1
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Martins WF, Severo DDS, Longhi DA, de Aragão GMF. Comparison of SYBR® Green qPCR assay and plate count method to describe growth of Weissella viridescens and Leuconostoc mesenteroides in pure and mixed cultivation. Food Microbiol 2024; 119:104452. [PMID: 38225053 DOI: 10.1016/j.fm.2023.104452] [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: 06/15/2023] [Revised: 11/28/2023] [Accepted: 12/18/2023] [Indexed: 01/17/2024]
Abstract
The current study was conducted to statistically compare the SYBR® Green quantitative polymerase chain reaction (qPCR) assay and the conventional plate counting (PC) method to construct growth curves of a cocktail of Weissella viridescens in pure culture under different isothermal storage conditions (4, 8, 14, and 30 °C) and in mixed culture with Leuconostoc mesenteroides at 8 °C. The efficiency and specificity of the qPCR standard curves were confirmed, and both methods were adequate to quantify the growth kinetics of W. viridescens at all isothermal temperatures, demonstrating a good correlation and agreement. The efficiencies of the standard curves varied between 98% and 102%. The SYBR® Green qPCR assay was also able to differentiate the growth curves of W. viridescens and L. mesenteroides in the mixed culture at 8 °C. Additionally, the SYBR® Green qPCR method was considered a faster and more sensitive alternative to construct growth curves under different isothermal conditions and differentiate morphologically similar lactic acid bacteria. Overall, the results suggest that the SYBR® Green qPCR method is a reliable and efficient tool to study microbial growth kinetics in pure and mixed cultures.
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Affiliation(s)
- Wiaslan Figueiredo Martins
- Department of Food Technology, Goiano Federal Institute of Education, Science, and Technology, IF Goiano/Morrinhos Campus, Zip Code 75650-000, Morrinhos, GO, Brazil; Chemical and Food Engineering Department, Federal University of Santa Catarina, EQA/UFSC, Zip Code 88040-900, Florianopolis, SC, Brazil.
| | - Danielle de Sousa Severo
- Chemical and Food Engineering Department, Federal University of Santa Catarina, EQA/UFSC, Zip Code 88040-900, Florianopolis, SC, Brazil
| | - Daniel Angelo Longhi
- LaBeM - Laboratory of Bioactives and Microbiology, School of Food Engineering, Federal University of Paraná, UFPR/Jandaia do Sul Campus, Zip Code 86900-000, Jandaia do Sul, PR, Brazil
| | - Gláucia Maria Falcão de Aragão
- Chemical and Food Engineering Department, Federal University of Santa Catarina, EQA/UFSC, Zip Code 88040-900, Florianopolis, SC, Brazil
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2
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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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3
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Kim E, Yang SM, Choi CH, Shin MK, Kim HY. Droplet digital PCR method for the absolute quantitative detection and monitoring of Lacticaseibacillus casei. Food Microbiol 2023; 113:104265. [PMID: 37098421 DOI: 10.1016/j.fm.2023.104265] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/12/2023]
Abstract
Droplet digital polymerase chain reaction (ddPCR) is an emerging molecular detection assay that provides an absolute quantification of targets. Despite its emerging applications in the detection of food microorganisms, there are limited reports of its use for the monitoring of microorganisms utilized as starters in the dairy industry. This study investigated the applicability of ddPCR as a detection platform for Lacticaseibacillus casei, a probiotic found in fermented foods and exerts beneficial effects on human health. In addition, this study compared the performance of ddPCR with that of real-time PCR. The ddPCR targeting the haloacid dehalogenase-like hydrolase (LBCZ_1793) exhibited high specificity against 102 nontarget bacteria, including Lacticaseibacillus species that is very closely related to L. casei. The ddPCR exhibited high linearity and efficiency within the quantitation range (105-100 CFU/ml), with the limit of detection being 100 CFU/ml. The ddPCR also demonstrated a higher sensitivity than real-time PCR in detecting low bacterial concentration in spiked milk samples. Furthermore, it provided an accurate absolute quantification of the concentration of L. casei, without the need for standard calibration curves. This study demonstrated that ddPCR is a useful method for monitoring starter cultures in dairy fermentations and detecting L. casei in foods.
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4
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Kim E, Lee GY, Yang SM, Kim HY. Rapid and accurate on-site identification of Lactobacillus delbrueckii subspecies in dairy products using direct polymerase chain reaction with microfluidic chip. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
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5
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Rapid identification and absolute quantitation of zero tolerance-Salmonella enterica subsp. enterica serovar Thompson using droplet digital polymerase chain reaction. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2022.114333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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6
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Yao Z, Zhu Y, Wu Q, Xu Y. Challenges and perspectives of quantitative microbiome profiling in food fermentations. Crit Rev Food Sci Nutr 2022; 64:4995-5015. [PMID: 36412251 DOI: 10.1080/10408398.2022.2147899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Spontaneously fermented foods are consumed and appreciated for thousands of years although they are usually produced with fluctuated productivity and quality, potentially threatening both food safety and food security. To guarantee consistent fermentation productivity and quality, it is essential to control the complex microbiota, the most crucial factor in food fermentations. The prerequisite for the control is to comprehensively understand the structure and function of the microbiota. How to quantify the actual microbiota is of paramount importance. Among various microbial quantitative methods evolved, quantitative microbiome profiling, namely to quantify all microbial taxa by absolute abundance, is the best method to understand the complex microbiota, although it is still at its pioneering stage for food fermentations. Here, we provide an overview of microbial quantitative methods, including the development from conventional methods to the advanced quantitative microbiome profiling, and the application examples of these methods. Moreover, we address potential challenges and perspectives of quantitative microbiome profiling methods, as well as future research needs for the ultimate goal of rational and optimal control of microbiota in spontaneous food fermentations. Our review can serve as reference for the traditional food fermentation sector for stable fermentation productivity, quality and safety.
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Affiliation(s)
- Zhihao Yao
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education; State Key Laboratory of Food Science and Technology; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yang Zhu
- Bioprocess Engineering, Wageningen University and Research, Wageningen, The Netherlands
| | - Qun Wu
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education; State Key Laboratory of Food Science and Technology; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education; State Key Laboratory of Food Science and Technology; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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7
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Kim E, Yang SM, Kim IS, Lee SY, Kim HY. Identification of Leuconostoc species based on novel marker genes identified using real-time PCR via computational pangenome analysis. Front Microbiol 2022; 13:1014872. [PMID: 36212836 PMCID: PMC9537375 DOI: 10.3389/fmicb.2022.1014872] [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: 08/09/2022] [Accepted: 09/06/2022] [Indexed: 11/29/2022] Open
Abstract
Leuconostoc species are important microorganisms in food fermentation but also cause food spoilage. Although these species are commercially important, their taxonomy is still based on inaccurate identification methods. Here, we used computational pangenome analysis to develop a real-time PCR-based method for identifying and differentiating the 12 major Leuconostoc species found in food. Analysis of pan and core-genome phylogenies showed clustering of strains into 12 distinct groups according to the species. Pangenome analysis of 130 Leuconostoc genomes from these 12 species enabled the identification of each species-specific gene. In silico testing of the species-specific genes against 143 publicly available Leuconostoc and 100 other lactic acid bacterial genomes showed that all the assays had 100% inclusivity/exclusivity. We also verified the specificity for each primer pair targeting each specific gene using 23 target and 124 non-target strains and found high specificity (100%). The sensitivity of the real-time PCR method was 102 colony forming units (CFUs)/ml in pure culture and spiked food samples. All standard curves showed good linear correlations, with an R2 value of ≥0.996, suggesting that screened targets have good specificity and strong anti-interference ability from food sample matrices and non-target strains. The real-time PCR method can be potentially used to determine the taxonomic status and identify the Leuconostoc species in foods.
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Kim E, Kim DS, Yang SM, Kim HY. The accurate identification and quantification of six Enterococcus species using quantitative polymerase chain reaction based novel DNA markers. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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9
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da Cunha ET, Pedrolo AM, Bueno JCF, Pereira TP, Soares CRFS, Arisi ACM. Inoculation of Herbaspirillum seropedicae strain SmR1 increases biomass in maize roots DKB 390 variety in the early stages of plant development. Arch Microbiol 2022; 204:373. [PMID: 35672591 DOI: 10.1007/s00203-022-02986-8] [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: 12/10/2021] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 11/26/2022]
Abstract
Herbaspirillum seropedicae is a plant growth-promoting bacteria isolated from diverse plant species. In this work, the main objective was to investigate the efficiency of H. seropedicae strain SmR1 in colonizing and increasing maize growth (DKB 390 variety) in the early stages of development under greenhouse conditions. Inoculation with H. seropedicae resulted in 19.43 % (regarding High and Low N controls) and 10.51% (regarding Low N control) in mean of increase of root biomass, for 1st and 2nd greenhouse experiments, respectively, mainly in the initial stages of plant development, at 21 days after emergence (DAE). Quantification of H. seropedicae in roots and leaves was performed by quantitative PCR. H. seropedicae was detected only in maize inoculated roots by qPCR, and a slight decrease in DNA copy number g-1 of fresh root weight was observed from 7 to 21 DAE, suggesting that there was initial effective colonization on maize plants. H. seropedicae strain SmR1 efficiently increased maize root biomass exhibiting its potential to be used as inoculant in agricultures systems.
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Affiliation(s)
- Elisandra Triches da Cunha
- Food Science and Technology Department, CAL CCA UFSC, Federal University of Santa Catarina, Rod Admar Gonzaga, 1346, Florianópolis, SC, 88034-001, Brazil
| | - Ana Marina Pedrolo
- Food Science and Technology Department, CAL CCA UFSC, Federal University of Santa Catarina, Rod Admar Gonzaga, 1346, Florianópolis, SC, 88034-001, Brazil
| | - Jessica Cavalheiro Ferreira Bueno
- Food Science and Technology Department, CAL CCA UFSC, Federal University of Santa Catarina, Rod Admar Gonzaga, 1346, Florianópolis, SC, 88034-001, Brazil
| | - Tomás Pelizzaro Pereira
- Food Science and Technology Department, CAL CCA UFSC, Federal University of Santa Catarina, Rod Admar Gonzaga, 1346, Florianópolis, SC, 88034-001, Brazil
- Public Policy Coordination Department, EPAGRI, Santa Catarina Agricultural Research and Rural Extension Company, Rio do Sul, SC, Brazil
| | - Cláudio Roberto Fônseca Sousa Soares
- Microbiology, Immunology and Parasitology Department, MIP CCB UFSC, Federal University of Santa Catarina, Av Prof Henrique da Silva Fontes, 2754, Florianópolis, SC, 88040-900, Brazil
| | - Ana Carolina Maisonnave Arisi
- Food Science and Technology Department, CAL CCA UFSC, Federal University of Santa Catarina, Rod Admar Gonzaga, 1346, Florianópolis, SC, 88034-001, Brazil.
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Kim E, Yang SM, Kim IS, Kim HY. Identification of novel molecular targets for Weissella species-specific real-time PCR based on pangenome analysis. Appl Microbiol Biotechnol 2022; 106:4157-4168. [PMID: 35672470 DOI: 10.1007/s00253-022-12003-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 01/24/2023]
Abstract
Some Weissella species are used in probiotic products because of their beneficial effects in humans, whereas some species are considered as opportunistic pathogens that cause infections in humans. Therefore, an accurate and rapid identification of Weissella species is essential to control pathogenic Weissella species or isolate new functional strains with probiotic effects from their habitat. The objective of our study was to extract novel molecular targets using pangenome analysis for the identification of major Weissella species present in food. With 50 genomes representing 11 Weissella species, novel molecular targets were mined based on their 100% presence in the respective strains of the target species and absence in the strains of non-target bacteria. Primers based on molecular targets showed positive results for the corresponding species, whereas 79 non-target strains showed negative results. Standard curves revealed good linearity in the range of 103-108 colony-forming units per reaction. Our method was successfully applied to 74 Weissella strains isolated from food samples to demonstrate that the molecular targets provided a viable alternative to the 16S rRNA sequence. Furthermore, it was possible to identify and quantify Weissella communities in fermented foods. These results demonstrate that our method can be used for effective and accurate screening for the presence of Weissella species in foods. KEY POINTS: • This is first study to mine novel targets for differentiating 11 Weissella species. • The novel targets showed higher resolution than the 16S rRNA gene sequence. • The PCR method effectively detected Weissella species with opposing properties.
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Affiliation(s)
- Eiseul Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Seung-Min Yang
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Ik-Seon Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea.
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11
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Choi CH, Kim E, Yang SM, Kim DS, Suh SM, Lee GY, Kim HY. Comparison of Real-Time PCR and Droplet Digital PCR for the Quantitative Detection of Lactiplantibacillus plantarum subsp. plantarum. Foods 2022; 11:foods11091331. [PMID: 35564054 PMCID: PMC9105557 DOI: 10.3390/foods11091331] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/26/2022] [Accepted: 04/30/2022] [Indexed: 12/04/2022] Open
Abstract
Droplet digital polymerase chain reaction (ddPCR) is one of the newest and most promising tools providing absolute quantification of target DNA molecules. Despite its emerging applications in microorganisms, few studies reported its use for detecting lactic acid bacteria. This study evaluated the applicability of a ddPCR assay targeting molecular genes obtained from in silico analysis for detecting Lactiplantibacillus plantarum subsp. plantarum, a bacterium mainly used as a starter or responsible for fermentation in food. The performance characteristics of a ddPCR were compared to those of a quantitative real-time PCR (qPCR). To compare the linearity and sensitivity of a qPCR and ddPCR, the calibration curve for a qPCR and the regression curve for a ddPCR were obtained using genomic DNA [102−108 colony-forming units (CFU)/mL] extracted from a pure culture and spiked food sample. Both the qPCR and ddPCR assays exhibited good linearity with a high coefficient of determination in the pure culture and spiked food sample (R2 ≥ 0.996). The ddPCR showed a 10-fold lower limit of detection, suggesting that a ddPCR is more sensitive than a qPCR. However, a ddPCR has limitations in the absolute quantitation of high bacterial concentrations (>106 CFU/mL). In conclusion, a ddPCR can be a reliable method for detecting and quantifying lactic acid bacteria in food.
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Affiliation(s)
| | | | | | | | | | | | - Hae-Yeong Kim
- Correspondence: ; Tel.: +82-31-201-2600; Fax: +82-31-204-8116
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12
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Ma P, Duan N, Ye H, Xia Y, Ding Z, Wang Z. Selection, truncation and fluorescence polarization based aptasensor for Weissella viridescens detection. Talanta 2022; 246:123499. [PMID: 35594734 DOI: 10.1016/j.talanta.2022.123499] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/27/2022] [Accepted: 04/19/2022] [Indexed: 01/09/2023]
Abstract
Weissella viridescens is a spoilage bacterium commonly found in low-temperature meat products. In this work, after fifteen rounds including three counter selection rounds of whole-cell systemic evolution of ligands by exponential enrichment (SELEX) in vitro, a novel aptamer L3 that can specifically recognize W. viridescens was obtained with a dissociation constant (Kd) value of 68.25 ± 5.32 nM. The sequence of aptamer L3 was optimized by truncation and a new aptamer sequence TL43 was obtained with a lower Kd value of 32.11 ± 3.01 nM. Finally, a simple and rapid fluorescence polarization (FP) platform was constructed to detect W. viridescens, in which FAM-labeled complementary sequence (FAM-cDNA) was employed to generate FP signal and streptavidin was used to amplify FP signal. In the presence of target bacteria, FP value decreased owning to the dissociation of FAM-cDNA from streptavidin/biotin-TL43/FAM-cDNA complex. Under optimal conditions, the concentration of W. viridescens and FP value displayed a good linear relationship with the detection range from 102 to 106 cfu/mL. Moreover, the designed detection system had a good recovery rate of 90.6%-107.7% in smoked ham samples compared with classical plate counting method, indicating the great potential of the selected and truncated aptamer in practical biosensing applications.
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Affiliation(s)
- Pengfei Ma
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology Jiangnan University, Wuxi, 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Nuo Duan
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology Jiangnan University, Wuxi, 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Hua Ye
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Yu Xia
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology Jiangnan University, Wuxi, 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Zhongyang Ding
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology Jiangnan University, Wuxi, 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China.
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Kim E, Kim D, Yang SM, Kim HY. Validation of probiotic species or subspecies identity in commercial probiotic products using high-resolution PCR method based on large-scale genomic analysis. Food Res Int 2022; 154:111011. [DOI: 10.1016/j.foodres.2022.111011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 02/10/2022] [Accepted: 02/12/2022] [Indexed: 12/18/2022]
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14
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Multiplex SYBR Green real-time PCR for Lactobacillus acidophilus group species targeting biomarker genes revealed by a pangenome approach. Microbiol Res 2022; 259:127013. [DOI: 10.1016/j.micres.2022.127013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 02/16/2022] [Accepted: 03/16/2022] [Indexed: 11/19/2022]
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15
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Effect of lysozyme and Chinese liquor on Staphylococcus aureus growth, microbiome, flavor profile, and the quality of dry fermented sausage. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.112059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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16
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Kim E, Yang SM, Kim HY. Differentiation of Lacticaseibacillus zeae Using Pan-Genome Analysis and Real-Time PCR Method Targeting a Unique Gene. Foods 2021; 10:foods10092112. [PMID: 34574222 PMCID: PMC8468013 DOI: 10.3390/foods10092112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 11/16/2022] Open
Abstract
Lacticaseibacillus zeae strains, isolated from raw milk and fermented dairy products, are closely related to the Lacticaseibacillus species that has beneficial probiotic properties. However, it is difficult to distinguish those using conventional methods. In this study, a unique gene was revealed to differentiate L. zeae from other strains of the Lacticaseibacillus species and other species by pan-genome analysis, and a real-time PCR method was developed to rapidly and accurately detect the unique gene. The genome analysis of 141 genomes yielded an 17,978 pan-genome. Among them, 18 accessory genes were specifically present in five genomes of L. zeae. The glycosyltransferase family 8 was identified as a unique gene present only in L. zeae and not in 136 other genomes. A primer designed from the unique gene accurately distinguished L. zeae in pure and mixed DNA and successfully constructed the criterion for the quantified standard curve in real-time PCR. The real-time PCR method was applied to 61 strains containing other Lacticaseibacillus species and distinguished L. zeae with 100% accuracy. Also, the real-time PCR method was proven to be superior to the 16S rRNA gene method in the identification of L. zeae.
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Affiliation(s)
| | | | - Hae-Yeong Kim
- Correspondence: ; Tel.: +82-31-201-2600; Fax: +82-31-204-8116
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17
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Real-time PCR method for qualitative and quantitative detection of Lactobacillus sakei group species targeting novel markers based on bioinformatics analysis. Int J Food Microbiol 2021; 355:109335. [PMID: 34343716 DOI: 10.1016/j.ijfoodmicro.2021.109335] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/06/2021] [Accepted: 07/17/2021] [Indexed: 11/21/2022]
Abstract
Latilactobacillus sakei group comprises four closely related species, making it difficult to accurately distinguish them with standard markers such as the 16S rRNA gene. The objective of our study was to mine novel markers for PCR detection and discrimination of L. sakei group species and L. sakei subspecies by comparative pan-genomic analysis. A total of 63 genome sequences of L. sakei group species consisted of 119,899 coding genes, yielding 5741 pan-genomes, 831 core-genomes, 3347 accessory-genomes, and 1563 unique-genomes. The accessory-genome was compared to extract unique candidate genes common only to genomes of the same species. The candidate genes were then aligned with the other bacterial genomes to select marker genes present in all genomes of a given species, but not in the genomes of other species. We identified the arginine/ornithine antiporter, putative cell surface protein precursor, sodium:solute symporter, PRD domain protein, PTS sugar transporter subunit IIC, and phosphoenolpyruvate-dependent sugar phosphotransferase system EIIC as marker genes for L. sakei, L. sakei subsp. sakei, L. sakei subsp. carnosus, L. curvatus, L. graminis, and L. fuchuensis, respectively. Primer pairs were designed for each marker and showed 100% specificity for 48 lactic acid bacterial reference strains. The PCR method developed in this study was used to evaluate 106 strains isolated from fermented foods to demonstrate that the marker genes provided a viable alternative to the 16S rRNA gene. We also applied the method to the monitoring of kimchi samples to quantify L. sakei group species or subspecies. Our PCR method based on novel markers can rapidly identify L. sakei group with high accuracy and high throughput.
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18
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Kim E, Kim HB, Yang SM, Kim D, Kim HY. Real-time PCR assay for detecting Lactobacillus plantarum group using species/subspecies-specific genes identified by comparative genomics. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110789] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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19
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Kim HB, Kim E, Yang SM, Lee S, Kim MJ, Kim HY. Development of Real-Time PCR Assay to Specifically Detect 22 Bifidobacterium Species and Subspecies Using Comparative Genomics. Front Microbiol 2020; 11:2087. [PMID: 33013760 PMCID: PMC7493681 DOI: 10.3389/fmicb.2020.02087] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/07/2020] [Indexed: 01/03/2023] Open
Abstract
Bifidobacterium species are used as probiotics to provide beneficial effects to humans. These effects are specific to some species or subspecies of Bifidobacterium. However, some Bifidobacterium species or subspecies are not distinguished because similarity of 16S rRNA and housekeeping gene sequences within Bifidobacterium species is very high. In this study, we developed a real-time polymerase chain reaction (PCR) assay to rapidly and accurately detect 22 Bifidobacterium species by selecting genetic markers using comparative genomic analysis. A total of 210 Bifidobacterium genome sequences were compared to select species- or subspecies-specific genetic markers. A phylogenetic tree based on pan-genomes generated clusters according to Bifidobacterium species or subspecies except that two strains were not grouped with their subspecies. Based on pan-genomes constructed, species- or subspecies-specific genetic markers were selected. The specificity of these markers was confirmed by aligning these genes against 210 genome sequences. Real-time PCR could detect 22 Bifidobacterium specifically. We constructed the criterion for quantification by standard curves. To further test the developed assay for commercial food products, we monitored 26 probiotic products and 7 dairy products. Real-time PCR results and labeling data were then compared. Most of these products (21/33, 63.6%) were consistent with their label claims. Some products labeled at species level only can be detected up to subspecies level through our developed assay.
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Affiliation(s)
- Hyeon-Be Kim
- Department of Food Science and Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin, South Korea
| | - Eiseul Kim
- Department of Food Science and Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin, South Korea
| | - Seung-Min Yang
- Department of Food Science and Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin, South Korea
| | - Shinyoung Lee
- Department of Food Science and Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin, South Korea
| | - Mi-Ju Kim
- Department of Food Science and Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin, South Korea
| | - Hae-Yeong Kim
- Department of Food Science and Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin, South Korea
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Hu Y, Zhang L, Liu Q, Wang Y, Chen Q, Kong B. The potential correlation between bacterial diversity and the characteristic volatile flavour of traditional dry sausages from Northeast China. Food Microbiol 2020; 91:103505. [PMID: 32539975 DOI: 10.1016/j.fm.2020.103505] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 10/24/2022]
Abstract
The objective of this study was to explore the correlation between bacterial communities and volatile compounds in traditional dry sausages from different regions in Northeast China. The bacterial community structure of dry sausages from five different regions as determined by high-throughput sequencing technology demonstrated that Firmicutes and Proteobacteria were the predominant phyla; Lactobacillus, Staphylococcus, Leuconostoc, Lactococcus and Weissella were the predominant genera; and Staphylococcus xylosus, Lactobacillus sakei, Weissella hellenica, Leuconostoc citreum, Lactococcus raffinolactis and Lactobacillus plantarum were the predominant species. Meanwhile, a total of 120 volatile compounds were detected in sausages from five different regions and mainly included alcohols, acids, aldehydes, ketones, esters and terpenes. Furthermore, the potential correlations between the core bacteria and major volatile compounds (64) were explored based on Spearman's correlation analysis. Positive correlations were found between W. hellenica, Lb. sakei, Lactococcus lactis, Lactobacillus alimentarius, Lb. plantarum and carboxylic acids and alcohols. Lc. lactis, Lb. alimentarius and Lb. plantarum were associated with the production of most esters, aldehydes and ketones. This study provides a deep insight into the relationship between the bacterial community and the volatile flavour profile of dry sausages, which may be helpful for the production of fermented dry sausages.
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Affiliation(s)
- Yingying Hu
- College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Lang Zhang
- College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Qian Liu
- College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Yan Wang
- Shimadzu (China) Co., LTD., Shenyang, Liaoning, 110000, China
| | - Qian Chen
- College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China.
| | - Baohua Kong
- College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China.
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21
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Azospirillum brasilense viable cells enumeration using propidium monoazide-quantitative PCR. Arch Microbiol 2020; 202:1653-1662. [DOI: 10.1007/s00203-020-01877-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 01/23/2020] [Accepted: 04/01/2020] [Indexed: 01/05/2023]
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22
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Kim E, Yang SM, Cho EJ, Kim HY. Novel real-time PCR assay for Lactobacillus casei group species using comparative genomics. Food Microbiol 2020; 90:103485. [PMID: 32336352 DOI: 10.1016/j.fm.2020.103485] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 12/20/2019] [Accepted: 03/11/2020] [Indexed: 12/14/2022]
Abstract
The Lactobacillus casei group, which includes the closely related species L. casei, L. paracasei, L. rhamnosus, and L. chiayiensis, has been under debate regarding its taxonomy because of the difficulty in distinguishing the species from each other. In the present study, we developed a novel real-time PCR assay for distinguishing the L. casei group species. The pan-genome, as determined by the genomes of 44 strains, comprised 6789 genes, comparative genomic analysis showed that L. casei group strains were classified by species. Based on these results, species-specific genes were identified, and primers were designed from those genes. Real-time PCR clearly distinguished each species of the L. casei group and specifically amplified only to the target species. The method was applied to 29 probiotic products, and the detected results and label claims were compared. Total 23 products were in accordance with the label claims, and the remaining products contained species different from those stated in the label claims. Our method can rapidly and accurately distinguish the L. casei group species in a single reaction. Hence, our assay can be applied to identify L. casei group species from food or environmental samples and to accurately determine the nomenclature of the species.
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Affiliation(s)
- Eiseul Kim
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
| | - Seung-Min Yang
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
| | - Eun-Ji Cho
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, South Korea.
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Martins WF, Longhi DA, de Aragão GMF, Melero B, Rovira J, Diez AM. A mathematical modeling approach to the quantification of lactic acid bacteria in vacuum-packaged samples of cooked meat: Combining the TaqMan-based quantitative PCR method with the plate-count method. Int J Food Microbiol 2019; 318:108466. [PMID: 31865245 DOI: 10.1016/j.ijfoodmicro.2019.108466] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 11/04/2019] [Accepted: 11/27/2019] [Indexed: 01/01/2023]
Abstract
The TaqMan-based quantitative Polymerase Chain Reaction (qPCR) method and the Plate Count (PC) method are both used in combination with primary and secondary mathematical modeling, to describe the growth curves of Leuconostoc mesenteroides and Weissella viridescens in vacuum-packaged meat products during storage under different isothermal conditions. Vacuum-Packaged Morcilla (VPM), a typical cooked blood sausage, is used as a representative meat product, with the aim of improving shelf-life prediction methods for those sorts of meat products. The standard curves constructed by qPCR showed good linearity between the cycle threshold (CT) and log10 CFU/g, demonstrating the high precision and the reproducible results of the qPCR method. The curves were used for the quantification of L. mesenteroides and W. viridescens in artificially inoculated VPM samples under isothermal storage (5, 8, 13 and 18 °C). Primally, both the qPCR and the PC methods were compared, and a linear regression analysis demonstrated a statistically significant linear correlation between the methods. Secondly, the Baranyi and Roberts model was fitted to the growth curve data to estimate the kinetic parameters of L. mesenteroides and W. viridescens under isothermal conditions, and secondary models were used to establish the dependence of the maximum specific growth rate on the temperature. The results proved that primary and secondary models were adequate for describing the growth curves of both methods in relation to both bacteria. In conclusion, the results of all the experiments proved that the qPCR method in combination with the PC method can be used to construct microbial growth kinetics and that primary and secondary mathematical modeling can be successfully applied to describe the growth of L. mesenteroides and W. viridescens in vacuum-packaged morcilla and, by extension, other cooked meat products with similar characteristics.
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Affiliation(s)
- Wiaslan Figueiredo Martins
- Federal University of Santa Catarina, Department of Chemical Engineering and Food Engineering, Center of Technology, Florianópolis, SC 88040-901, Brazil; Federal Institute of Education, Science and Technology of Goiano, Food Technology, Campus Morrinhos, Morrinhos, GO 75650-000, Brazil
| | - Daniel Angelo Longhi
- Federal University of Paraná, Food Engineering, Campus Jandaia do Sul, Jandaia do Sul, PR 86900-000, Brazil
| | - Gláucia Maria Falcão de Aragão
- Federal University of Santa Catarina, Department of Chemical Engineering and Food Engineering, Center of Technology, Florianópolis, SC 88040-901, Brazil
| | - Beatriz Melero
- University of Burgos, Department of Biotechnology and Food Science, Burgos 09001, Spain
| | - Jordi Rovira
- University of Burgos, Department of Biotechnology and Food Science, Burgos 09001, Spain
| | - Ana M Diez
- University of Burgos, Department of Biotechnology and Food Science, Burgos 09001, Spain.
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Piotrowska-Cyplik A, Myszka K, Czarny J, Ratajczak K, Kowalski R, Biegańska-Marecik R, Staninska-Pięta J, Nowak J, Cyplik P. Characterization of specific spoilage organisms (SSOs) in vacuum-packed ham by culture-plating techniques and MiSeq next-generation sequencing technologies. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:659-668. [PMID: 27144959 DOI: 10.1002/jsfa.7785] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 04/07/2016] [Accepted: 04/27/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND Knowledge regarding microaerophilic and anaerobic specific spoilage organisms (SSOs) is crucial for an appropriate evaluation of vacuum-packed ham. The objective of this study was to characterize the SSO community in vacuum-packed ham by a culture-dependent technique and MiSeq next-generation sequencing (NGS) platform. The relation between changes among the SSO group in the ham and changes in sensory characteristics of the product was also assessed. RESULTS In the study, conventional microbiological analyses were employed in order to establish the participation of several groups of microorganisms in the deterioration of vacuum-packed ham. The diversity of the SSO group in the product was further assessed with the use of MiSeq NGS technology. The bacteria identified in sliced cooked ham belonged mostly to four phyla, namely Actinobacteria, Proteobacteria, Firmicutes and Bacteroidetes. A temperature of 4 °C favoured the development of mesophilic and psychrophilic/psychrotrophic flora, mainly Lactobacillaceae, Enterobacteriaceae and Micrococcaceae families. A high ratio of Brochothrix thermosphacta species and new, cold-tolerant Clostridium spp. was also observed. The growth of these microorganisms facilitated changes in the pH value and organoleptic characteristics of the product. CONCLUSION This study confirms that the combination of culturing and MiSeq NGS technology improves the microbial evaluation of food. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Agnieszka Piotrowska-Cyplik
- Institute of Food Technology of Plant Origin, Poznań University of Life Sciences, Wojska Polskiego 31, PL-60-624, Poznań, Poland
| | - Kamila Myszka
- Department of Biotechnology and Food Microbiology, Poznań University of Life Sciences, Wojska Polskiego 48, PL-60-627, Poznań, Poland
| | - Jakub Czarny
- Institute of Forensic Genetics, Al. Mickiewicza 3/4, PL-85-071, Bydgoszcz, Poland
| | - Katarzyna Ratajczak
- Institute of Food Technology of Plant Origin, Poznań University of Life Sciences, Wojska Polskiego 31, PL-60-624, Poznań, Poland
| | - Ryszard Kowalski
- Institute of Meat Technology, Wojska Polskiego 31, PL-60-624, Poznań, Poland
| | - Róża Biegańska-Marecik
- Institute of Food Technology of Plant Origin, Poznań University of Life Sciences, Wojska Polskiego 31, PL-60-624, Poznań, Poland
| | - Justyna Staninska-Pięta
- Department of Biotechnology and Food Microbiology, Poznań University of Life Sciences, Wojska Polskiego 48, PL-60-627, Poznań, Poland
| | - Jacek Nowak
- Institute of Food Technology of Plant Origin, Poznań University of Life Sciences, Wojska Polskiego 31, PL-60-624, Poznań, Poland
| | - Paweł Cyplik
- Department of Biotechnology and Food Microbiology, Poznań University of Life Sciences, Wojska Polskiego 48, PL-60-627, Poznań, Poland
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Liang H, Zhang A, Wu Z, Liu C, Zhang W. Characterization of Microbial Community during the Fermentation of Chinese Homemade paocai, a Traditional Fermented Vegetable Food. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2016. [DOI: 10.3136/fstr.22.467] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Huipeng Liang
- College of Light Industry, Textile and Food Engineering, Sichuan University
| | - An Zhang
- College of Light Industry, Textile and Food Engineering, Sichuan University
| | - Zhengyun Wu
- College of Light Industry, Textile and Food Engineering, Sichuan University
| | - Chaolan Liu
- Chengdu University, Sichuan Industrial Institute of Antibiotics
| | - Wenxue Zhang
- College of Light Industry, Textile and Food Engineering, Sichuan University
- School of Liquor-Making Engineering, Sichuan University Jinjiang College
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