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Lahmamsi H, Ananou S, Lahlali R, Tahiri A. Lactic acid bacteria as an eco-friendly approach in plant production: Current state and prospects. Folia Microbiol (Praha) 2024; 69:465-489. [PMID: 38393576 DOI: 10.1007/s12223-024-01146-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/31/2024] [Indexed: 02/25/2024]
Abstract
Since the late nineteenth century, the agricultural sector has experienced a tremendous increase in chemical use in response to the growing population. Consequently, the intensive and indiscriminate use of these substances caused serious damage on several levels, including threatening human health, disrupting soil microbiota, affecting wildlife ecosystems, and causing groundwater pollution. As a solution, the application of microbial-based products presents an interesting and ecological restoration tool. The use of Plant Growth-Promoting Microbes (PGPM) affected positive production, by increasing its efficiency, reducing production costs, environmental pollution, and chemical use. Among these microbial communities, lactic acid bacteria (LAB) are considered an interesting candidate to be formulated and applied as effective microbes. Indeed, these bacteria are approved by the European Food Safety Authority (EFSA) and Food and Drug Administration (FDA) as Qualified Presumption of Safety statute and Generally Recognized as Safe for various applications. To do so, this review comes as a road map for future research, which addresses the different steps included in LAB formulation as biocontrol, bioremediation, or plant growth promoting agents from the isolation process to their field application passing by the different identification methods and their various uses. The plant application methods as well as challenges limiting their use in agriculture are also discussed.
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Affiliation(s)
- Haitam Lahmamsi
- Laboratoire de Biotechnologie Microbienne et Molécules Bioactives, Faculté des Sciences et Techniques, Université Sidi Mohamed Ben Abdellah, Route Immouzer BP 2202, Fez, Morocco
- Unité de Phytopathologie, Département de Protection des Plantes, Ecole Nationale d'Agriculture, Km10, Rt Haj Kaddour, BP S/40, 50001, Meknes, Morocco
| | - Samir Ananou
- Laboratoire de Biotechnologie Microbienne et Molécules Bioactives, Faculté des Sciences et Techniques, Université Sidi Mohamed Ben Abdellah, Route Immouzer BP 2202, Fez, Morocco
| | - Rachid Lahlali
- Unité de Phytopathologie, Département de Protection des Plantes, Ecole Nationale d'Agriculture, Km10, Rt Haj Kaddour, BP S/40, 50001, Meknes, Morocco.
| | - Abdessalem Tahiri
- Unité de Phytopathologie, Département de Protection des Plantes, Ecole Nationale d'Agriculture, Km10, Rt Haj Kaddour, BP S/40, 50001, Meknes, Morocco.
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2
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Muñoz R, Rivas BDL, Rodríguez H, Esteban-Torres M, Reverón I, Santamaría L, Landete JM, Plaza-Vinuesa L, Sánchez-Arroyo A, Jiménez N, Curiel JA. Food phenolics and Lactiplantibacillus plantarum. Int J Food Microbiol 2024; 412:110555. [PMID: 38199014 DOI: 10.1016/j.ijfoodmicro.2023.110555] [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: 11/30/2023] [Revised: 12/21/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024]
Abstract
Phenolic compounds are important constituents of plant food products. These compounds play a key role in food characteristics such as flavor, astringency and color. Lactic acid bacteria are naturally found in raw vegetables, being Lactiplantibacillus plantarum the most commonly used commercial starter for the fermentation of plant foods. Hence, the metabolism of phenolic compounds of L. plantarum has been a subject of study in recent decades. Such studies confirm that L. plantarum, in addition to presenting catalytic capacity to transform aromatic alcohols and phenolic glycosides, exhibits two main differentiated metabolic routes that allow the biotransformation of dietary hydroxybenzoic and hydroxycinnamic acid-derived compounds. These metabolic pathways lead to the production of new compounds with new biological and organoleptic properties. The described metabolic pathways involve the action of specialized esterases, decarboxylases and reductases that have been identified through genetic analysis and biochemically characterized. The purpose of this review is to provide a comprehensive and up-to-date summary of the current knowledge of the metabolism of food phenolics in L. plantarum.
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Affiliation(s)
- Rosario Muñoz
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain.
| | - Blanca de Las Rivas
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain
| | - Héctor Rodríguez
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain
| | - María Esteban-Torres
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain
| | - Inés Reverón
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain
| | - Laura Santamaría
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain
| | - José Maria Landete
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain
| | - Laura Plaza-Vinuesa
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain
| | - Ana Sánchez-Arroyo
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain
| | - Natalia Jiménez
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain
| | - José Antonio Curiel
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain.
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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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He Z, Chen K, Huang C, Xin X, Tan H, Jiang J, Wu X, Zhai J. Microbial metabolism and health risk assessment of kitchen waste odor VOCs. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:108946-108958. [PMID: 37759058 DOI: 10.1007/s11356-023-30053-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023]
Abstract
Kitchen waste (KW) generates odors comprising complex volatile organic compounds (VOCs). We used gas chromatography-mass spectrometry to analyze VOCs, and 16S gene sequencing was used to analyze the microbial community composition and microbial metabolic mechanism. The results showed that the major odor-causing VOCs were hydrogen sulfide, methanethiol, methyl sulfide, dimethyl disulfide, and ethyl acetate. As the temperature increased, the VOCs and microbial community composition became more complex, and the microbial community related to VOC production included Leuconostoc, Pediococcus, Acetobacter, and Weissella. Based on PICRUSt2 analysis, the possibility of typical VOC interconversion by microbial metabolism was low. It was more likely that precursor substances were catalyzed by enzymes to generate the corresponding VOCs. Attention should be given to trichloromethane and 1,2-dichloroethane, which may cause adverse health effects through long-term inhalation. The study results provide guidance for controlling VOCs from KW.
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Affiliation(s)
- Zijun He
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, China
- College of Environment and Ecology, Chongqing University, Chongqing, 400044, China
| | - Kejin Chen
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, China
- College of Environment and Ecology, Chongqing University, Chongqing, 400044, China
| | - Chuan Huang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, China.
- College of Environment and Ecology, Chongqing University, Chongqing, 400044, China.
| | - Xiaobu Xin
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, China
- College of Environment and Ecology, Chongqing University, Chongqing, 400044, China
| | - Hanyue Tan
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, China
- College of Environment and Ecology, Chongqing University, Chongqing, 400044, China
| | - Jing Jiang
- Ecological and Environment Monitoring Center of Chongqing, Chongqing, 400010, China
| | - Xiaoyan Wu
- Ecological and Environment Monitoring Center of Chongqing, Chongqing, 400010, China
| | - Jinru Zhai
- Ecological and Environment Monitoring Center of Chongqing, Chongqing, 400010, China
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Abdulsalam RA, Ijabadeniyi OA, Cason ED, Sabiu S. Characterization of Microbial Diversity of Two Tomato Cultivars through Targeted Next-Generation Sequencing 16S rRNA and ITS Techniques. Microorganisms 2023; 11:2337. [PMID: 37764180 PMCID: PMC10534366 DOI: 10.3390/microorganisms11092337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Even though the nutritional and economic values of Solanum lycopersicum (tomato) are substantially impacted by microbial spoilage, the available data on its microbial community, particularly during spoilage, are limited and have primarily been characterized using conventional culture-dependent methods. This study employed a targeted high-throughput next-generation sequencing method to longitudinally characterize the microbial diversity of two South African tomato cultivars (jam and round) at varied storage intervals (1, 6, and 12 days). Throughout the storage period, the bacterial communities of the two cultivars were more diverse than the fungal communities. The microbial diversity of both bacteria and fungi was greater and comparable between the cultivars on day 1, but becomes distinct as the storage period increases, with round tomatoes being more diverse than jam tomato, though, on day 12, jam tomato develops greater diversity than round tomato. Overall, the most abundant phyla (though Proteobacteria was most dominant) were Proteobacteria, Firmicutes, and Bacteriodota in the bacterial communities, while Ascomycota and Basidiomycota formed most fungal communities with Ascomycota being dominant. At the genus level, Pantoea and Klebsiella (bacteria), Hanseniaspora, Stemphylium, and Alternaria (fungi) were prevalent. Taken together, this study casts light on a broad microbial diversity profile thus, confirms the cultivars' diversity and abundance differences.
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Affiliation(s)
- Rukayat Abiola Abdulsalam
- Department of Biotechnology and Food Science, Durban University of Technology, Durban 4000, South Africa
| | | | - Errol D. Cason
- Department of Animal Science, University of the Free State, Bloemfontein 9300, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Durban University of Technology, Durban 4000, South Africa
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Ko HI, Jeong CH, Park SJ, Kim SR, Eun JB, Kim TW. Influence of Isolation Temperature on Isolating Diverse Lactic Acid Bacteria from Kimchi and Cultural Characteristics of Psychrotrophs. J Microbiol Biotechnol 2023; 33:1066-1075. [PMID: 37280779 PMCID: PMC10468671 DOI: 10.4014/jmb.2303.03047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 06/08/2023]
Abstract
Kimchi is a traditional Korean fermented vegetable that is stored and fermented at low temperatures. However, kimchi lactic acid bacteria (LAB) are typically isolated under mesophilic conditions, which may be inappropriate for isolating the diverse LAB. Therefore, this study investigated the suitable conditions for isolating various LAB from kimchi. Here, LAB were isolated from four kimchi samples using MRS, PES, and LBS media and varying isolation temperatures (30, 20, 10, and 5°C). Then, MRS was selected as the suitable medium for LAB isolation. A comparison of culture-dependent and culture-independent approaches indicated that 5°C was not a suitable isolation temperature. Thus, the number and diversity of LAB were determined at 30, 20, and 10°C using 12 additional kimchi samples to elucidate the effect of isolation temperature. With the exception of two samples, most samples did not substantially differ in LAB number. However, Leuconostoc gelidum, Leuconostoc gasicomitatum, Leuconostoc inhae, Dellaglioa algida, Companilactobacillus kimchiensis, Leuconostoc miyukkimchii, Leuconostoc holzapfelii, and Leuconostoc carnosum were isolated only at 10 and 20°C. The growth curves of these isolates, except Leu. holzapfelii and Leu. carnosum, showed poor growth at 30°C. This confirmed their psychrotrophic characteristics. In Weissella koreensis, which was isolated at all isolation temperatures, there was a difference in the fatty acid composition of membranes between strains that could grow well at 30°C and those that could not. These findings can contribute to the isolation of more diverse psychrotrophic strains that were not well isolated under mesophilic temperatures.
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Affiliation(s)
- Hye In Ko
- Technology Innovation Research Division, World Institute of Kimchi, Gwangju 61755, Republic of Korea
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Chang Hee Jeong
- Technology Innovation Research Division, World Institute of Kimchi, Gwangju 61755, Republic of Korea
- Honam National Institute of Biological Resources, Mokpo 587262, Republic of Korea
| | - Se-Jin Park
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - So-Rim Kim
- Technology Innovation Research Division, World Institute of Kimchi, Gwangju 61755, Republic of Korea
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jong-Bang Eun
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Tae-Woon Kim
- Technology Innovation Research Division, World Institute of Kimchi, Gwangju 61755, Republic of Korea
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Kim E, Yang SM, Jung DH, Kim HY. Differentiation between Weissella cibaria and Weissella confusa Using Machine-Learning-Combined MALDI-TOF MS. Int J Mol Sci 2023; 24:11009. [PMID: 37446188 DOI: 10.3390/ijms241311009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Although Weissella cibaria and W. confusa are essential food-fermenting bacteria, they are also opportunistic pathogens. Despite these species being commercially crucial, their taxonomy is still based on inaccurate identification methods. In this study, we present a novel approach for identifying two important Weissella species, W. cibaria and W. confusa, by combining matrix-assisted laser desorption/ionization and time-of-flight mass spectrometer (MALDI-TOF MS) data using machine-learning techniques. After on- and off-plate protein extraction, we observed that the BioTyper database misidentified or could not differentiate Weissella species. Although Weissella species exhibited very similar protein profiles, these species can be differentiated on the basis of the results of a statistical analysis. To classify W. cibaria, W. confusa, and non-target Weissella species, machine learning was used for 167 spectra, which led to the listing of potential species-specific mass-to-charge (m/z) loci. Machine-learning techniques including artificial neural networks, principal component analysis combined with the K-nearest neighbor, support vector machine (SVM), and random forest were used. The model that applied the Radial Basis Function kernel algorithm in SVM achieved classification accuracy of 1.0 for training and test sets. The combination of MALDI-TOF MS and machine learning can efficiently classify closely-related species, enabling accurate microbial identification.
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Affiliation(s)
- Eiseul Kim
- Institute of Life Sciences and Resources, Yongin 17104, Republic of Korea
- Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Seung-Min Yang
- Institute of Life Sciences and Resources, Yongin 17104, Republic of Korea
- Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Dae-Hyun Jung
- Institute of Life Sciences and Resources, Yongin 17104, Republic of Korea
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences and Resources, Yongin 17104, Republic of Korea
- Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
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Molecular Detection and Identification of Plant-Associated Lactiplantibacillus plantarum. Int J Mol Sci 2023; 24:ijms24054853. [PMID: 36902287 PMCID: PMC10003612 DOI: 10.3390/ijms24054853] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Lactiplantibacillus plantarum is a lactic acid bacterium often isolated from a wide variety of niches. Its ubiquity can be explained by a large, flexible genome that helps it adapt to different habitats. The consequence of this is great strain diversity, which may make their identification difficult. Accordingly, this review provides an overview of molecular techniques, both culture-dependent, and culture-independent, currently used to detect and identify L. plantarum. Some of the techniques described can also be applied to the analysis of other lactic acid bacteria.
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Zhong H, Wei S, Kang M, Sun Q, Xia Q, Wang Z, Han Z, Liu Y, Liu M, Liu S. Effects of different storage conditions on microbial community and quality changes of greater amberjack (Seriola dumerili) fillets. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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Lee W, Kim MH, Park J, Kim YJ, Kim E, Heo EJ, Kim SH, Kim G, Shin H, Kim SH, Kim HY. Seasonal Changes in the Microbial Communities on Lettuce ( Lactuca sativa L.) in Chungcheong-do, South Korea. J Microbiol Biotechnol 2023; 33:219-227. [PMID: 36524338 PMCID: PMC9998205 DOI: 10.4014/jmb.2210.10001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022]
Abstract
Lettuce is one of the most consumed vegetables worldwide. However, it has potential risks associated with pathogenic bacterial contamination because it is usually consumed raw. In this study, we investigated the changes in the bacterial community on lettuce (Lactuca sativa L.) in Chungcheong-do, South Korea, and the prevalence of foodborne pathogens on lettuce in different seasons using 16S rRNA gene-based sequencing. Our data revealed that the Shannon diversity index showed the same tendency in term of the number of OTUs, with the index being greatest for summer samples in comparison to other seasons. Moreover, the microbial communities were significantly different between the four seasons. The relative abundance of Actinobacteriota varied according to the season. Family Micrococcaceae was most dominant in all samples except summer, and Rhizobiaceae was predominant in the microbiome of the summer sample. At the genus level, the relative abundance of Bacillus was greatest in spring samples, whereas Pseudomonas was greatest in winter samples. Potential pathogens, such as Staphylococcus and Clostridium, were detected with low relative abundance in all lettuce samples. We also performed metagenome shotgun sequencing analysis on the selected summer and winter samples, which were expected to be contaminated with foodborne pathogens, to support 16S rRNA gene-based sequencing dataset. Moreover, we could detect seasonal biomarkers and microbial association networks of microbiota on lettuce samples. Our results suggest that seasonal characteristics of lettuce microbial communities, which include diverse potential pathogens, can be used as basic data for food safety management to predict and prevent future outbreaks.
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Affiliation(s)
- Woojung Lee
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Min-Hee Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Juyeon Park
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - You Jin Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Eiseul Kim
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Eun Jeong Heo
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Seung Hwan Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Gyungcheon Kim
- Department of Food Science and Biotechnology, and Carbohydrate Bioproduct Research Center, College of Life Science, Sejong University, Seoul 05006, Republic of Korea
| | - Hakdong Shin
- Department of Food Science and Biotechnology, and Carbohydrate Bioproduct Research Center, College of Life Science, Sejong University, Seoul 05006, Republic of Korea
| | - Soon Han Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
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Li L, Liu D, Li X, Zhang B, Li C, Xiao Z, Liu M, Fang F, Deng N, Wang J. The dynamic changes of microbial diversity and biogenic amines in different parts of bighead carp (Aristichthys nobilis) head during storage at -2℃. J Food Compost Anal 2023. [DOI: 10.1016/j.jfca.2023.105228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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12
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Kim E, Yang SM, Kim HY. Weissella and the two Janus faces of the genus. Appl Microbiol Biotechnol 2023; 107:1119-1127. [PMID: 36680587 DOI: 10.1007/s00253-023-12387-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/22/2023]
Abstract
The genus Weissella belongs to the lactic acid bacteria group. It occurs naturally in foods and is a component of the human microbiome. A few Weissella species are candidate probiotics due to their potential for survival under the harsh conditions present in the gastrointestinal tract of humans and animals. Various species have also shown potential for treating and preventing periodontal disease, skin pathologies, and atopic dermatitis; some are used as starters for the fermentation of foods due to their production of exopolysaccharides; and others are used as protective cultures due to their production of weissellicin, a bacteriocin. However, a few Weissella species are opportunistic pathogens, such as W. ceti, which is the etiological agent of weissellosis, a disease in rainbow trout. Additionally, most Weissella species are intrinsically vancomycin-resistant. Thus, the Weissella genus is important from both medical and industrial points of view, and the Janus faces of this genus should be considered in any expected biotechnological applications. In this review, we present an overview of the probiotic potential and pathogenic cases of the Weissella genus reported in the literature.
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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
| | - 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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Teixeira CG, da Silva Rodrigues R, Lucau-Danila A, Nero LA, de Carvalho AF, Drider D. Genome analyses of Weissella strains isolated from Campos das Vertentes, Minas Gerais, Brazil revealed new bacteriocins with a large spectrum of activity. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2023.102421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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14
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Boyaci Gunduz CP, Agirman B, Erten H. Identification of yeasts in fermented foods and beverages using MALDI-TOF MS. FEMS Yeast Res 2022; 22:6823700. [PMID: 36367538 DOI: 10.1093/femsyr/foac056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/21/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022] Open
Abstract
Yeasts are an important group of microorganisms and contribute to the fermentation of a broad range of foods and beverages spontaneously or as a starter culture. Rapid and reliable microbial species identification is essential to evaluate biodiversity in fermented foods and beverages. Nowadays, high-throughput omics technologies and bioinformatics tools produce large-scale molecular-level data in many fields. These omics technologies generate data at different expression levels and are used to identify microorganisms. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a powerful analytical technique in proteomic technology. It is a tool used to analyze the peptides or proteins of microorganisms for identification. MALDI-TOF MS has been used for the taxonomic identification of microorganisms as a fast, high-throughput, and cost-effective method. This review briefly discussed the application of MALDI-TOF MS in identifying yeasts in fermented foods and beverages.
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Affiliation(s)
- Cennet Pelin Boyaci Gunduz
- Department of Food Engineering, Faculty of Engineering, Cukurova University, TR-01330 Adana, Turkey.,Department of Food Engineering, Faculty of Engineering, Adana Alparslan Turkes Science and Technology University, Adana 01250, Turkey
| | - Bilal Agirman
- Department of Food Engineering, Faculty of Engineering, Cukurova University, TR-01330 Adana, Turkey
| | - Huseyin Erten
- Department of Food Engineering, Faculty of Engineering, Cukurova University, TR-01330 Adana, Turkey
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15
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Pinar-Méndez A, Galofré B, Blanch AR, García-Aljaro C. Culture and molecular methods as complementary tools for water quality management. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157789. [PMID: 35931155 DOI: 10.1016/j.scitotenv.2022.157789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/30/2022] [Accepted: 07/30/2022] [Indexed: 06/15/2023]
Abstract
Bacterial communities in a full-scale drinking water treatment plant (DWTP) were characterized using matrix-assisted laser desorption/ionization time of flight mass-spectrometry (MALDI-TOF MS) to identify HPC isolates and the obtained results were compared to 16S rRNA (V4) metabarcoding data acquired in a previous study. Sixty-three samples were collected at nine stages of the potabilization process: river water and groundwater intake, decantation, sand filtration, ozonization, carbon filtration, reverse osmosis, the mixing chamber and post-chlorination drinking water. In total, 1807 bacterial colonies were isolated, 32 % of which were successfully identified to at least the genus level by MALDI-TOF MS using our previously developed Drinking Water Library. Trends in diversity were similar by both approaches, but differences were observed in the detection of taxa, especially at lower hierarchy levels. High bacterial diversity was observed in river and groundwater, where Proteobacteria predominated. The diversity decreased significantly after the chlorination step, where Bacillus sp. (Firmicutes) and an unknown genus of Obscuribacteraceae (Cyanobacteria) were the most prevalent genera according to MALDI-TOF MS and metabarcoding, respectively. The two approaches gave similar results for the decantation, sand filtration and mixing chamber steps, where the most abundant taxon was Flavobacterium. The combined use of these culture-based and culture-independent methods to characterize microbial populations may help to better understand the role of bacteria in water treatment and quality, which will be of value for DWTP management.
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Affiliation(s)
- Anna Pinar-Méndez
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, Barcelona, Spain; Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), Barcelona, Spain.
| | - Belén Galofré
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, Barcelona, Spain
| | - Anicet R Blanch
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), Barcelona, Spain
| | - Cristina García-Aljaro
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), Barcelona, Spain.
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16
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Lv J, Ye Y, Zhong Y, Liu W, Chen M, Guo A, Lv J, Ma H. Microbial diversity and functional genes of red vinasse acid based on metagenome analysis. Front Microbiol 2022; 13:1025886. [PMID: 36312974 PMCID: PMC9611532 DOI: 10.3389/fmicb.2022.1025886] [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: 08/23/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Red vinasse acid has a distinct flavor and a vivid red color that are directly tied to the intricate metabolic activities of microorganisms that produce it. In this study, metagenomic technology was used to mine its functional genes and examine the microbial diversity of red vinasse acid. The findings revealed the identification of 2,609 species, 782 genera, and 63 phyla of microorganisms, and the dominant genus was Lactobacillus. Amino acid metabolism and carbohydrate metabolism were significant activities among the 16,093 and 49,652 genes that were annotated in the evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. In gluconeogenesis, red vinasse acid encodes 194 genes controlling the transporter protein systems of different sugars and has key enzyme genes that catalyze the conversion of intracellular sugars into glycolytic intermediates. In amino acid flavor formation, red vinasse acid contains 32 control genes for branched-chain aminotransferase (BCAT), 27 control genes for aromatic-amino-acid transaminase (ArAT), 60 control genes for keto acid invertase, 123 control genes for alcohol/aldehyde dehydrogenase, and 27 control genes for acetyl esterase, which have the basis for the formation of strong flavor substances from amino acids.
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Affiliation(s)
- Jianman Lv
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yaolu Ye
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuan Zhong
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wukang Liu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Meilin Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ailing Guo
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Jun Lv, ; Ailing Guo,
| | - Jun Lv
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, China
- *Correspondence: Jun Lv, ; Ailing Guo,
| | - Huawei Ma
- Aquatic Preservation and Processing Technology, Guangxi Academy of Fishery Science, Nanning, China
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17
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Kim SY, Park SY, Jin JE, Hong KS, Kim DJ, Kim YK, Shin HC, Cho SK, Kang DH. Comparing the VITEK 2 ANC card, species-specific PCR, and MALDI-TOF mass spectrometry methods for identification of lactic acid bacteria. J Food Sci 2022; 87:5099-5106. [PMID: 36201398 DOI: 10.1111/1750-3841.16343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/15/2022] [Accepted: 09/06/2022] [Indexed: 11/30/2022]
Abstract
Lactic acid bacteria (LAB) are not only the most common probiotics in the food and feed industry but are also used as plant probiotics. Therefore, precise identification of LAB at the species level is required. In this study, we compared three different methods, the VITEK 2 ANC card, species-specific PCR, and MALDI-TOF MS, to identify six LAB (Lacticaseibacillus casei, Lacticaseibacillus paracasei, Lacticaseibacillus rhamnosus, Lactiplantibacillus plantarum, Lentilactobacillus buchneri, and Limosilactobacillus fermentum) species previously assigned to the genus Lactobacillus that are used as biofertilizers. Twenty-two strains of six LAB species were analyzed using the VITEK 2 ANC card, species-specific PCR, and MALDI-TOF MS, and identification rates at the species level were 45.5%, 95.5%, and 95.5%, respectively. There were cross-reactions between L. casei and L. parpacasei, and one strain of L. casei could not be identified by these three methods. PCR assays and MALDI-TOF MS were applicable for LAB identification. PRACTICAL APPLICATION: LAB are the most common probiotics in the food and feed industry, so precise identification and classification of LAB at the species level are required. This study aimed at comparing three different methods for the effective identification of six LAB species: biochemical testing using VITEK 2 ANC card, species-specific PCR, and MALDI-TOF MS analysis.
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Affiliation(s)
- Sung-Youn Kim
- Experiment Research Institute, National Agricultural Products Quality Management Service, Gimcheon, Republic of Korea.,Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sol Yi Park
- Experiment Research Institute, National Agricultural Products Quality Management Service, Gimcheon, Republic of Korea
| | - Ji-Eun Jin
- Experiment Research Institute, National Agricultural Products Quality Management Service, Gimcheon, Republic of Korea
| | - Kyong-Suk Hong
- Experiment Research Institute, National Agricultural Products Quality Management Service, Gimcheon, Republic of Korea
| | - Dae-Jung Kim
- Experiment Research Institute, National Agricultural Products Quality Management Service, Gimcheon, Republic of Korea
| | - Yong-Kyoung Kim
- Experiment Research Institute, National Agricultural Products Quality Management Service, Gimcheon, Republic of Korea
| | - Hee-Chang Shin
- Experiment Research Institute, National Agricultural Products Quality Management Service, Gimcheon, Republic of Korea
| | - Soon-Kil Cho
- Experiment Research Institute, National Agricultural Products Quality Management Service, Gimcheon, Republic of Korea
| | - Dong-Hyun Kang
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul, Republic of Korea
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18
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Sulfite-free treatment combined with modified atmosphere packaging to extend trimmed young coconut shelf life during cold storage. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Ferrocino I, Rantsiou K, Cocolin L. Microbiome and -omics application in food industry. Int J Food Microbiol 2022; 377:109781. [DOI: 10.1016/j.ijfoodmicro.2022.109781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 11/30/2022]
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20
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Chang L, Mu G, Wang M, Zhao T, Tuo Y, Zhu X, Qian F. Microbial Diversity and Quality-Related Physicochemical Properties of Spicy Cabbage in Northeastern China and Their Correlation Analysis. Foods 2022; 11:foods11101511. [PMID: 35627081 PMCID: PMC9141884 DOI: 10.3390/foods11101511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/14/2022] [Accepted: 05/14/2022] [Indexed: 02/05/2023] Open
Abstract
Chinese spicy cabbage (CSC) is a popular special fermented food in Northeast China. The bacterial community and quality of CSC from different regions of northeastern China (Group_J: Jilin province, Group_L: Liaoning province, Group_H: Heilongjiang province) at retail (Group_P) and home-made (Group_C) were investigated in this study. The determination of the microbial community was achieved using high-throughput sequencing and the quality-related physicochemical characteristics included pH, salinity, total acid (TA), amino acid nitrogen (AAN), reducing sugar (RS), nitrite, and biogenic amines (BAs). Based on OPLS-DA analysis, there was a difference between the quality of Group_C and Group_P. No significant difference was observed in province grouping. Proteobacteria and Firmicutes were the dominant phyla, and the dominant genera were Lactobacillus, Pantoea, Weissella, and Pseudomonas. All groups had significant differences in community structure (p < 0.05). Compared with Group_C, the relative abundance of opportunistic pathogens (Pseudomonas and Serratia) in Group_P was lower. Pseudomonas and Serratia were the biomarkers in Group_H. At the genus level, Lactobacilluss and Weissella had a positive correlation with pH, Cadaverrine, and salinity (p < 0.05), however, they were negatively related to tryptamine. Pseudomonas was negatively correlated with salinity (p < 0.05). Bacterial community and physicochemical parameters of CSC, as well as the correlation between them, were discussed in this study, providing a reference for future studies on CSC inoculation and fermentation.
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Affiliation(s)
- Lixuan Chang
- School of Food Science and Technology, Dalian Polytechnic University, No. 1 Qinggongyuan, Ganjingzi District, Dalian 116034, China; (L.C.); (G.M.); (M.W.); (Y.T.); (X.Z.)
| | - Guangqing Mu
- School of Food Science and Technology, Dalian Polytechnic University, No. 1 Qinggongyuan, Ganjingzi District, Dalian 116034, China; (L.C.); (G.M.); (M.W.); (Y.T.); (X.Z.)
| | - Mingxu Wang
- School of Food Science and Technology, Dalian Polytechnic University, No. 1 Qinggongyuan, Ganjingzi District, Dalian 116034, China; (L.C.); (G.M.); (M.W.); (Y.T.); (X.Z.)
| | - Tong Zhao
- Dalian Center for Certification and Food and Drug Control, Dalian 116021, China;
| | - Yanfeng Tuo
- School of Food Science and Technology, Dalian Polytechnic University, No. 1 Qinggongyuan, Ganjingzi District, Dalian 116034, China; (L.C.); (G.M.); (M.W.); (Y.T.); (X.Z.)
| | - Xuemei Zhu
- School of Food Science and Technology, Dalian Polytechnic University, No. 1 Qinggongyuan, Ganjingzi District, Dalian 116034, China; (L.C.); (G.M.); (M.W.); (Y.T.); (X.Z.)
| | - Fang Qian
- School of Food Science and Technology, Dalian Polytechnic University, No. 1 Qinggongyuan, Ganjingzi District, Dalian 116034, China; (L.C.); (G.M.); (M.W.); (Y.T.); (X.Z.)
- Correspondence: ; Tel.: +86-13130035327; Fax: +86-41186322121
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21
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Kim E, Yang SM, Kim HJ, Kim HY. Differentiating between Enterococcusfaecium and Enterococcuslactis by Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry. Foods 2022; 11:foods11071046. [PMID: 35407133 PMCID: PMC8997568 DOI: 10.3390/foods11071046] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 03/30/2022] [Accepted: 04/04/2022] [Indexed: 12/10/2022] Open
Abstract
Unlike Enterococcus faecium strains, some Enterococcus lactis strains are considered potential probiotic strains as they lack particular virulence and antibiotic resistance genes. However, these closely related species are difficult to distinguish via conventional taxonomic methods. Here, for the first time, we used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with BioTyper and in-house databases to distinguish between E. faecium and E. lactis. A total of 58 reference and isolated strains (89.2%) were correctly identified at the species level using MALDI-TOF MS with in-house databases. However, seven strains (10.8%) were not accurately differentiated as a single colony was identified as a different species with a similar score value. Specific mass peaks were identified by analyzing reference strains, and mass peaks at 10,122 ± 2 m/z, 3650 ± 1 m/z, and 7306 ± 1 m/z were unique to E. faecium and E. lactis reference strains, respectively. Mass peaks verified reproducibility in 60 isolates and showed 100% specificity, whereas 16S rRNA sequencing identified two different candidates for some isolates (E. faecium and E. lactis). Our specific mass peak method helped to differentiate two species, with high accuracy and high throughput, and provided a viable alternative to 16S rRNA sequencing.
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Affiliation(s)
| | | | | | - Hae-Yeong Kim
- Correspondence: ; Tel.: +82-31-201-2600; Fax: +82-31-204-8116
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22
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Diversity of a Lactic Acid Bacterial Community during Fermentation of Gajami-Sikhae, a Traditional Korean Fermented Fish, as Determined by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. Foods 2022; 11:foods11070909. [PMID: 35406996 PMCID: PMC8997922 DOI: 10.3390/foods11070909] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 12/04/2022] Open
Abstract
Gajami-sikhae is a traditional Korean fermented fish food made by naturally fermenting flatfish (Glyptocephalus stelleri) with other ingredients. This study was the first to investigate the diversity and dynamics of lactic acid bacteria in gajami-sikhae fermented at different temperatures using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). A total of 4824 isolates were isolated from the fermented gajami-sikhae. These findings indicated that Latilactobacillus, Lactiplantibacillus, Levilactobacillus, Weissella, and Leuconostoc were the dominant genera during fermentation, while the dominant species were Latilactobacillus sakei, Lactiplantibacillus plantarum, Levilactobacillus brevis, Weissella koreensis, and Leuconostoc mesenteroides. At all temperatures, L. sakei was dominant at the early stage of gajami-sikhae fermentation, and it maintained dominance until the later stage of fermentation at low temperatures (5 °C and 10 °C). However, L. plantarum and L. brevis replaced it at higher temperatures (15 °C and 20 °C). The relative abundance of L. plantarum and L. brevis reached 100% at the later fermentation stage at 20 °C. These results suggest that the optimal fermentation temperatures for gajami-sikhae are low rather than high temperatures. This study could allow for the selection of an adjunct culture to control gajami-sikhae fermentation.
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23
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Ashfaq MY, Da'na DA, Al-Ghouti MA. Application of MALDI-TOF MS for identification of environmental bacteria: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 305:114359. [PMID: 34959061 DOI: 10.1016/j.jenvman.2021.114359] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/07/2021] [Accepted: 12/18/2021] [Indexed: 05/22/2023]
Abstract
Bacteria play a variety of roles in the environment. They maintain the balance in the ecosystem and provide different ecosystem services such as in biogeochemical cycling of nutrients, biodegradation of toxic pollutants, and others. Therefore, isolation and identification of different environmental bacteria are important to most environmental research. Due to the high cost and time associated with the conventional molecular techniques, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has gained considerable attention for routine identification of bacteria. This review aims to provide an overview of the application of MALDI-TOF MS in various environmental studies through bibliometric analysis and literature review. The bibliometric analysis helped to understand the time-variable application of MALDI-TOF MS in various environmental studies. The categorical literature review covers various environmental studies comprising areas like ecology, food microbiology, environmental biotechnology, agriculture, and plant sciences, which show the application of the technique for identification and characterization of pollutant-degrading, plant-associated, disease-causing, soil-beneficial, and other environmental bacteria. Further research should focus on bridging the gap between the phylogenetic identity of bacteria and their specific environmental functions or metabolic traits that can help in rapid advancements in environmental research, thereby, improving time and cost savings.
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Affiliation(s)
- Mohammad Y Ashfaq
- Environmental Science program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Dana A Da'na
- Environmental Science program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Mohammad A Al-Ghouti
- Environmental Science program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar.
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24
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Grujović MŽ, Mladenović KG, Semedo-Lemsaddek T, Laranjo M, Stefanović OD, Kocić-Tanackov SD. Advantages and disadvantages of non-starter lactic acid bacteria from traditional fermented foods: Potential use as starters or probiotics. Compr Rev Food Sci Food Saf 2022; 21:1537-1567. [PMID: 35029033 DOI: 10.1111/1541-4337.12897] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022]
Abstract
Traditional fermented foods are a significant source of starter and/or non-starter lactic acid bacteria (nsLAB). Moreover, these microorganisms are also known for their role as probiotics. The potential of nsLAB is huge; however, there are still challenges to be overcome with respect to characterization and application. In the present review, the most important steps that autochthonous lactic acid bacteria isolated from fermented foods need to overcome, to qualify as novel starter cultures, or as probiotics, in food technology and biotechnology, are considered. These different characterization steps include precise identification, detection of health-promoting properties, and safety evaluation. Each of these features is strain specific and needs to be accurately determined. This review highlights the advantages and disadvantages of nsLAB, isolated from traditional fermented foods, discussing safety aspects and sensory impact.
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Affiliation(s)
- Mirjana Ž Grujović
- Department of Science, Institute for Information Technologies, University of Kragujevac, Kragujevac, Republic of Serbia.,Department of Biology and Ecology, Faculty of Science, University of Kragujevac, Kragujevac, Republic of Serbia
| | - Katarina G Mladenović
- Department of Science, Institute for Information Technologies, University of Kragujevac, Kragujevac, Republic of Serbia.,Department of Biology and Ecology, Faculty of Science, University of Kragujevac, Kragujevac, Republic of Serbia
| | - Teresa Semedo-Lemsaddek
- CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisboa, Portugal
| | - Marta Laranjo
- MED-Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada, Universidade de Évora, Évora, Portugal
| | - Olgica D Stefanović
- Department of Biology and Ecology, Faculty of Science, University of Kragujevac, Kragujevac, Republic of Serbia
| | - Sunčica D Kocić-Tanackov
- Department of Food Preservation Engineering, Faculty of Technology, University of Novi Sad, Novi Sad, Republic of Serbia
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25
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Lee W, Choi HJ, Zin H, Kim E, Yang SM, Hwang J, Kwak HS, Kim SH, Kim HY. Effect of Enterotoxigenic Escherichia coli on Microbial Communities during Kimchi Fermentation. J Microbiol Biotechnol 2021; 31:1552-1558. [PMID: 34489379 PMCID: PMC9705866 DOI: 10.4014/jmb.2108.08038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 12/15/2022]
Abstract
The diverse microbial communities in kimchi are dependent on fermentation period and temperature. Here, we investigated the effect of enterotoxigenic Escherichia coli (ETEC) during the fermentation of kimchi at two temperatures using high-throughput sequencing. There were no differences in pH between the control group, samples not inoculated with ETEC, and the ETEC group, samples inoculated with ETEC MFDS 1009477. The pH of the two groups, which were fermented at 10 and 25°C, decreased rapidly at the beginning of fermentation and then reached pH 3.96 and pH 3.62. In both groups, the genera Lactobacillus, Leuconostoc, and Weissella were predominant. Our result suggests that microbial communities during kimchi fermentation may be affected by the fermentation parameters, such as temperature and period, and not enterotoxigenic E. coli (ETEC).
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Affiliation(s)
- Woojung Lee
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea,Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Hyo Ju Choi
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Hyunwoo Zin
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Eiseul Kim
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Seung-Min Yang
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Jinhee Hwang
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Hyo-Sun Kwak
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea,Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Soon Han Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea,Corresponding authors S.H. Kim E-mail:
| | - Hae-Yeong Kim
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea,
H.Y. Kim Phone: +82-31-201-2123 Fax: +82-31-204-8116 E-mail:
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26
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Wang H, Su W, Mu Y, Zhao C. Correlation Between Microbial Diversity and Volatile Flavor Compounds of Suan zuo rou, a Fermented Meat Product From Guizhou, China. Front Microbiol 2021; 12:736525. [PMID: 34745037 PMCID: PMC8564356 DOI: 10.3389/fmicb.2021.736525] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/01/2021] [Indexed: 11/17/2022] Open
Abstract
Suan zuo rou (SZR), a traditional fermented meat from Guizhou province, China, is loved by local people for its unique flavor and nutritional value. However, the microbial communities and related flavor characteristics of SZR from different regions of Guizhou are unclear. We studied the correlation between the microbial communities and the physicochemical properties and volatile flavor compounds (VFCs) of 15 SZR samples from three regions in Guizhou province. The microbial community structure of SZR was determined by high-throughput sequencing and VFCs were identified by headspace-solid phase microextraction combined with gas chromatography-mass spectrometry. The results indicated that the microbial communities of SZR varied among the regions, as evidenced by the relative abundance of Weissella, Staphylococcus, Brochothrix, Kazachstania, and Debaryomces. There were also significant differences in pH, water activity, NaCl, and total volatile basic nitrogen (P < 0.05). Based on orthogonal projections to latent structures and Pearson’s correlation coefficient, we showed that Wickerhamomyces, Kazachstania, Lactobacillus, Weissella, Brochothrix, Debaryomyces, Staphylococcus, Pediococcus, Pichia, Candida, and Leuconostoc were highly correlated with 48 VFCs (| ρ| > 0.8, P < 0.05). Redundancy analysis showed that most of the dominant bacteria were positively related to water activity, whereas Lactobacillus was positively related with pH, and negatively related with total volatile basic nitrogen.
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Affiliation(s)
- Hanyu Wang
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China.,Guizhou Key Laboratory for Storage and Processing of Agricultural and Animal Products, Guizhou University, Guiyang, China.,Animal Disease Control and Prevention Center of Guizhou Province, Guizhou University, Guiyang, China
| | - Wei Su
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China.,Guizhou Key Laboratory for Storage and Processing of Agricultural and Animal Products, Guizhou University, Guiyang, China
| | - Yingchun Mu
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Chi Zhao
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China.,Guizhou Key Laboratory for Storage and Processing of Agricultural and Animal Products, Guizhou University, Guiyang, China
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Wang X, Du G, Chen H, Zeng X, Liu B, Guo C, Sheng Q, Yuan Y, Yue T. Comparative Metagenomics Reveals Microbial Communities and Their Associated Functions in Two Types of Fuzhuan Brick Tea. Front Microbiol 2021; 12:705681. [PMID: 34603231 PMCID: PMC8481837 DOI: 10.3389/fmicb.2021.705681] [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: 05/06/2021] [Accepted: 08/19/2021] [Indexed: 12/28/2022] Open
Abstract
Fuzhuan brick tea (FBT) is a unique post-fermented tea product, naturally co-fermented by microorganisms, and has gained global popularity due to its potential health benefits for humans. Considerable efforts have been made toward elucidating the microbial diversity within FBT, but an understanding of the underlying FBT community interactions and functions remains poorly studied. Consequently, the microbial communities of two types of FBT, originating from Hunan and Shaanxi provinces, were investigated using comparative shotgun metagenomic sequencing and functional annotations. Metagenomic analysis indicated that two communities shared similar taxonomic and functional attributes. Two samples shared 486 genera, in which Pseudomonas contributed most to the abundant functions within the two samples. The carbohydrate active enzyme functions of the communities primarily comprised GH (32.92%), GT (26.8%), CEs (20.43%), and AAs (18.04%). Furthermore, the overall metabolic pathways encoded by the metagenomes were largely associated with carbohydrate and amino acid metabolism, with nine metabolic pathways that were differential between two groups including penicillin and cephalosporin biosynthesis. Significantly, a total of 35 potential probiotics were inferred, with Pseudomonas putida being the most abundant inferred probiotic (80%) within the FBT communities. This study provides new insights into FBT microbial communities on their potential functions and roles in FBT characteristics.
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Affiliation(s)
- Xin Wang
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China.,Laboratory of Quality & Safety Risk Assessment for Agro-Products (Yangling), Ministry of Agriculture, Xianyang, China
| | - Gengan Du
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China.,Laboratory of Quality & Safety Risk Assessment for Agro-Products (Yangling), Ministry of Agriculture, Xianyang, China
| | - Hong Chen
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China.,Laboratory of Quality & Safety Risk Assessment for Agro-Products (Yangling), Ministry of Agriculture, Xianyang, China
| | - Xuejun Zeng
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China.,Laboratory of Quality & Safety Risk Assessment for Agro-Products (Yangling), Ministry of Agriculture, Xianyang, China
| | - Bin Liu
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China.,Laboratory of Quality & Safety Risk Assessment for Agro-Products (Yangling), Ministry of Agriculture, Xianyang, China
| | - Chunfeng Guo
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China.,Laboratory of Quality & Safety Risk Assessment for Agro-Products (Yangling), Ministry of Agriculture, Xianyang, China
| | - Qinglin Sheng
- College of Food Science and Technology, Northwest University, Xi'an, China
| | - Yahong Yuan
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China.,Laboratory of Quality & Safety Risk Assessment for Agro-Products (Yangling), Ministry of Agriculture, Xianyang, China
| | - Tianli Yue
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China.,Laboratory of Quality & Safety Risk Assessment for Agro-Products (Yangling), Ministry of Agriculture, Xianyang, China.,College of Food Science and Technology, Northwest University, Xi'an, China
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Taban BM, Numanoglu Cevik Y. The efficiency of MALDI-TOF MS method in detecting Staphylococcus aureus isolated from raw milk and artisanal dairy foods. CYTA - JOURNAL OF FOOD 2021. [DOI: 10.1080/19476337.2021.1977392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Birce Mercanoglu Taban
- Dairy Technology Department, Faculty of Agriculture, Veterinary and Agriculture Campus, Ankara University, Diskapi, Ankara, Turkey
| | - Yasemin Numanoglu Cevik
- Microbiology and Reference Laboratory and Biological Products Department, General Directorate of Public Health, Ministry of Health, Ankara, Turkey
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Hurtado-Romero A, Del Toro-Barbosa M, Gradilla-Hernández MS, Garcia-Amezquita LE, García-Cayuela T. Probiotic Properties, Prebiotic Fermentability, and GABA-Producing Capacity of Microorganisms Isolated from Mexican Milk Kefir Grains: A Clustering Evaluation for Functional Dairy Food Applications. Foods 2021; 10:foods10102275. [PMID: 34681324 PMCID: PMC8534820 DOI: 10.3390/foods10102275] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 01/13/2023] Open
Abstract
Isolation and functional characterization of microorganisms are relevant steps for generating starter cultures with functional properties, and more recently, those related to improving mental health. Milk kefir grains have been recently investigated as a source of health-related strains. This study focused on the evaluation of microorganisms from artisanal Mexican milk kefir grains regarding probiotic properties, in vitro fermentability with commercial prebiotics (lactulose, inulin, and citrus pectin), and γ-aminobutyric acid (GABA)-producing capacity. Microorganisms were identified belonging to genera Lactococcus, Lactobacillus, Leuconostoc, and Kluyveromyces. The probiotic properties were assessed by aggregation abilities, antimicrobial activity, antibiotic susceptibility, and resistance to in vitro gastrointestinal digestion, showing a good performance compared with commercial probiotics. Most of isolates maintained a concentration above 6 log colony forming units/mL after the intestinal phase. Specific isolates of Kluyveromyces (BIOTEC009 and BIOTEC010), Leuconostoc (BIOTEC011 and BIOTEC012), and Lactobacillus (BIOTEC014 and BIOTEC15) showed a high fermentability in media supplemented with commercial prebiotics. The capacity to produce GABA was classified as medium for L. lactis BIOTEC006, BIOTEC007, and BIOTEC008; K. lactis BIOTEC009; L. pseudomesenteroides BIOTEC012; and L. kefiri BIOTEC014, and comparable to that obtained for commercial probiotics. Finally, a multivariate approach was performed, allowing the grouping of 2-5 clusters of microorganisms that could be further considered new promising cultures for functional dairy food applications.
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Ayhan K, Coşansu S, Orhan-Yanıkan E, Gülseren G. Advance methods for the qualitative and quantitative determination of microorganisms. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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31
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Ryu JA, Kim E, Yang SM, Lee S, Yoon SR, Jang KS, Kim HY. High-throughput sequencing of the microbial community associated with the physicochemical properties of meju (dried fermented soybean) and doenjang (traditional Korean fermented soybean paste). Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111473] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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32
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Culture-independent analysis of the bacterial community in Chinese fermented vegetables and genomic analysis of lactic acid bacteria. Arch Microbiol 2021; 203:4693-4703. [PMID: 34189594 DOI: 10.1007/s00203-021-02375-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 12/26/2022]
Abstract
Six different fermented vegetables were collected from Zhejiang Province, China, to explore the associated bacterial community using a high-throughput sequencing platform. A total of 24 phyla, 274 families and 569 genera were identified from 6 samples. Firmicutes and Proteobacteria were the main phyla in all of the samples. Brevibacterium was the major genus in Xiaoshan pickled radish. Lactobacillus-related genera and Vibrio were the major genera in fermented potherb mustard and its brine. Enterobacter and Cobetia were the major genera in fermented radish and its brine. Chromohalobacter was the major genus in the tuber mustard. These results indicated clear differences were there between the bacterial genera present in Xiaoshan pickled radish, fermented potherb mustard, fermented radish, and tuber mustard. This demonstrated the possible influences of raw materials and manufacturing processes. Furthermore, a large number of lactic acid bacteria were isolated and identified by culture-dependent and 16S rRNA gene sequence analysis, which accounted for more than 68% of all the isolates. In addition, whole-genome analysis of Levilactobacillus suantsaii, Latilactobacillus sakei subsp. sakei, and Weissella cibaria showed that they had large numbers of genes associated with carbohydrate metabolism. This may explain why these three bacterial strains can grow in fermented vegetable environments.
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Zhang J, Zhang C, Xin X, Liu D, Zhang W. Comparative Analysis of Traditional and Modern Fermentation for Xuecai and Correlations Between Volatile Flavor Compounds and Bacterial Community. Front Microbiol 2021; 12:631054. [PMID: 33995294 PMCID: PMC8118120 DOI: 10.3389/fmicb.2021.631054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/07/2021] [Indexed: 01/28/2023] Open
Abstract
Differences in flavor compounds and bacterial communities of Xuecai by traditional and modern fermentation are poorly understood. Allyl isothiocyanate (E9), ethyl acetate (E1), 3-butenenitrile (N1), phenol (P1), ethanol (A1), and 3-(2,6,6-trimethyl-1-cyclohexen-1-yl) acrylaldehyde (L11) were the main flavor compounds that differed between Xuecai produced by traditional and modern fermentation. Among these compounds, the contents of N1 and E9 were higher in modern fermentation Xuecai. Traditional fermentation Xuecai possessed higher contents of A1, P1, E1, and L11. High-throughput sequencing showed that Lactobacillus-related genera was the most abundant genus (50%) in modern fermentation Xuecai. However, in traditional fermentation Xuecai, Halanaerobium (29.06%) and Halomonas (12.96%) were the dominant genera. Halophilic bacteria (HB) positively contribute to the flavor of Xuecai. Carbohydrate metabolism and amino acid metabolism were the most abundant pathways associated with the bacterial communities of the Xuecai. This indicated that Xuecai flavor formation is mainly dependent on protein and carbohydrate degradation. This study provides a novel insight that HB may be important for flavor formation of Xuecai.
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Affiliation(s)
- Jianming Zhang
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Chengcheng Zhang
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaoting Xin
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Daqun Liu
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Wenwu Zhang
- Hangzhou Trendbiotech Co., Ltd, Hangzhou, China
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Kim E, Yang SM, Kim HY. Analysis of Cultivable Microbial Community during Kimchi Fermentation Using MALDI-TOF MS. Foods 2021; 10:foods10051068. [PMID: 34066045 PMCID: PMC8151656 DOI: 10.3390/foods10051068] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 04/28/2021] [Accepted: 05/08/2021] [Indexed: 12/31/2022] Open
Abstract
Kimchi, a traditional Korean fermented vegetable, has received considerable attention for its health-promoting effects. This study analyzes the cultivable microbial community in kimchi fermented at different temperatures using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to comprehensively understand the factors affecting the quality of kimchi. Of the 5204 strains isolated from kimchi, aligned with the in-house database, 4467 (85.8%) were correctly identified at the species level. The fermentation temperature affected the microbial community by varying the pH and acidity, which was mainly caused by temperature-dependent competition between the different lactic acid bacteria (LAB) species in kimchi. LAB, such as Levilactobacillus (Lb.) brevis and Lactiplantibacillus (Lpb.) plantarum associated with rancidity and tissue softening, proliferated faster at higher temperatures than at low temperature. In addition, LAB, such as Latilactobacillus (Lat.) sakei and Leuconostoc (Leu.) mesenteroides, which produce beneficial substances and flavor, were mainly distributed in kimchi fermented at 4 °C. This study shows as a novelty that MALDI-TOF MS is a robust and economically affordable method for investigating viable microbial communities in kimchi.
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Affiliation(s)
| | | | - Hae-Yeong Kim
- Correspondence: ; Tel.: +82-31-201-2600; Fax: +82-31-204-8116
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35
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Zhang C, Zhang J, Liu D. Biochemical changes and microbial community dynamics during spontaneous fermentation of Zhacai, a traditional pickled mustard tuber from China. Int J Food Microbiol 2021; 347:109199. [PMID: 33878643 DOI: 10.1016/j.ijfoodmicro.2021.109199] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023]
Abstract
Zhacai is a traditional fermented vegetable that has been consumed in China for centuries. It is currently manufactured by spontaneous fermentation and therefore mostly relies on the activities of autochthonous microorganisms. Here, we characterized microbial community dynamics and associated biochemical changes in 12% salted Zhacai during a 90-day spontaneous fermentation process using high-throughput sequencing and chromatography-based approaches to identify associations between microorganisms and fermentation characteristics. Amplicon sequencing targeting bacterial 16S rRNA genes revealed that bacterial communities were dominated by halophilic bacteria (HAB, i.e., Halomonas and Idiomarina) and lactic acid bacteria (LAB, i.e., Lactobacillus-related genera and Weissella) after 30 days of fermentation. In addition, the relative abundances of the fungal genera Debaryomyces, Sterigmatomyces, and Sporidiobolus increased as fermentation progressed. Concomitantly, pH decreased while titratable acidity increased during fermentation, along with associated variation in biochemical profiles. Overall, the levels of organic acids (i.e., lactic and acetic acid), free amino acids (i.e., alanine, lysine, and glutamic acid), and volatiles (i.e., alcohols, esters, aldehydes, and ketones) increased in mature Zhacai. In addition, the abundances of Lactobacillus-related species, Halomonas spp., Idiomarina loihiensis, as well as that of the yeast Debaryomyces hansenii, were strongly correlated with increased concentrations of organic acids, amino acids, biogenic amines, and volatiles. This study provides new detailed insights into the succession of microbial communities and their potential roles in Zhacai fermentation.
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Affiliation(s)
- Chengcheng Zhang
- Food Science Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jianming Zhang
- Food Science Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Daqun Liu
- Food Science Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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Saraiva JP, Worrich A, Karakoç C, Kallies R, Chatzinotas A, Centler F, Nunes da Rocha U. Mining Synergistic Microbial Interactions: A Roadmap on How to Integrate Multi-Omics Data. Microorganisms 2021; 9:microorganisms9040840. [PMID: 33920040 PMCID: PMC8070991 DOI: 10.3390/microorganisms9040840] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/13/2021] [Accepted: 04/08/2021] [Indexed: 11/24/2022] Open
Abstract
Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data. Our meta-analysis indicates that genetic potential alone does not resolve all issues involving mining of microbial interactions. Nevertheless, it can be used as the starting point to infer synergistic interspecies interactions and to limit the search space (i.e., number of species and metabolic reactions) to a manageable size. A reduced search space decreases the number of additional experiments necessary to validate the inferred putative interactions. As validation experiments, we examine how multi-omics and state of the art imaging techniques may further improve our understanding of species interactions’ role in ecosystem processes. Finally, we analyze pros and cons from the current methods to infer microbial interactions from genetic potential and propose a new theoretical framework based on: (i) genomic information of key members of a community; (ii) information of ecosystem processes involved with a specific hypothesis or research question; (iii) the ability to identify putative species’ contributions to ecosystem processes of interest; and, (iv) validation of putative microbial interactions through integration of other data sources.
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Affiliation(s)
- Joao Pedro Saraiva
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Anja Worrich
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Canan Karakoç
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Rene Kallies
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, 04103 Leipzig, Germany
| | - Florian Centler
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- Correspondence:
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Altakhis M, Pillidge CJ, Osborn AM, Torley PJ, Kaur M. Assessment of the potential use of MALDI-TOF MS for the identification of bacteria associated with chilled vacuum-packaged lamb meat. Meat Sci 2021; 177:108508. [PMID: 33798992 DOI: 10.1016/j.meatsci.2021.108508] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/09/2021] [Accepted: 03/19/2021] [Indexed: 10/21/2022]
Abstract
The focus of this study was to compare the effectiveness of MALDI-TOF MS and partial 16S rRNA gene sequencing for the identification of bacteria isolated from VP lamb meat stored chilled at 5 °C for 21 days, at the same time gaining insights into bacterial changes over time. The identity of bacterial isolates on non-selective and selective agars was determined by both methods and results compared. Results showed that total bacterial numbers increased over the 21 days (as expected) with Staphylococcus and Pseudomonas (day 0) being replaced by Carnobacterium, Brochothrix and members of the Enterobacteriaceae family by day 21. A high level of agreement (86-100%) for bacterial isolates' identity at genus level was observed between MALDI-TOF MS and partial 16S rRNA gene-based sequencing for isolates where identification was possible. With its cheaper cost and faster turnaround time, once optimized, MALDI-TOF MS could become a useful alternative to 16S rRNA gene-sequencing for the rapid identification of red meat bacterial isolates.
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Affiliation(s)
- Mohammed Altakhis
- Biosciences and Food Technology, School of Science, RMIT University, Melbourne, Australia
| | - Christopher J Pillidge
- Biosciences and Food Technology, School of Science, RMIT University, Melbourne, Australia
| | - A Mark Osborn
- Biosciences and Food Technology, School of Science, RMIT University, Melbourne, Australia
| | - Peter J Torley
- Biosciences and Food Technology, School of Science, RMIT University, Melbourne, Australia
| | - Mandeep Kaur
- Biosciences and Food Technology, School of Science, RMIT University, Melbourne, Australia.
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Ryu JA, Kim E, Kim MJ, Lee S, Yoon SR, Ryu JG, Kim HY. Physicochemical Characteristics and Microbial Communities in Gochujang, a Traditional Korean Fermented Hot Pepper Paste. Front Microbiol 2021; 11:620478. [PMID: 33537020 PMCID: PMC7848209 DOI: 10.3389/fmicb.2020.620478] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/21/2020] [Indexed: 12/11/2022] Open
Abstract
Gochujang is a Korean fermented hot pepper paste beneficial to human health by providing various nutrients. In this study, its physicochemical characteristics were identified, and its microbial communities were analyzed by high-throughput sequencing. The interrelationship between physicochemical characteristics and microbial composition was investigated to reveal the properties of gochujang before and after fermentation. After fermentation, all samples showed decreased salt concentration, pH, and reducing sugar content, while the acidity and amino-type nitrogen increased. The water content, salt concentration, amino-type nitrogen, and reducing sugar differed according to the batches of samples. Bacillus, Aerosakkonema, and Enterococcus were identified as the predominant bacterial genera. Furthermore, Aerosakkonema was the most abundant genus before fermentation; however, it was replaced by Bacillus as it decreased after fermentation. For the fungi, Aspergillus dominated before fermentation, whereas Zygosaccharomyces and Millerozyma dominated after fermentation. The high level of amino-type nitrogen in gochujang was related to the relative abundance of B. haynesii/B. licheniformis before fermentation. Additionally, the high abundance of Z. rouxii after fermentation was related to the flavor of gochujang. This comprehensive analysis of the microbial community associated with the physicochemical properties of gochujang could help in understanding the factors affecting the quality of the product.
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Affiliation(s)
- Jung-A Ryu
- Gyeongsangbuk-do Agricultural Research and Extension Services, Daegu, South Korea.,Department of Horticulture, Kyungpook National University, Daegu, South Korea
| | - Eiseul Kim
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Mi-Ju Kim
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Shinyoung Lee
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Sung-Ran Yoon
- Gyeongsangbuk-do Agricultural Research and Extension Services, Daegu, South Korea
| | - Jung-Gi Ryu
- Gyeongsangbuk-do Agricultural Research and Extension Services, Daegu, South Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, South Korea
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