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Thierry A, Madec MN, Chuat V, Bage AS, Picard O, Grondin C, Rué O, Mariadassou M, Marché L, Valence F. Microbial communities of a variety of 75 homemade fermented vegetables. Front Microbiol 2023; 14:1323424. [PMID: 38163080 PMCID: PMC10757351 DOI: 10.3389/fmicb.2023.1323424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/15/2023] [Indexed: 01/03/2024] Open
Abstract
Fermentation is an ancient practice of food preservation. Fermented vegetables are popular in Eastern European and Asian countries. They have received a growing interest in Western countries, where they are mainly manufactured at domestic and artisanal scales and poorly characterized. Our aim was to investigate the microbial communities and the safety of French homemade fermented vegetables, in the frame of a citizen science project. Fermented vegetables and the data associated with their manufacture were collected from citizens and characterized for pH, NaCl concentration, and microbiology by culturomics and 16S DNA metabarcoding analysis. Lactic acid bacteria (LAB) and yeast isolates were identified by 16S rRNA gene sequencing and D1/D2 domains of the large subunit of the rRNA gene, respectively. The 75 collected samples contained 23 types of vegetables, mainly cabbage, followed by carrots and beets, and many mixtures of vegetables. They were 2 weeks to 4 years old, and their median pH was 3.56, except for two samples with a pH over 4.5. LAB represented the dominant viable bacteria. LAB concentrations ranged from non-detectable values to 8.7 log colony-forming units (CFU)/g and only depended on the age of the samples, with the highest most frequently observed in the youngest samples (<100 days). The 93 LAB isolates identified belonged to 23 species, the two mains being Lactiplantibacillus pentosus/plantarum and Levilactobacillus brevis. The other microbial groups enumerated (total aerobic bacteria, halotolerant bacteria, Gram-negative bacteria, and acetic acid bacteria) generally showed lower concentrations compared to LAB concentrations. No pathogenic bacteria were detected. Viable yeasts were observed in nearly half the samples, at concentrations reaching up to 8.0 log CFU/g. The 33 yeast clones identified belonged to 16 species. Bacterial metabarcoding showed two main orders, namely, Lactobacillales (i.e., LAB, 79% of abundance, 177 of the 398 total ASVs) and Enterobacterales (19% of abundance, 191 ASVs). Fifteen LAB genera were identified, with Lactiplantibacillus and Levilactobacillus as the most abundant, with 41 and 12% of total reads, respectively. Enterobacterales members were mainly represented by Enterobacteriaceae and Yersiniaceae. This study is the first wide description of the microbiota of a large variety of homemade fermented vegetables and documents their safety.
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Affiliation(s)
| | | | | | | | | | - Cécile Grondin
- INRAE, Université de Montpellier, Institut Agro, URM SPO, Montpellier, France
| | - Olivier Rué
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Jouy-en-Josas, France
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Kim JY, Park SE, Kim EJ, Seo SH, Whon TW, Cho KM, Kwon SJ, Roh SW, Son HS. Long-term population dynamics of viable microbes in a closed ecosystem of fermented vegetables. Food Res Int 2022; 154:111044. [DOI: 10.1016/j.foodres.2022.111044] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/16/2022] [Accepted: 02/18/2022] [Indexed: 11/25/2022]
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3
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Fentie EG, Jeong M, Emire SA, Demsash HD, Kim MA, Shin JH. Fermentation dynamics of spontaneously fermented Ethiopian honey wine, Tej. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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4
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Dunn RR, Wilson J, Nichols LM, Gavin MC. Toward a Global Ecology of Fermented Foods. CURRENT ANTHROPOLOGY 2021. [DOI: 10.1086/716014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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5
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Real-time PCR assays for the quantitative detection of Kazachstania servazzii and Candida sake related to undesirable white colony on kimchi. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.107984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Lavefve L, Cureau N, Rodhouse L, Marasini D, Walker LM, Ashley D, Lee S, Gadonna‐Widehem P, Anton PM, Carbonero F. Microbiota profiles and dynamics in fermented plant‐based products and preliminary assessment of their in vitro gut microbiota modulation. FOOD FRONTIERS 2021. [DOI: 10.1002/fft2.75] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Laura Lavefve
- Department of Food Science University of Arkansas Fayetteville AR USA
| | - Natacha Cureau
- Department of Food Science University of Arkansas Fayetteville AR USA
| | - Lindsey Rodhouse
- Department of Food Science University of Arkansas Fayetteville AR USA
| | - Daya Marasini
- Department of Food Science University of Arkansas Fayetteville AR USA
| | - Laura M. Walker
- Department of Biology Washington University in Saint‐Louis St Louis MO USA
| | - Danielle Ashley
- Department of Food Science University of Arkansas Fayetteville AR USA
| | - Sun‐Ok Lee
- Department of Food Science University of Arkansas Fayetteville AR USA
| | - Pascale Gadonna‐Widehem
- Transformations & Agroresources, ULR7519 Institut Polytechnique UniLaSalle, Universite d’Artois Beauvais France
| | - Pauline M. Anton
- Transformations & Agroresources, ULR7519 Institut Polytechnique UniLaSalle, Universite d’Artois Beauvais France
| | - Franck Carbonero
- Department of Food Science University of Arkansas Fayetteville AR USA
- Department of Nutrition and Exercise Physiology Elson Floyd School of Medicine Washington State University‐Spokane Spokane WA USA
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7
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Development of Leuconostoc lactis–Specific Quantitative PCR and its Application for Identification and Enumeration in Fermented Foods. FOOD ANAL METHOD 2020. [DOI: 10.1007/s12161-020-01720-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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8
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Comparison of Six Commercial Meat Starter Cultures for the Fermentation of Yellow Mealworm ( Tenebrio molitor) Paste. Microorganisms 2019; 7:microorganisms7110540. [PMID: 31717367 PMCID: PMC6920846 DOI: 10.3390/microorganisms7110540] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 10/30/2019] [Accepted: 11/05/2019] [Indexed: 12/23/2022] Open
Abstract
In this study, six commercial meat starters, each consisting of a pure strain of a lactic acid-fermenting bacterium (including Lactococcus lactis, Lactobacillus curvatus, L. farciminis, L. plantarum, L. sakei, and Pediococcus acidilactici), were tested for their ability to ferment a paste produced from the yellow mealworm (Tenebrio molitor). During fermentation, microbial counts, pH, and the bacterial community composition were determined. In addition, UPLC-MS was applied to monitor the consumption of glucose and the production of glutamic (Glu) and aspartic (Asp) acid. All tested starters were able to ferment the mealworm paste, judged by a pH reduction from 6.68 to 4.60–4.95 within 72 h. Illumina amplicon sequencing showed that all starters were able to colonize the substrate efficiently. Moreover, the introduction of the starter cultures led to the disappearance of Bacillus and Clostridium species, which were the dominant microorganisms in un-inoculated samples. Of the six cultures tested, Lactobacillus farciminis was most promising as its application resulted in the largest increase (±25 mg/100 g of paste) in the content of free glutamic and aspartic acid. These amino acids are responsible for the appreciated umami flavour in fermented food products and might stimulate the acceptance of insects and their consumption.
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Xia X, Dai Y, Wu H, Liu X, Wang Y, Yin L, Wang Z, Li X, Zhou J. Kombucha fermentation enhances the health-promoting properties of soymilk beverage. J Funct Foods 2019. [DOI: 10.1016/j.jff.2019.103549] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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10
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Agyirifo DS, Wamalwa M, Otwe EP, Galyuon I, Runo S, Takrama J, Ngeranwa J. Metagenomics analysis of cocoa bean fermentation microbiome identifying species diversity and putative functional capabilities. Heliyon 2019; 5:e02170. [PMID: 31388591 PMCID: PMC6667825 DOI: 10.1016/j.heliyon.2019.e02170] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/05/2019] [Accepted: 07/24/2019] [Indexed: 12/17/2022] Open
Abstract
Fermentation of Theobroma cacao L. beans is the most critical stage in the production of cocoa products such as chocolates and its derivatives. There is a limited understanding of the complex response of microbial diversity during cocoa bean fermentation. The aim of the present study was to investigate microbial communities in the cocoa bean fermentation heap using a culture-independent approach to elucidate microbial diversity, structure, functional annotation and mapping unto metabolic pathways. Genomic DNA was extracted and purified from a sample of cocoa beans fermentation heap and was followed by library preparations. Sequence data was generated on Illumina Hiseq 2000 paired-end technology (Macrogen Inc). Taxonomic analysis based on genes predicted from the metagenome identified a high percentage of Bacteria (90.0%), Yeast (9%), and bacteriophages (1%) from the cocoa microbiome. Lactobacillus (20%), Gluconacetobacter (9%), Acetobacter (7%) and Gluconobacter (6%) dominated this study. The mean species diversity, measured by Shannon alpha-diversity index, was estimated at 142.81. Assignment of metagenomic sequences to SEED database categories at 97% sequence similarity identified a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates and aromatic amino acids. Metabolism of aromatic compounds, amino acids and their derivatives and carbohydrates occupied 0.6%, 8% and 13% respectively. Overall, these results provide insights into the cocoa microbiome, identifying fermentation processes carried out broadly by complex microbial communities and metabolic pathways encoding aromatic compounds such as phenylacetaldehyde, butanediol, acetoin, and theobromine that are required for flavour and aroma production. The results obtained will help develop targeted inoculations to produce desired chocolate flavour or targeted metabolic pathways for the selection of microbes for good aroma and flavour compounds formation.
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Affiliation(s)
- Daniel S Agyirifo
- Biochemistry and Biotechnology Department, Kenyatta University, Kenya.,Department of Molecular Biology and Biotechnology, University of Cape Coast, Ghana
| | - Mark Wamalwa
- Biochemistry and Biotechnology Department, Kenyatta University, Kenya.,International Livestock Research Institute-Bioscience East and Central Africa, Kenya
| | - Emmanuel Plas Otwe
- Department of Molecular Biology and Biotechnology, University of Cape Coast, Ghana
| | - Isaac Galyuon
- Department of Molecular Biology and Biotechnology, University of Cape Coast, Ghana
| | - Steven Runo
- Biochemistry and Biotechnology Department, Kenyatta University, Kenya
| | - Jemmy Takrama
- Department of Molecular Biology and Biotechnology, University of Cape Coast, Ghana.,Cocoa Research Institute of Ghana, Ghana
| | - Joseph Ngeranwa
- Biochemistry and Biotechnology Department, Kenyatta University, Kenya
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11
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Jung MJ, Kim MS, Yun JH, Lee JY, Kim PS, Lee HW, Ha JH, Roh SW, Bae JW. Viral community predicts the geographical origin of fermented vegetable foods more precisely than bacterial community. Food Microbiol 2018; 76:319-327. [DOI: 10.1016/j.fm.2018.06.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 06/11/2018] [Accepted: 06/15/2018] [Indexed: 12/18/2022]
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12
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Soltan Dallal M, Zamaniahari S, Davoodabadi A, Hosseini M, Rajabi Z. Identification and characterization of probiotic lactic acid bacteria isolated from traditional persian pickled vegetables. GMS HYGIENE AND INFECTION CONTROL 2017; 12:Doc15. [PMID: 28989854 PMCID: PMC5627144 DOI: 10.3205/dgkh000300] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Background: The pickle, a traditional fermented product, is popular among Iranians. Much research has been conducted worldwide on this food group. Due to a lack of related data in Iran, this study was conducted to isolate and identify dominant lactic acid bacteria (LAB) in pickles and salted pickles. Materials and methods: Seventy samples were collected from different regions of Iran. The isolated bacteria were identified as LAB by Gram staining and catalase by using MRS agar. Then, those strains were identified at the species level by physiological tests (e.g., gas production from glucose, arginine hydrolysis, CO2 production from glucose in MRS broth, carbohydrate fermentation) and growth at temperatures of 15°C, 30°C, and 45°C in MRS broth for 3 days. The probiotic characteristics of these bacteria were studied using acid and bile tolerance. The corresponding results were verified using PCR analyses of the 16S rDNA region. Results: 114 presumptive lactic acid bacteria (LAB) with Gram-positive and catalase-negative properties were obtained from the samples. The results revealed that all isolated bacteria were identfied as Lactobacillus (L.) plantarum, L. brevis, L. pentosus, L. casei, L. paracasei and Leuconostoc mesenteroides. The predominant LAB in these pickles was L. plantarum, which was isolated from most of the samples. Among the 114 LAB, 7 isolated species have probiotic potential. Six out of seven were recognized as L. plantarum and one remained unidentifiable by biochemical testing. PCR analysis and sequencing of the 16S rDNA region using 27f and 1522r primers showed that all of the probiotic strains were L. plantarum. Conclusion: The results of this study showed that the dominant LAB in traditional Persian pickled vegetables are L. plantarum, L. brevis, L. pentosus, L. casei, L. paracasei, and Leuconostoc mesenteroides. Moreover, L. plantarum was recognized as a probiotic species in pickled vegetables. The raw data obtained from this study can be used in the pickling industry to improve the nutritional value of products.
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Affiliation(s)
- M.M. Soltan Dallal
- Food Microbiology Research Center, Tehran University of Medical Sciences (TUMS), Tehran, Iran
- Division of Food Microbiology, Department of Pathobiology, School of Public Health, TUMS, Tehran, Iran
| | - S. Zamaniahari
- Division of Food Microbiology, Department of Pathobiology, School of Public Health, TUMS, Tehran, Iran
| | - A. Davoodabadi
- Department of Microbiology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - M. Hosseini
- Medical Statistics, Department of Epidemiology and Biostatics, School of Public Health, Tehran University of Medical Sciences. Tehran, Iran
| | - Z. Rajabi
- Food Microbiology Research Center, Tehran University of Medical Sciences (TUMS), Tehran, Iran
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13
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Gibtan A, Park K, Woo M, Shin JK, Lee DW, Sohn JH, Song M, Roh SW, Lee SJ, Lee HS. Diversity of Extremely Halophilic Archaeal and Bacterial Communities from Commercial Salts. Front Microbiol 2017; 8:799. [PMID: 28539917 PMCID: PMC5423978 DOI: 10.3389/fmicb.2017.00799] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 04/19/2017] [Indexed: 11/21/2022] Open
Abstract
Salting is one of the oldest food preservation techniques. However, salt is also the source of living halophilic microorganisms that may affect human health. In order to determine the microbial communities of commercial salts, an investigation were done using amplicon sequencing approach in four commercial salts: Ethiopian Afdera salt (EAS), Ethiopian rock salt (ERS), Korean Jangpan salt (KJS), and Korean Topan salt (KTS). Using domain-specific primers, a region of the 16S rRNA gene was amplified and sequenced using a Roche 454 instrument. The results indicated that these microbial communities contained 48.22–61.4% Bacteria, 37.72–51.26% Archaea, 0.51–0.86% Eukarya, and 0.005–0.009% unclassified reads. Among bacteria, the communities in these salts were dominated by the phyla Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes. Of the archaea, 91.58% belonged to the class Halobacteria, whereas the remaining 7.58, 0.83, and 0.01% were Nanoarchaea, Methanobacteria, and Thermococci, respectively. This comparison of microbial diversity in salts from two countries showed the presence of many archaeal and bacterial genera that occurred in salt samples from one country but not the other. The bacterial genera Enterobacter and Halovibrio were found only in Korean and Ethiopian salts, respectively. This study indicated the occurrence and diversity of halophilic bacteria and archaea in commercial salts that could be important in the gastrointestinal tract after ingestion.
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Affiliation(s)
- Ashagrie Gibtan
- Major in Food Biotechnology, Division of Bioindustry, Silla UniversityBusan, South Korea
| | - Kyounghee Park
- Major in Food Biotechnology, Division of Bioindustry, Silla UniversityBusan, South Korea
| | - Mingyeong Woo
- Major in Food Biotechnology, Division of Bioindustry, Silla UniversityBusan, South Korea
| | - Jung-Kue Shin
- Department of Korean Cusine, Jeonju UniversityJeonju, South Korea
| | - Dong-Woo Lee
- School of Applied Biosciences, Kyungpook National UniversityDaegu, South Korea
| | - Jae Hak Sohn
- Major in Food Biotechnology, Division of Bioindustry, Silla UniversityBusan, South Korea.,Research Center for Extremophiles and Marine Microbiology, Silla UniversityBusan, South Korea
| | - Minjung Song
- Major in Food Biotechnology, Division of Bioindustry, Silla UniversityBusan, South Korea
| | - Seong Woon Roh
- Microbiology and Functionality Research Group, World Institute of KimchiGwangju, South Korea
| | - Sang-Jae Lee
- Major in Food Biotechnology, Division of Bioindustry, Silla UniversityBusan, South Korea.,Research Center for Extremophiles and Marine Microbiology, Silla UniversityBusan, South Korea
| | - Han-Seung Lee
- Major in Food Biotechnology, Division of Bioindustry, Silla UniversityBusan, South Korea.,Research Center for Extremophiles and Marine Microbiology, Silla UniversityBusan, South Korea
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14
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Exploring flavour-producing core microbiota in multispecies solid-state fermentation of traditional Chinese vinegar. Sci Rep 2016; 6:26818. [PMID: 27241188 PMCID: PMC4886211 DOI: 10.1038/srep26818] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/18/2016] [Indexed: 11/09/2022] Open
Abstract
Multispecies solid-state fermentation (MSSF), a natural fermentation process driven by reproducible microbiota, is an important technique to produce traditional fermented foods. Flavours, skeleton of fermented foods, was mostly produced by microbiota in food ecosystem. However, the association between microbiota and flavours and flavour-producing core microbiota are still poorly understood. Here, acetic acid fermentation (AAF) of Zhenjiang aromatic vinegar was taken as a typical case of MSSF. The structural and functional dynamics of microbiota during AAF process was determined by metagenomics and favour analyses. The dominant bacteria and fungi were identified as Acetobacter, Lactobacillus, Aspergillus, and Alternaria, respectively. Total 88 flavours including 2 sugars, 9 organic acids, 18 amino acids, and 59 volatile flavours were detected during AAF process. O2PLS-based correlation analysis between microbiota succession and flavours dynamics showed bacteria made more contribution to flavour formation than fungi. Seven genera including Acetobacter, Lactobacillus, Enhydrobacter, Lactococcus, Gluconacetobacer, Bacillus and Staphylococcus were determined as functional core microbiota for production of flavours in Zhenjiang aromatic vinegar, based on their dominance and functionality in microbial community. This study provides a perspective for bridging the gap between the phenotype and genotype of ecological system, and advances our understanding of MSSF mechanisms in Zhenjiang aromatic vinegar.
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Ripari V, Gänzle MG, Berardi E. Evolution of sourdough microbiota in spontaneous sourdoughs started with different plant materials. Int J Food Microbiol 2016; 232:35-42. [PMID: 27240218 DOI: 10.1016/j.ijfoodmicro.2016.05.025] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 04/24/2016] [Accepted: 05/20/2016] [Indexed: 11/26/2022]
Abstract
The preparation of sourdough in bakeries may include the use of inocula, e.g. fruits, flowers or rumen cuts to accelerate the process of selection of suitable microorganisms. The aim of this work was to investigate the effect of these inocula on the microbial evolution in sourdoughs. First, the microbiota of nineteen traditional sourdoughs that were initially started with diverse inocula was identified. Second, de novo sourdoughs were started with plant materials and the evolution of sourdough microbiota was investigated by culture, and by high-resolution melting curve quantitative PCR (HRM-qPCR). This study developed a new protocol for HRM-qPCR analysis of yeast microbiota in sourdough, and indicates this independent culture method suitable for characterization of yeasts. Microbiota of traditional sourdoughs were largely independent from the use of inoculum, however, Acetobacter spp. were identified only in sourdoughs started with apple flowers or apple pulp. In de novo sourdoughs started with plant materials, microbiota rapidly stabilized, and were characterized by Lactobacillus sanfranciscensis, Lactobacillus plantarum, Lactobacillus graminis, or Lactobacillus rossiae, and Saccharomyces cerevisiae as dominant species. Competition experiments revealed that the ecological fitness of L. plantarum, L. graminis, and L. rossiae in wheat or rye malt sourdoughs was lower when compared to L. sanfranciscensis, demonstrating that their presence in de novo sourdoughs reflects dispersal limitation. In conclusion, establishment of microbiota in de novo sourdoughs is dispersal limited. This study provides scientific support for the artisanal practice to inoculate de novo sourdoughs with flowers, berries, or related plant material.
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Affiliation(s)
- Valery Ripari
- Università Politecnica delle Marche, Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Ancona 62010, Italy; University of Alberta, Dept. of Agricultural, Food and Nutritional Science, Edmonton, AB T6G 2P5, Canada
| | - Michael G Gänzle
- University of Alberta, Dept. of Agricultural, Food and Nutritional Science, Edmonton, AB T6G 2P5, Canada.
| | - Enrico Berardi
- Università Politecnica delle Marche, Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Ancona 62010, Italy
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Tamang JP, Watanabe K, Holzapfel WH. Review: Diversity of Microorganisms in Global Fermented Foods and Beverages. Front Microbiol 2016; 7:377. [PMID: 27047484 PMCID: PMC4805592 DOI: 10.3389/fmicb.2016.00377] [Citation(s) in RCA: 332] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 03/08/2016] [Indexed: 01/03/2023] Open
Abstract
Culturalable and non-culturable microorganisms naturally ferment majority of global fermented foods and beverages. Traditional food fermentation represents an extremely valuable cultural heritage in most regions, and harbors a huge genetic potential of valuable but hitherto undiscovered strains. Holistic approaches for identification and complete profiling of both culturalable and non-culturable microorganisms in global fermented foods are of interest to food microbiologists. The application of culture-independent technique has thrown new light on the diversity of a number of hitherto unknown and non-cultural microorganisms in naturally fermented foods. Functional bacterial groups ("phylotypes") may be reflected by their mRNA expression in a particular substrate and not by mere DNA-level detection. An attempt has been made to review the microbiology of some fermented foods and alcoholic beverages of the world.
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Affiliation(s)
- Jyoti P. Tamang
- Department of Microbiology, School of Life Sciences, Sikkim UniversityTadong, India
| | - Koichi Watanabe
- Department of Animal Science and Technology, National Taiwan UniversityTaipei, Taiwan
| | - Wilhelm H. Holzapfel
- Advance Green Energy and Environment Institute, Handong Global UniversityPohang-si, South Korea
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Sattler T, Pikalo J, Wodak E, Schmoll F. Performance of ELISAs for detection of antibodies against porcine respiratory and reproductive syndrome virus in serum of pigs after PRRSV type 2 live vaccination and challenge. Porcine Health Manag 2015; 1:19. [PMID: 28405425 PMCID: PMC5382508 DOI: 10.1186/s40813-015-0015-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 12/05/2015] [Indexed: 11/10/2022] Open
Abstract
Background The aim of the study was to evaluate the performance of different newly developed and/or commercially available ELISAs for detection of PRRSV specific antibodies. Consequently, ten PRRSV negative piglets (group V) were vaccinated with a PRRSV type 2 vaccine. Blood samples were taken before as well as seven, 21 and 42 days after vaccination. At day 42 after vaccination (day 0 of the study) all of the piglets from group V and 10 non-prevaccinated PRRSV negative piglets (group N) were challenged with an HP PRRSV type 2 field strain. Blood samples were taken before and at days 3, 7, 10, 14, 21 and 28 after challenge. The success of vaccination and challenge was measured with RT qPCR. All serum samples were tested with six ELISAs for detection of PRRSV antibodies. Three of them are nucleocapsid-based, two use a glycoprotein extract and one uses inactivated whole virus as antigen. The specificity of the ELISAs was evaluated using 301 serum samples of piglets from PRRSV negative herds. Results The piglets from group V tested positive by RT qPCR at day 7 after vaccination and all piglets tested positive at day 3 after challenge. PRRSV specific antibodies were seen with all nucleocapsid-based ELISAs from day 21 after vaccination onwards in group V and from day 10 after challenge in group N. The glycoprotein-based ELISAs detected antibodies from day 42 after vaccination (group V) and day 21 after challenge (group N). The agreement according to kappa-coefficient was almost perfect. The glycoprotein-based ELISAs were able to distinguish PRRSV type 2, although with some cross reactions. Regarding specificity, the ELISAs performed differently (specificity between 97.4 % and 100 %), whereas most of the ELISAs with higher sensitivity had a slightly lower specificity. Conclusions All tested ELISA were able to detect PRRSV antibodies in the serum of pigs vaccinated with a PRRSV type 2 vaccine and after challenge with an HP PRRSV type 2 field strain. The onset on antibody detection differed, depending on the type of antigen used in the ELISAs. Most of the ELISAs with a higher sensitivity had a lower specificity.
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Affiliation(s)
- Tatjana Sattler
- Large Animal Clinic for Internal Medicine, University of Leipzig, An den Tierkliniken 11, 04103 Leipzig, Germany.,Institute for Veterinary Disease Control, AGES, Robert-Koch-Gasse 17, 2340 Mödling, Austria
| | - Jutta Pikalo
- Institute for Veterinary Disease Control, AGES, Robert-Koch-Gasse 17, 2340 Mödling, Austria
| | - Eveline Wodak
- Institute for Veterinary Disease Control, AGES, Robert-Koch-Gasse 17, 2340 Mödling, Austria
| | - Friedrich Schmoll
- Institute for Veterinary Disease Control, AGES, Robert-Koch-Gasse 17, 2340 Mödling, Austria
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18
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Wu ZF, Sun L, Zhang X, Shen XQ, Weng PF. Quantitative analysis of predominant yeasts and volatile compounds in the process of pickled wax gourd. CYTA - JOURNAL OF FOOD 2015. [DOI: 10.1080/19476337.2015.1052018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Kyung KH, Medina Pradas E, Kim SG, Lee YJ, Kim KH, Choi JJ, Cho JH, Chung CH, Barrangou R, Breidt F. Microbial Ecology of Watery Kimchi. J Food Sci 2015; 80:M1031-8. [DOI: 10.1111/1750-3841.12848] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 02/17/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Kyu Hang Kyung
- Dept. of Food Science; Sejong Univ; 98 Gunja-dong Gwangjin-gu Seoul 143-747 South Korea
| | - Eduardo Medina Pradas
- Inst. de la Grasa (CSIC); Av. Padre Garcia Tejero 4; 41012 Seville Spain
- Dept. of Food, Bioprocessing and Nutrition Sciences; 400 Dan Allen Drive, North Carolina State Univ; Raleigh NC 27695-7624 U.S.A
| | - Song Gun Kim
- Microbial Resource Center/KCTC; Korea Research Inst. of Bioscience and Biotechnology; Daejeon 305-806 Republic of Korea
| | - Yong Jae Lee
- Microbial Resource Center/KCTC; Korea Research Inst. of Bioscience and Biotechnology; Daejeon 305-806 Republic of Korea
| | - Kyong Ho Kim
- Dept. of Microbiology; Pukyong Natl. Univ; Pusan 608-737 South Korea
| | - Jin Joo Choi
- Dept. of Culinary Science and Food Service Management; Sejong Univ; 98 Gunja-dong Gwangjin-gu Seoul 143-747 South Korea
| | - Joo Hyong Cho
- Dept. of Culinary Science and Food Service Management; Sejong Univ; 98 Gunja-dong Gwangjin-gu Seoul 143-747 South Korea
| | - Chang Ho Chung
- Dept. of Culinary Science and Food Service Management; Sejong Univ; 98 Gunja-dong Gwangjin-gu Seoul 143-747 South Korea
| | - Rodolphe Barrangou
- Dept. of Food, Bioprocessing and Nutrition Sciences; 400 Dan Allen Drive, North Carolina State Univ; Raleigh NC 27695-7624 U.S.A
| | - Frederick Breidt
- USDA-ARS; SAA Food Science Research Unit; 322 Schaub Hall, Box 7624, North Carolina State Univ; Raleigh NC 27695-7624 U.S.A
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20
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Kim DH, Chon JW, Kim HS, Yim JH, Kim H, Seo KH. Rapid detection of Lactobacillus kefiranofaciens in kefir grain and kefir milk using newly developed real-time PCR. J Food Prot 2015; 78:855-8. [PMID: 25836417 DOI: 10.4315/0362-028x.jfp-14-329] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Lactobacillus kefiranofaciens is an indicator microorganism for kefir and a key factor in kefir grain formation and kefiran production. We designed a novel real-time PCR primer and probe set, LKF_KU504, for the rapid detection of L. kefiranofaciens. In inclusivity and exclusivity tests, only 14 L. kefiranofaciens strains were positive among 61 microorganisms, indicating 100 % sensitivity and specificity. The LKF_KU504 set also differentiated kefir milk from 30 commercial nonkefir yogurts. The levels of L. kefiranofaciens in kefir grain and kefir milk were significantly different, indicating L. kefiranofaciens was more concentrated in kefir grain than in kefir milk.
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Affiliation(s)
- Dong-Hyeon Kim
- Center for Food Safety, College of Veterinary Medicine, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Korea
| | - Jung-Whan Chon
- Center for Food Safety, College of Veterinary Medicine, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Korea
| | - Hong-Seok Kim
- Center for Food Safety, College of Veterinary Medicine, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Korea
| | - Jin-Hyeok Yim
- Center for Food Safety, College of Veterinary Medicine, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Korea
| | - Hyunsook Kim
- Center for Food Safety, College of Veterinary Medicine, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Korea
| | - Kun-Ho Seo
- Center for Food Safety, College of Veterinary Medicine, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Korea.
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21
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Ahn GH, Moon JS, Shin SY, Min WK, Han NS, Seo JH. A competitive quantitative polymerase chain reaction method for characterizing the population dynamics during kimchi fermentation. J Ind Microbiol Biotechnol 2014; 42:49-55. [PMID: 25475752 DOI: 10.1007/s10295-014-1553-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 11/19/2014] [Indexed: 01/05/2023]
Abstract
The aim of this study was to develop a competitive quantitative-PCR (CQ-PCR) method for rapid analysis of the population dynamics of lactic acid bacteria (LAB) in kimchi. For this, whole chromosome sequences of Leuconostoc mesenteroides, Lactobacillus plantarum, and Lb. brevis were compared and species-specific PCR primers targeting dextransucrase, 16S rRNA, and surface layer protein D (SlpD) genes, respectively, were constructed. The tested strains were quantified both in medium and kimchi by CQ-PCR and the results were compared with the data obtained using a conventional plate-counting method. As a result, the three species were successfully detected and quantified by the indicated primer sets. Our results show that the CQ-PCR method targeting species-specific genes is suitable for rapid estimation of LAB population to be used in the food fermentation industry.
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Affiliation(s)
- Gee-Hyun Ahn
- Department of Agricultural Biotechnology and Center for Food and Bioconvergence, Seoul National University, Seoul, 151-921, South Korea
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22
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Kim DH, Chon JW, Kim H, Kim HS, Choi D, Hwang DG, Seo KH. Detection and Enumeration of Lactic Acid Bacteria, Acetic Acid Bacteria and Yeast in Kefir Grain and Milk Using Quantitative Real-Time PCR. J Food Saf 2014. [DOI: 10.1111/jfs.12153] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Dong-Hyeon Kim
- KU Center for Food Safety; College of Veterinary Medicine; Konkuk University; Hwayang-dong, Gwangjin-gu Seoul 143-701 Korea
| | - Jung-Whan Chon
- KU Center for Food Safety; College of Veterinary Medicine; Konkuk University; Hwayang-dong, Gwangjin-gu Seoul 143-701 Korea
| | - Hyunsook Kim
- KU Center for Food Safety; College of Veterinary Medicine; Konkuk University; Hwayang-dong, Gwangjin-gu Seoul 143-701 Korea
| | - Hong-Seok Kim
- KU Center for Food Safety; College of Veterinary Medicine; Konkuk University; Hwayang-dong, Gwangjin-gu Seoul 143-701 Korea
| | - Dasom Choi
- KU Center for Food Safety; College of Veterinary Medicine; Konkuk University; Hwayang-dong, Gwangjin-gu Seoul 143-701 Korea
| | - Dae-Geun Hwang
- KU Center for Food Safety; College of Veterinary Medicine; Konkuk University; Hwayang-dong, Gwangjin-gu Seoul 143-701 Korea
| | - Kun-Ho Seo
- KU Center for Food Safety; College of Veterinary Medicine; Konkuk University; Hwayang-dong, Gwangjin-gu Seoul 143-701 Korea
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23
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Lu M, Wang X, Sun G, Qin B, Xiao J, Yan S, Pan Y, Wang Y. Fine structure of Tibetan kefir grains and their yeast distribution, diversity, and shift. PLoS One 2014; 9:e101387. [PMID: 24977409 PMCID: PMC4076316 DOI: 10.1371/journal.pone.0101387] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 06/06/2014] [Indexed: 02/03/2023] Open
Abstract
Tibetan kefir grains (TKGs), a kind of natural starter for fermented milk in Tibet, China, host various microorganisms of lactic acid bacteria, yeasts, and occasionally acetic acid bacteria in a polysaccharide/protein matrix. In the present study, the fine structure of TKGs was studied to shed light on this unusual symbiosis with stereomicroscopy and thin sections. The results reveal that TKGs consist of numerous small grain units, which are characterized by a hollow globular structure with a diameter between 2.0 and 9.0 mm and a wall thickness of approximately 200 µm. A polyhedron-like net structure, formed mainly by the bacteria, was observed in the wall of the grain units, which has not been reported previously to our knowledge. Towards the inside of the grain unit, the polyhedron-like net structures became gradually larger in diameter and fewer in number. Such fine structures may play a crucial role in the stability of the grains. Subsequently, the distribution, diversity, and shift of yeasts in TKGs were investigated based on thin section, scanning electron microscopy, cloning and sequencing of D1/D2 of the 26S rRNA gene, real-time quantitative PCR, and in situ hybridization with specific fluorescence-labeled oligonucleotide probes. These show that (i) yeasts appear to localize on the outer surface of the grains and grow normally together to form colonies embedded in the bacterial community; (ii) the diversity of yeasts is relatively low on genus level with three dominant species – Saccharomyces cerevisiae, Kluyveromyces marxianus, and Yarrowia lipolytica; (iii) S. cerevisiae is the stable predominant yeast species, while the composition of Kluyveromyces and Yarrowia are subject to change over time. Our results indicate that TKGs are relatively stable in structure, and culture conditions to some extent shape the microbial community and interaction in kefir grains. These findings pave the way for further study of the specific symbiotic associations between S. cerevisiae and Lactobacillus bacteria in TKGs.
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Affiliation(s)
- Man Lu
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Xingxing Wang
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Guowei Sun
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Bing Qin
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jinzhou Xiao
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Shuling Yan
- Institute of Biochemistry and Molecular Cell Biology, University of Goettingen, Goettingen, Germany
| | - Yingjie Pan
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yongjie Wang
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
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A systematic strain selection approach for halotolerant and halophilic bioprocess development: a review. Extremophiles 2014; 18:629-39. [DOI: 10.1007/s00792-014-0659-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 05/18/2014] [Indexed: 10/25/2022]
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Park EJ, Chun J, Cha CJ, Park WS, Jeon CO, Bae JW. Bacterial community analysis during fermentation of ten representative kinds of kimchi with barcoded pyrosequencing. Food Microbiol 2012; 30:197-204. [DOI: 10.1016/j.fm.2011.10.011] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 10/06/2011] [Accepted: 10/07/2011] [Indexed: 12/23/2022]
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Yu J, Gao W, Qing M, Sun Z, Wang W, Liu W, Pan L, Sun T, Wang H, Bai N, Zhang H. Identification and characterization of lactic acid bacteria isolated from traditional pickles in Sichuan, China. J GEN APPL MICROBIOL 2012; 58:163-72. [DOI: 10.2323/jgam.58.163] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Jung JY, Lee SH, Lee HJ, Seo HY, Park WS, Jeon CO. Effects of Leuconostoc mesenteroides starter cultures on microbial communities and metabolites during kimchi fermentation. Int J Food Microbiol 2011; 153:378-87. [PMID: 22189023 DOI: 10.1016/j.ijfoodmicro.2011.11.030] [Citation(s) in RCA: 179] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 11/20/2011] [Accepted: 11/28/2011] [Indexed: 12/20/2022]
Abstract
Kimchi fermentation usually relies upon the growth of naturally-occurring various heterofermentative lactic acid bacteria (LAB). This sometimes makes it difficult to produce kimchi with uniform quality. The use of Leuconostoc mesenteroides as a starter has been considered to produce commercial fermented kimchi with uniform and good quality in Korea. In this study, a combination of a barcoded pyrosequencing strategy and a (1)H NMR technique was used to investigate the effects of Leu. mesenteroides strain B1 as a starter culture for kimchi fermentation. Baechu (Chinese cabbage) and Chonggak (radish) kimchi with and without Leu. mesenteroides inoculation were prepared, respectively and their characteristics that included pH, cell number, bacterial community, and metabolites were monitored periodically for 40 days. Barcoded pyrosequencing analysis showed that the numbers of bacterial operational taxonomic units (OTU) in starter kimchi decreased more quickly than that in non-starter kimchi. Members of the genera Leuconostoc, Lactobacillus, and Weissella were dominant LAB regardless of the kimchi type or starter inoculation. Among the three genera, Leuconostoc was the most abundant, followed by Lactobacillus and Weissella. The use of Leu. mesenteroides as a starter increased the Leuconostoc proportions and decreased the Lactobacillus proportions in both type of kimchi during kimchi fermentation. However, interestingly, the use of the kimchi starter more highly maintained the Weissella proportions of starter kimchi compared to that in the non-starter kimchi until fermentation was complete. Metabolite analysis using the (1)H NMR technique showed that both Baechu and Chonggak kimchi with the starter culture began to consume free sugars earlier and produced a little greater amounts of lactic and acetic acids and mannitol. Metabolite analysis demonstrated that kimchi fermentation using Leu. mesenteroides as a starter was completed earlier with more production of kimchi metabolites compared to that not using a starter, which coincided with the decreases in pH and the increases in bacterial cell number. The PCA strategy using all kimchi components including carbohydrates, amino acids, organic acids, and others also showed that starter kimchi fermented faster with more organic acid and mannitol production. In conclusion, the combination of the barcoded pyrosequencing strategy and the (1)H NMR technique was used to effectively monitor microbial succession and metabolite production and allowed for a greater understanding of the relationships between the microbial community and metabolite production in kimchi fermentation.
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Affiliation(s)
- Ji Young Jung
- School of Biological Sciences, Chung-Ang University, Seoul, 156-756, Republic of Korea
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28
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Abstract
Kimchi, a traditional food in the Korean culture, is made from vegetables by fermentation. In this study, metagenomic approaches were used to monitor changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation process. Metagenomic DNA was extracted from kimchi samples obtained periodically and was sequenced using a 454 GS FLX Titanium system, which yielded a total of 701,556 reads, with an average read length of 438 bp. Phylogenetic analysis based on 16S rRNA genes from the metagenome indicated that the kimchi microbiome was dominated by members of three genera: Leuconostoc, Lactobacillus, and Weissella. Assignment of metagenomic sequences to SEED categories of the Metagenome Rapid Annotation using Subsystem Technology (MG-RAST) server revealed a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates, which was supported by the detection of mannitol, lactate, acetate, and ethanol as fermentation products. When the metagenomic reads were mapped onto the database of completed genomes, the Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 and Lactobacillus sakei subsp. sakei 23K genomes were highly represented. These same two genera were confirmed to be important in kimchi fermentation when the majority of kimchi metagenomic sequences showed very high identity to Leuconostoc mesenteroides and Lactobacillus genes. Besides microbial genome sequences, a surprisingly large number of phage DNA sequences were identified from the cellular fractions, possibly indicating that a high proportion of cells were infected by bacteriophages during fermentation. Overall, these results provide insights into the kimchi microbial community and also shed light on fermentation processes carried out broadly by complex microbial communities.
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