] [Accepted: 08/29/2014] [Indexed: 02/01/2023]
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18
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Takahashi M, Kita Y, Kusaka K, Mizuno A, Goto-Yamamoto N. Evaluation of microbial diversity in the pilot-scale beer brewing process by culture-dependent and culture-independent method. J Appl Microbiol 2015; 118:454-69. [DOI: 10.1111/jam.12712] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 11/06/2014] [Accepted: 11/24/2014] [Indexed: 11/29/2022]
Affiliation(s)
- M. Takahashi
- National Research Institute of Brewing (NRIB); Higashi-Hiroshima Japan
| | - Y. Kita
- National Research Institute of Brewing (NRIB); Higashi-Hiroshima Japan
| | - K. Kusaka
- National Research Institute of Brewing (NRIB); Higashi-Hiroshima Japan
| | - A. Mizuno
- National Research Institute of Brewing (NRIB); Higashi-Hiroshima Japan
| | - N. Goto-Yamamoto
- National Research Institute of Brewing (NRIB); Higashi-Hiroshima Japan
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Mayo B, Rachid CTCC, Alegría A, Leite AMO, Peixoto RS, Delgado S. Impact of next generation sequencing techniques in food microbiology. Curr Genomics 2014; 15:293-309. [PMID: 25132799 PMCID: PMC4133952 DOI: 10.2174/1389202915666140616233211] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 06/04/2014] [Accepted: 06/13/2014] [Indexed: 02/07/2023] Open
Abstract
Understanding the Maxam-Gilbert and Sanger sequencing as the first generation, in recent years there has been an explosion of newly-developed sequencing strategies, which are usually referred to as next generation sequencing (NGS) techniques. NGS techniques have high-throughputs and produce thousands or even millions of sequences at the same time. These sequences allow for the accurate identification of microbial taxa, including uncultivable organisms and those present in small numbers. In specific applications, NGS provides a complete inventory of all microbial operons and genes present or being expressed under different study conditions. NGS techniques are revolutionizing the field of microbial ecology and have recently been used to examine several food ecosystems. After a short introduction to the most common NGS systems and platforms, this review addresses how NGS techniques have been employed in the study of food microbiota and food fermentations, and discusses their limits and perspectives. The most important findings are reviewed, including those made in the study of the microbiota of milk, fermented dairy products, and plant-, meat- and fish-derived fermented foods. The knowledge that can be gained on microbial diversity, population structure and population dynamics via the use of these technologies could be vital in improving the monitoring and manipulation of foods and fermented food products. They should also improve their safety.
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Affiliation(s)
- Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300-Villaviciosa, Asturias, Spain
| | - Caio T C C Rachid
- Instituto de Microbiologia, Departamento de Microbiologia Geral, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, 21941904-Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Angel Alegría
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300-Villaviciosa, Asturias, Spain
| | - Analy M O Leite
- Instituto de Microbiologia, Departamento de Microbiologia Geral, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, 21941904-Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Raquel S Peixoto
- Instituto de Microbiologia, Departamento de Microbiologia Geral, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, 21941904-Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Susana Delgado
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300-Villaviciosa, Asturias, Spain
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Pyrosequencing Analysis of Microbiota inKaburazushi, a Traditional Medieval Sushi in Japan. Biosci Biotechnol Biochem 2014; 77:2125-30. [DOI: 10.1271/bbb.130550] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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21
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Kuda T, Tomomi K, Kawahara M, Takahashi H, Kimura B. Inhibitory effects of Leuconostoc mesenteroides 1RM3 isolated from narezushi on lipopolysaccharide-induced inflammation in RAW264.7 mouse macrophage cells and dextran sodium sulphate-induced inflammatory bowel disease in mice. J Funct Foods 2014. [DOI: 10.1016/j.jff.2013.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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Dai Z, Li Y, Wu J, Zhao Q. Diversity of Lactic Acid Bacteria during Fermentation of a Traditional Chinese Fish Product,Chouguiyu(Stinky Mandarinfish). J Food Sci 2013; 78:M1778-83. [DOI: 10.1111/1750-3841.12289] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 09/14/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Zhiyuan Dai
- College of Food Science and Biotechnology and, Inst. of Aquatic Products Processing; Zhejiang Gongshang Univ.; Hangzhou Zhejiang 310035 China
| | - Yan Li
- College of Food Science and Biotechnology and, Inst. of Aquatic Products Processing; Zhejiang Gongshang Univ.; Hangzhou Zhejiang 310035 China
| | - Jiajia Wu
- College of Food Science and Biotechnology and, Inst. of Aquatic Products Processing; Zhejiang Gongshang Univ.; Hangzhou Zhejiang 310035 China
| | - Qiaoling Zhao
- College of Food Science and Biotechnology and, Inst. of Aquatic Products Processing; Zhejiang Gongshang Univ.; Hangzhou Zhejiang 310035 China
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Marsh AJ, O’Sullivan O, Hill C, Ross RP, Cotter PD. Sequencing-based analysis of the bacterial and fungal composition of kefir grains and milks from multiple sources. PLoS One 2013; 8:e69371. [PMID: 23894461 PMCID: PMC3716650 DOI: 10.1371/journal.pone.0069371] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 06/07/2013] [Indexed: 12/25/2022] Open
Abstract
Kefir is a fermented milk-based beverage to which a number of health-promoting properties have been attributed. The microbes responsible for the fermentation of milk to produce kefir consist of a complex association of bacteria and yeasts, bound within a polysaccharide matrix, known as the kefir grain. The consistency of this microbial population, and that present in the resultant beverage, has been the subject of a number of previous, almost exclusively culture-based, studies which have indicated differences depending on geographical location and culture conditions. However, culture-based identification studies are limited by virtue of only detecting species with the ability to grow on the specific medium used and thus culture-independent, molecular-based techniques offer the potential for a more comprehensive analysis of such communities. Here we describe a detailed investigation of the microbial population, both bacterial and fungal, of kefir, using high-throughput sequencing to analyse 25 kefir milks and associated grains sourced from 8 geographically distinct regions. This is the first occasion that this technology has been employed to investigate the fungal component of these populations or to reveal the microbial composition of such an extensive number of kefir grains or milks. As a result several genera and species not previously identified in kefir were revealed. Our analysis shows that the bacterial populations in kefir are dominated by 2 phyla, the Firmicutes and the Proteobacteria. It was also established that the fungal populations of kefir were dominated by the genera Kazachstania, Kluyveromyces and Naumovozyma, but that a variable sub-dominant population also exists.
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Affiliation(s)
- Alan J. Marsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Microbiology Department, University College Cork, Cork, Ireland
| | | | - Colin Hill
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Microbiology Department, University College Cork, Cork, Ireland
- * E-mail: (CH); (PDC)
| | - R. Paul Ross
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- * E-mail: (CH); (PDC)
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24
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High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology. Appl Environ Microbiol 2013; 79:3148-55. [PMID: 23475615 DOI: 10.1128/aem.00256-13] [Citation(s) in RCA: 312] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Following recent trends in environmental microbiology, food microbiology has benefited from the advances in molecular biology and adopted novel strategies to detect, identify, and monitor microbes in food. An in-depth study of the microbial diversity in food can now be achieved by using high-throughput sequencing (HTS) approaches after direct nucleic acid extraction from the sample to be studied. In this review, the workflow of applying culture-independent HTS to food matrices is described. The current scenario and future perspectives of HTS uses to study food microbiota are presented, and the decision-making process leading to the best choice of working conditions to fulfill the specific needs of food research is described.
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25
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Song S, Jarvie T, Hattori M. Our second genome-human metagenome: how next-generation sequencer changes our life through microbiology. Adv Microb Physiol 2013; 62:119-44. [PMID: 23481336 DOI: 10.1016/b978-0-12-410515-7.00003-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Next-generation sequencing has greatly expanded our ability to query the identity and genetic composition of entire communities of microbial organisms. This area of research, known as metagenomics, does not rely upon culturing the individual organisms. Rather, the genetic material from the entire community is processed and sequenced simultaneously. From this sequence data, researchers are able to determine the relative population of organisms within the community as well as determine which genes and metabolic pathways are present and expressed in the microbial community. While these techniques have been applied to a wide range of environmental samples, metagenomics is also the focus of intensive research on human-associated microbial communities. The scope of these human metagenomics studies are quite varied, but all have a common goal of attempting to understand the important role that human commensal microbial communities play in health and disease. The early results from studying the human metagenome indicate a vital role that microbial communities play in immunity, health, and disease. Going forward, human metagenomics is a wide open field of research with many unanswered questions such as which factors are responsible for the variation of composition of an individual's microbiome, how does the microbiome respond to disturbance, and what beneficial functions are the microorganisms performing?
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Affiliation(s)
- Shuolin Song
- Genome Sequencing Department, Applied Science, Roche Diagnostics K. K., Tokyo, Japan.
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26
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Bokulich NA, Mills DA. Next-generation approaches to the microbial ecology of food fermentations. BMB Rep 2012; 45:377-89. [PMID: 22831972 DOI: 10.5483/bmbrep.2012.45.7.148] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Food fermentations have enhanced human health since the dawn of time and remain a prevalent means of food processing and preservation. Due to their cultural and nutritional importance, many of these foods have been studied in detail using molecular tools, leading to enhancements in quality and safety. Furthermore, recent advances in high-throughput sequencing technology are revolutionizing the study of food microbial ecology, deepening insight into complex fermentation systems. This review provides insight into novel applications of select molecular techniques, particularly next-generation sequencing technology, for analysis of microbial communities in fermented foods. We present a guideline for integrated molecular analysis of food microbial ecology and a starting point for implementing next-generation analysis of food systems.
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Affiliation(s)
- Nicholas A Bokulich
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
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