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Lee DH, Lee W, Shin D, Im H, Jung G, Lee YB, Choi J. Genomic and metabolomic analysis of Latilactobacillus sakei DCF0720 for black soybean yogurt fermentation. Int J Food Microbiol 2024; 425:110897. [PMID: 39241349 DOI: 10.1016/j.ijfoodmicro.2024.110897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 08/28/2024] [Accepted: 08/28/2024] [Indexed: 09/09/2024]
Abstract
Lactic acid bacteria are commonly used in plant-based fermentation to reduce off-flavor and improve sensory characteristics. However, there have been few studies on Latilactobacillus sakei for plant-based yogurt fermentation and, particularly, its metabolic features at the genomic level remain unclear. This study aims to analyze the fermentation characteristics of the L. sakei DCF0720 strain and compare genetics and metabolic relations. For this, DCF0720 was used to ferment the black soybean milk and conduct the physicochemical analysis and sensory test. The genomic and metabolic analyses were performed by complete genome sequencing and 500 MHz 1H NMR, respectively. As a result, DCF0720 exhibited enhanced fermentation performance and sensory evaluations at 37 °C compared to 30 °C, which is generally recognized as the optimal growth temperature for most L. sakei strains. It also produced flavor enhancing volatile compounds such as acetoin and hydroxyacetone, possessing all three key genes for acetoin biosynthesis. DCF0720 lacks 2,3-butanediol dehydrogenase, which leads to the inhibition of acetoin production. DCF0720 possesses a complete pathway to utilize primary black soybean carbon sources such as sucrose, raffinose, and stachyose. DCF0720 also possesses genes for the GH28 family, including the key enzymes in the hydrolysis of pectin substances, which means eliminating the main soybean nonstarch polysaccharides. This study demonstrates that DCF0720 is a suitable starter for plant-based yogurt fermentation, providing a better understanding of fermentation conditions with genetic and metabolic features for black soybean yogurt. Various carbon source utilization abilities with depth metabolic pathway analysis provide that DCF0720 can be employed to develop enhanced starter cultures for black soybean yogurt and diverse plant-based yogurts.
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Affiliation(s)
- Dong Hyeon Lee
- Central Research Institute, Dr. Chung's Food Co., Ltd., Cheongju-si, Republic of Korea.
| | - Wonjong Lee
- Central Research Institute, Dr. Chung's Food Co., Ltd., Cheongju-si, Republic of Korea.
| | - Dongho Shin
- Central Research Institute, Dr. Chung's Food Co., Ltd., Cheongju-si, Republic of Korea.
| | - Haecheon Im
- Central Research Institute, Dr. Chung's Food Co., Ltd., Cheongju-si, Republic of Korea.
| | - Guhun Jung
- Central Research Institute, Dr. Chung's Food Co., Ltd., Cheongju-si, Republic of Korea.
| | - Yoon-Bok Lee
- Central Research Institute, Dr. Chung's Food Co., Ltd., Cheongju-si, Republic of Korea.
| | - Jaekwon Choi
- Central Research Institute, Dr. Chung's Food Co., Ltd., Cheongju-si, Republic of Korea.
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2
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Jaeger I, Köhn CR, Evans JD, Frazzon J, Renault P, Kothe CI. Nutritional and microbial profiles of ripened plant-based cheese analogs collected from the European market. Food Res Int 2024; 191:114724. [PMID: 39059920 DOI: 10.1016/j.foodres.2024.114724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024]
Abstract
Plant-based cheese analogs have emerged as a novel global market trend driven by sustainability concerns for our planet. This study examines eleven soft ripened plant-based cheese analogs produced in Europe, primarily with bloomy rinds and cashew nuts as the main ingredient. First, we focused on exploring the macronutrients and salt content stated on the labels, as well a detailed fatty acid analysis of the samples. Compared to dairy cheeses, plant-based cheeses share similarities in lipid content, but their fatty acid profiles diverge significantly, with higher ratio of mono- and polyunsaturated fatty acids such as oleic and linoleic acids. We also investigated the microbiota of these analog products, employing a culture-dependent and -independent approaches. We identified a variety of microorganisms in the plant-based cheeses, with Lactococcus lactis and Leuconostoc mesenteroides being the dominant bacterial species, and Geotrichum candidum and Penicillium camemberti the dominant fungal species. Most of the species characterized are similar to those present in dairy cheeses, suggesting that they have been inoculated as culture starters to contribute to the sensorial acceptance of plant-based cheeses. However, we also identify several species that are possibly intrinsic to plant matrices or originate from the production environment, such as Pediococcus pentosaceus and Enterococcus spp. This coexistence of typical dairy-associated organisms with plant associated species highlights the potential microbial dynamics inherent in the production of plant-based cheese. These findings will contribute to a better understanding of plant-based cheese alternatives, enable the development of sustainable products, and pave the way for future research exploring the use of plant-based substrates in the production of cheese analogues.
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Affiliation(s)
- Isabela Jaeger
- Food Science Institute, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, 91501-970 Porto Alegre, RS, Brazil; Université Paris-Saclay, INRAE, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Cecília R Köhn
- Food Science Institute, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, 91501-970 Porto Alegre, RS, Brazil
| | - Joshua D Evans
- Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Jeverson Frazzon
- Food Science Institute, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, 91501-970 Porto Alegre, RS, Brazil
| | - Pierre Renault
- Université Paris-Saclay, INRAE, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Caroline Isabel Kothe
- Université Paris-Saclay, INRAE, Micalis Institute, 78350 Jouy-en-Josas, France; Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark.
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Ardalani O, Phaneuf PV, Mohite OS, Nielsen LK, Palsson BO. Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits. mSystems 2024; 9:e0015624. [PMID: 38920366 PMCID: PMC11265412 DOI: 10.1128/msystems.00156-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 05/17/2024] [Indexed: 06/27/2024] Open
Abstract
Strains across the Lactobacillaceae family form the basis for a trillion-dollar industry. Our understanding of the genomic basis for their key traits is fragmented, however, including the metabolism that is foundational to their industrial uses. Pangenome analysis of publicly available Lactobacillaceae genomes allowed us to generate genome-scale metabolic network reconstructions for 26 species of industrial importance. Their manual curation led to more than 75,000 gene-protein-reaction associations that were deployed to generate 2,446 genome-scale metabolic models. Cross-referencing genomes and known metabolic traits allowed for manual metabolic network curation and validation of the metabolic models. As a result, we provide the first pangenomic basis for metabolism in the Lactobacillaceae family and a collection of predictive computational metabolic models that enable a variety of practical uses.IMPORTANCELactobacillaceae, a bacterial family foundational to a trillion-dollar industry, is increasingly relevant to biosustainability initiatives. Our study, leveraging approximately 2,400 genome sequences, provides a pangenomic analysis of Lactobacillaceae metabolism, creating over 2,400 curated and validated genome-scale models (GEMs). These GEMs successfully predict (i) unique, species-specific metabolic reactions; (ii) niche-enriched reactions that increase organism fitness; (iii) essential media components, offering insights into the global amino acid essentiality of Lactobacillaceae; and (iv) fermentation capabilities across the family, shedding light on the metabolic basis of Lactobacillaceae-based commercial products. This quantitative understanding of Lactobacillaceae metabolic properties and their genomic basis will have profound implications for the food industry and biosustainability, offering new insights and tools for strain selection and manipulation.
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Affiliation(s)
- O. Ardalani
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - P. V. Phaneuf
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - O. S. Mohite
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - L. K. Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
| | - B. O. Palsson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, California, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
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Dahar GY, Wang HW, Rajer FU, Jin P, Xu P, Abro MA, Qureshi AS, Karim A, Miao W. Comparative genomic analysis of Bacillus atrophaeus HAB-5 reveals genes associated with antimicrobial and plant growth-promoting activities. Front Microbiol 2024; 15:1384691. [PMID: 38989016 PMCID: PMC11233526 DOI: 10.3389/fmicb.2024.1384691] [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: 02/10/2024] [Accepted: 06/07/2024] [Indexed: 07/12/2024] Open
Abstract
Bacillus atrophaeus HAB-5 is a plant growth-promoting rhizobacterium (PGPR) that exhibits several biotechnological traits, such as enhancing plant growth, colonizing the rhizosphere, and engaging in biocontrol activities. In this study, we conducted whole-genome sequencing of B. atrophaeus HAB-5 using the single-molecule real-time (SMRT) sequencing platform by Pacific Biosciences (PacBio; United States), which has a circular chromosome with a total length of 4,083,597 bp and a G + C content of 44.21%. The comparative genomic analysis of B. atrophaeus HAB-5 with other strains, Bacillus amyloliquefaciens DSM7, B. atrophaeus SRCM101359, Bacillus velezensis FZB42, B. velezensis HAB-2, and Bacillus subtilis 168, revealed that these strains share 2,465 CDSs, while 599 CDSs are exclusive to the B. atrophaeus HAB-5 strain. Many gene clusters in the B. atrophaeus HAB-5 genome are associated with the production of antimicrobial lipopeptides and polypeptides. These gene clusters comprise distinct enzymes that encode three NRPs, two Transat-Pks, one terpene, one lanthipeptide, one T3PKS, one Ripp, and one thiopeptide. In addition to the likely IAA-producing genes (trpA, trpB, trpC, trpD, trpE, trpS, ywkB, miaA, and nadE), there are probable genes that produce volatile chemicals (acoA, acoB, acoR, acuB, and acuC). Moreover, HAB-5 contained genes linked to iron transportation (fbpA, fetB, feuC, feuB, feuA, and fecD), sulfur metabolism (cysC, sat, cysK, cysS, and sulP), phosphorus solubilization (ispH, pstA, pstC, pstS, pstB, gltP, and phoH), and nitrogen fixation (nif3-like, gltP, gltX, glnR, glnA, nadR, nirB, nirD, nasD, narl, narH, narJ, and nark). In conclusion, this study provides a comprehensive genomic analysis of B. atrophaeus HAB-5, pinpointing the genes and genomic regions linked to the antimicrobial properties of the strain. These findings advance our knowledge of the genetic basis of the antimicrobial properties of B. atrophaeus and imply that HAB-5 may employ a variety of commercial biopesticides and biofertilizers as a substitute strategy to increase agricultural output and manage a variety of plant diseases.
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Affiliation(s)
- Ghulam Yaseen Dahar
- Key Laboratory of Green Prevention and Control of Tropical Plant Disease and Pests, Ministry of Education, College of Plant Protection, Hainan University Haikou, Haikou, China
| | - Huan Wei Wang
- Key Laboratory of Green Prevention and Control of Tropical Plant Disease and Pests, Ministry of Education, College of Plant Protection, Hainan University Haikou, Haikou, China
| | - Faheem Uddin Rajer
- Department of Plant Pathology, Faculty of Crop Protection, Sindh Agriculture University, Tando Jam, Pakistan
| | - Pengfie Jin
- Key Laboratory of Green Prevention and Control of Tropical Plant Disease and Pests, Ministry of Education, College of Plant Protection, Hainan University Haikou, Haikou, China
| | - Peidong Xu
- Key Laboratory of Green Prevention and Control of Tropical Plant Disease and Pests, Ministry of Education, College of Plant Protection, Hainan University Haikou, Haikou, China
| | - Manzoor Ali Abro
- Department of Plant Pathology, Faculty of Crop Protection, Sindh Agriculture University, Tando Jam, Pakistan
| | - Abdul Sattar Qureshi
- Institute of Biotechnology and Genetic Engineering, University of Sindh, Jamshoro, Pakistan
| | - Asad Karim
- Jamil-Ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Weiguo Miao
- Key Laboratory of Green Prevention and Control of Tropical Plant Disease and Pests, Ministry of Education, College of Plant Protection, Hainan University Haikou, Haikou, China
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Roch FF, Dzieciol M, Quijada NM, Alteio LV, Mester PJ, Selberherr E. Microbial community structure of plant-based meat alternatives. NPJ Sci Food 2024; 8:27. [PMID: 38740858 DOI: 10.1038/s41538-024-00269-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
A reduction in animal-based diets has driven market demand for alternative meat products, currently raising a new generation of plant-based meat alternatives (PBMAs). It remains unclear whether these substitutes are a short-lived trend or become established in the long term. Over the last few years, the trend of increasing sales and diversifying product range has continued, but publication activities in this field are currently limited mainly to market research and food technology topics. As their popularity increases, questions emerge about the safety and nutritional risks of these novel products. Even though all the examined products must be heated before consumption, consumers lack experience with this type of product and thus further research into product safety, is desirable. To consider these issues, we examined 32 PBMAs from Austrian supermarkets. Based on 16S rRNA gene amplicon sequencing, the majority of the products were dominated by lactic acid bacteria (either Leuconostoc or Latilactobacillus), and generally had low alpha diversity. Pseudomonadota (like Pseudomonas and Shewanella) dominated the other part of the products. In addition to LABs, a high diversity of different Bacillus, but also some Enterobacteriaceae and potentially pathogenic species were isolated with the culturing approach. We assume that especially the dominance of heterofermentative LABs has high relevance for the product stability and quality with the potential to increase shelf life of the products. The number of isolated Enterobacteriaceae and potential pathogens were low, but they still demonstrated that these products are suitable for their presence.
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Affiliation(s)
- Franz-Ferdinand Roch
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Monika Dzieciol
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Narciso M Quijada
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185, Villamayor (Salamanca), Spain
| | - Lauren V Alteio
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, 3430, Tulln, Austria
| | - Patrick-Julian Mester
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Evelyne Selberherr
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria.
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Papadimitriou K, Georgalaki M, Anastasiou R, Alexandropoulou AM, Manolopoulou E, Zoumpopoulou G, Tsakalidou E. Study of the Microbiome of the Cretan Sour Cream Staka Using Amplicon Sequencing and Shotgun Metagenomics and Isolation of Novel Strains with an Important Antimicrobial Potential. Foods 2024; 13:1129. [PMID: 38611432 PMCID: PMC11011300 DOI: 10.3390/foods13071129] [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: 01/22/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Staka is a traditional Greek sour cream made mostly from spontaneously fermented sheep milk or a mixture of sheep and goat milk. At the industrial scale, cream separators and starter cultures may also be used. Staka is sometimes cooked with flour to absorb most of the fat. In this study, we employed culture-based techniques, amplicon sequencing, and shotgun metagenomics to analyze the Staka microbiome for the first time. The samples were dominated by Lactococcus or Leuconostoc spp. Most other bacteria were lactic acid bacteria (LAB) from the Streptococcus and Enterococcus genera or Gram-negative bacteria from the Buttiauxella, Pseudomonas, Enterobacter, Escherichia-Shigella, and Hafnia genera. Debaryomyces, Kluyveromyces, or Alternaria were the most prevalent genera in the samples, followed by other yeasts and molds like Saccharomyces, Penicillium, Aspergillus, Stemphylium, Coniospotium, or Cladosporium spp. Shotgun metagenomics allowed the species-level identification of Lactococcus lactis, Lactococcus raffinolactis, Streptococcus thermophilus, Streptococcus gallolyticus, Escherichia coli, Hafnia alvei, Streptococcus parauberis, and Enterococcus durans. Binning of assembled shotgun reads followed by recruitment plot analysis of single reads could determine near-complete metagenome assembled genomes (MAGs). Culture-dependent and culture-independent analyses were in overall agreement with some distinct differences. For example, lactococci could not be isolated, presumably because they had entered a viable but not culturable (VBNC) state or because they were dead. Finally, several LAB, Hafnia paralvei, and Pseudomonas spp. isolates exhibited antimicrobial activities against oral or other pathogenic streptococci, and certain spoilage and pathogenic bacteria establishing their potential role in food bio-protection or new biomedical applications. Our study may pave the way for additional studies concerning artisanal sour creams to better understand the factors affecting their production and the quality.
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Affiliation(s)
- Konstantinos Papadimitriou
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Marina Georgalaki
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (M.G.); (R.A.); (A.-M.A.); (E.M.); (G.Z.); (E.T.)
| | - Rania Anastasiou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (M.G.); (R.A.); (A.-M.A.); (E.M.); (G.Z.); (E.T.)
| | - Athanasia-Maria Alexandropoulou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (M.G.); (R.A.); (A.-M.A.); (E.M.); (G.Z.); (E.T.)
| | - Eugenia Manolopoulou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (M.G.); (R.A.); (A.-M.A.); (E.M.); (G.Z.); (E.T.)
| | - Georgia Zoumpopoulou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (M.G.); (R.A.); (A.-M.A.); (E.M.); (G.Z.); (E.T.)
| | - Effie Tsakalidou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (M.G.); (R.A.); (A.-M.A.); (E.M.); (G.Z.); (E.T.)
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Kim SJ, Ha S, Dang YM, Chang JY, Mun SY, Ha JH. Combined Non-Thermal Microbial Inactivation Techniques to Enhance the Effectiveness of Starter Cultures for Kimchi Fermentation. J Microbiol Biotechnol 2024; 34:622-633. [PMID: 37997263 PMCID: PMC11016767 DOI: 10.4014/jmb.2310.10010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023]
Abstract
For quality standardization, the application of functional lactic acid bacteria (LAB) as starter cultures for food fermentation is a well-known method in the fermented food industry. This study assessed the effect of adding a non-thermally microbial inactivated starter culture to kimchi, a traditional Korean food, in standardizing its quality. In this study, pretreatment based on sterilization processes, namely, slightly acidic electrolyzed water (SAEW) disinfection and ultraviolet C light-emitting diode (UVC-LED) of raw and subsidiary kimchi materials were used to reduce the initial microorganisms in them, thereby increasing the efficiency and value of the kimchi LAB starter during fermentation. Pretreatment sterilization effectively suppressed microorganisms that threatened the sanitary value and quality of kimchi. In addition, pretreatment based on sterilization effectively reduced the number of initial microbial colonies in kimchi, creating an environment in which kimchi LAB starters could settle or dominate, compared to non-sterilized kimchi. These differences in the initial microbial composition following the sterilization process and the addition of kimchi LAB starters led to differences in the metabolites that positively affect the taste and flavor of kimchi. The combined processing technology used in our study, that is, pre-sterilization and LAB addition, may be a powerful approach for kimchi quality standardization.
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Affiliation(s)
- Su-Ji Kim
- Hygienic Safety · Materials Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
- Department of Food Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Sanghyun Ha
- Hygienic Safety · Materials Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - Yun-Mi Dang
- Hygienic Safety · Materials Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - Ji Yoon Chang
- Fermentation Regulation Technology Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - So Yeong Mun
- Fermentation Regulation Technology Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - Ji-Hyoung Ha
- Hygienic Safety · Materials Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
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8
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Hye Baek J, Min Han D, Gyu Choi D, Ok Jeon C. Unraveling the carbohydrate metabolic characteristics of Leuconostoc mesenteroides J18 through metabolite and transcriptome analyses. Food Chem 2024; 435:137594. [PMID: 37804726 DOI: 10.1016/j.foodchem.2023.137594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 07/27/2023] [Accepted: 09/23/2023] [Indexed: 10/09/2023]
Abstract
The metabolic characteristics of Leuconostoc mesenteroides subsp. mesenteroides J18, which is mainly responsible for kimchi fermentation, on various carbon sources were investigated through carbon utilization, metabolite, and transcriptome analyses at different culture conditions (10 and 30 °C with/without 2.5% NaCl). The metabolic features of strain J18 were relatively similar across the four culture conditions. However, the metabolic characteristics of strain J18 showed significant variations depending on the carbon source. These distinct metabolic traits of strain J18 on various carbon sources were validated through transcriptomic analyses and the reconstruction of metabolic pathways. The transcriptional expression of the metabolic pathways in response to each carbon source consistently correlated with the production profiles of metabolites, including ethanol, acetoin, diacetyl, and riboflavin, in each carbon source. Our findings suggests that the abundance of Leu. mesenteroides during fermentation and the taste and flavor of fermented food products can be controlled by altering the carbon sources.
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Affiliation(s)
- Ju Hye Baek
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dong Min Han
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dae Gyu Choi
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.
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Sarker P, Mitro A, Hoque H, Hasan MN, Nurnabi Azad Jewel GM. Identification of potential novel therapeutic drug target against Elizabethkingia anophelis by integrative pan and subtractive genomic analysis: An in silico approach. Comput Biol Med 2023; 165:107436. [PMID: 37690289 DOI: 10.1016/j.compbiomed.2023.107436] [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: 11/30/2022] [Revised: 07/08/2023] [Accepted: 08/28/2023] [Indexed: 09/12/2023]
Abstract
Elizabethkingia anophelis is a human pathogen responsible for severe nosocomial infections in neonates and immunocompromised patients. The significantly higher mortality rate from E. anophelis infections and the lack of available regimens highlight the critical need to explore novel drug targets. The current study investigated effective novel drug targets by employing a comprehensive in silico subtractive genomic approach integrated with pangenomic analysis of E. anophelis strains. A total of 2809 core genomic proteins were found by pangenomic analysis of non-paralogous proteins. Subsequently, 156 pathogen-specific, 442 choke point, 202 virulence factor, 53 antibiotic resistant and 119 host-pathogen interacting proteins were identified in E. anophelis. By subtractive genomic approach, at first 791 proteins were found to be indispensable for the survival of E. anophelis. 558 and 315 proteins were detected as non-homologous to human and gut microflora respectively. Following that 245 cytoplasmic, 245 novel, and 23 broad-spectrum targets were selected and finally four proteins were considered as potential therapeutic targets of E. anophelis based on highest degree score in PPI network. Among those, three proteins were subjected to molecular docking and subsequent MD simulation as one protein did not contain a plausible binding pocket with sufficient surface area and volume. All the complexes were found to be stable and compact in 100 ns molecular dynamics simulation studies as measured by RMSD, RMSF, and Rg. These three short-listed targets identified in this study may lead to the development of novel antimicrobials capable of curing infections and pave the way to prevent and control the disease progression caused by the deadly agent E. anophelis.
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Affiliation(s)
- Parth Sarker
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh; Computational Biology and Bioinformatics Lab, Dept. of GEB, SUST, Sylhet-3114, Bangladesh
| | - Arnob Mitro
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh; Computational Biology and Bioinformatics Lab, Dept. of GEB, SUST, Sylhet-3114, Bangladesh
| | - Hammadul Hoque
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh
| | - Md Nazmul Hasan
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh
| | - G M Nurnabi Azad Jewel
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh; Computational Biology and Bioinformatics Lab, Dept. of GEB, SUST, Sylhet-3114, Bangladesh.
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Guse K, Sharma A, Weyenberg E, Davison S, Ma Y, Choi Y, Johnson AJ, Chen C, Gomez A. Regular consumption of lacto-fermented vegetables has greater effects on the gut metabolome compared with the microbiome. GUT MICROBIOME (CAMBRIDGE, ENGLAND) 2023; 4:e11. [PMID: 39295909 PMCID: PMC11406409 DOI: 10.1017/gmb.2023.9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/02/2023] [Accepted: 05/27/2023] [Indexed: 09/21/2024]
Abstract
The industrialisation of Western food systems has reduced the regular consumption of lacto-fermented vegetables (LFV). Consuming LFV may exert health benefits through the alteration of the gut microbiome, but the mechanisms involved remain unclear. To start understanding the possible benefits of LFV, we compared faecal microbial diversity and composition, as well as dietary habits between individuals who regularly consume LFV (n = 23) and those who do not (n = 24). We utilised microbial DNA amplicon sequencing (16S rRNA and ITS2) and untargeted metabolomics (LC-MS) to analyse stool samples. Study participants also provided three consecutive days of dietary data. Results show minor effects on microbiome composition; with the enrichment of a few microorganisms potentially associated with vegetable ferments, such as Leuconostoc mesenteroides and Rhodotorula mucilaginosa (P < 0.05), in LFV consumers. However, LFV consumption had greater effects on the faecal metabolome, with higher abundances of butyrate, acetate, and valerate (P < 0.05) and significantly greater metabolome diversity (P < 0.001). Overall, the observations of minor changes in the faecal microbiome and greater effects on the faecal metabolome from LFV consumption warrant further investigations on the health significance of LFV as regular components of the daily diet in humans.
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Affiliation(s)
- Kylene Guse
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN, USA
| | - Ashok Sharma
- Department of Animal Science, University of Minnesota, St. Paul, MN, USA
| | - Emily Weyenberg
- Department of Animal Science, University of Minnesota, St. Paul, MN, USA
| | - Sam Davison
- Department of Animal Science, University of Minnesota, St. Paul, MN, USA
| | - Yiwei Ma
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN, USA
| | - Yuni Choi
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Abigail J Johnson
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Chi Chen
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN, USA
- Department of Animal Science, University of Minnesota, St. Paul, MN, USA
| | - Andres Gomez
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN, USA
- Department of Animal Science, University of Minnesota, St. Paul, MN, USA
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11
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Kashyap AS, Manzar N, Meshram S, Sharma PK. Screening microbial inoculants and their interventions for cross-kingdom management of wilt disease of solanaceous crops- a step toward sustainable agriculture. Front Microbiol 2023; 14:1174532. [PMID: 37389335 PMCID: PMC10303155 DOI: 10.3389/fmicb.2023.1174532] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/18/2023] [Indexed: 07/01/2023] Open
Abstract
Microbial inoculants may be called magical bullets because they are small in size but have a huge impact on plant life and humans. The screening of these beneficial microbes will give us an evergreen technology to manage harmful diseases of cross-kingdom crops. The production of these crops is reducing as a result of multiple biotic factors and among them the bacterial wilt disease triggered by Ralstonia solanacearum is the most important in solanaceous crops. The examination of the diversity of bioinoculants has shown that more microbial species have biocontrol activity against soil-borne pathogens. Reduced crop output, lower yields, and greater cost of cultivation are among the major issues caused by diseases in agriculture around the world. It is universally true that soil-borne disease epidemics pose a greater threat to crops. These necessitate the use of eco-friendly microbial bioinoculants. This review article provides an overview of plant growth-promoting microorganisms bioinoculants, their various characteristics, biochemical and molecular screening insights, and modes of action and interaction. The discussion is concluded with a brief overview of potential future possibilities for the sustainable development of agriculture. This review will be useful for students and researchers to obtain existing knowledge of microbial inoculants, their activities, and their mechanisms, which will facilitate the development of environmentally friendly management strategies for cross-kingdom plant diseases.
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Affiliation(s)
- Abhijeet Shankar Kashyap
- Molecular Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Nazia Manzar
- Plant Pathology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Shweta Meshram
- Department of Plant Pathology, Lovely Professional University, Phagwara, Punjab, India
| | - Pawan Kumar Sharma
- Plant Pathology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
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12
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Vallejo-García LC, Sánchez-Olmos MDC, Gutiérrez-Ríos RM, López Munguía A. Glycosyltransferases Expression Changes in Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 Grown on Different Carbon Sources. Foods 2023; 12:foods12091893. [PMID: 37174431 PMCID: PMC10177778 DOI: 10.3390/foods12091893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Leuconostoc mesenteroides strains are common contributors in fermented foods producing a wide variety of polysaccharides from sucrose through glycosyltransferases (GTFs). These polymers have been proposed as protective barriers against acidity, dehydration, heat, and oxidative stress. Despite its presence in many traditional fermented products and their association with food functional properties, regulation of GTFs expression in Ln. mesenteroides is still poorly understood. The strain Ln. mesenteroides ATCC 8293 contains three glucansucrases genes not found in operons, and three fructansucrases genes arranged in two operons, levLX and levC-scrB, a Glycoside-hydrolase. We described the first differential gene expression analysis of this strain when cultivated in different carbon sources. We observed that while GTFs are expressed in the presence of most sugars, they are down-regulated in xylose. We ruled out the regulatory effect of CcpA over GTFs and did not find regulatory elements with a direct effect on glucansucrases in the condition assayed. Our findings suggest that only operon levLX is repressed in xylose by LexA and that both fructansucrases operons can be regulated by the VicK/VicR system and PerR. It is essential to further explore the effect of environmental conditions in Ln. mesenteroides bacteria to better understand GTFs regulation and polymer function.
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Affiliation(s)
- Luz Cristina Vallejo-García
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Col. Chamilpa, Cuernavaca 62210, Morelos, Mexico
| | - María Del Carmen Sánchez-Olmos
- Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Col. Chamilpa, Cuernavaca 62210, Morelos, Mexico
| | - Rosa María Gutiérrez-Ríos
- Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Col. Chamilpa, Cuernavaca 62210, Morelos, Mexico
| | - Agustín López Munguía
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Col. Chamilpa, Cuernavaca 62210, Morelos, Mexico
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13
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Kim SA, Lee DH, Ryu BH, Han NS. Strain-specific barcode PCR and quantitative PCR assay for identification and enumeration of kimchi starter, Leuconostoc mesenteroides DRC1506. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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14
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Miyamoto J, Shimizu H, Hisa K, Matsuzaki C, Inuki S, Ando Y, Nishida A, Izumi A, Yamano M, Ushiroda C, Irie J, Katayama T, Ohno H, Itoh H, Yamamoto K, Kimura I. Host metabolic benefits of prebiotic exopolysaccharides produced by Leuconostoc mesenteroides. Gut Microbes 2023; 15:2161271. [PMID: 36604628 PMCID: PMC9828693 DOI: 10.1080/19490976.2022.2161271] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Fermented foods demonstrate remarkable health benefits owing to probiotic bacteria or microproducts produced via bacterial fermentation. Fermented foods are produced by the fermentative action of several lactic acid bacteria, including Leuconostoc mesenteroides; however, the exact mechanism of action of these foods remains unclear. Here, we observed that prebiotics associated with L. mesenteroides-produced exopolysaccharides (EPS) demonstrate substantial host metabolic benefits. L. mesenteroides-produced EPS is an indigestible α-glucan, and intake of the purified form of EPS improved glucose metabolism and energy homeostasis through EPS-derived gut microbial short-chain fatty acids, and changed gut microbial composition. Our findings reveal an important mechanism that accounts for the effects of diet, prebiotics, and probiotics on energy homeostasis and suggests an approach for preventing lifestyle-related diseases by targeting bacterial EPS.
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Affiliation(s)
- Junki Miyamoto
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Japan,AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda-ku, Japan
| | - Hidenori Shimizu
- AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda-ku, Japan,Noster Inc. Kamiueno, Muko-shi, Kyoto, Japan
| | - Keiko Hisa
- AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda-ku, Japan,Noster Inc. Kamiueno, Muko-shi, Kyoto, Japan
| | - Chiaki Matsuzaki
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan
| | - Shinsuke Inuki
- AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda-ku, Japan,Department of Bioorganic Medicinal Chemistry and Chemogenomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yuna Ando
- Laboratory of Molecular Neurobiology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Akari Nishida
- Department of Molecular Neurobiology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Ayano Izumi
- Department of Molecular Neurobiology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Mayu Yamano
- Department of Molecular Neurobiology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Chihiro Ushiroda
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Japan,Department of Clinical Nutrition, Fujita Health University, Aichi, Japan
| | - Junichiro Irie
- AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda-ku, Japan,Department of Endocrinology, Metabolism and Nephrology, School of Medicine, Keio University, Shinjuku-ku, Japan
| | - Takane Katayama
- Laboratory of Molecular Biology and Bioresponse, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Hiroaki Ohno
- AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda-ku, Japan,Department of Bioorganic Medicinal Chemistry and Chemogenomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Hiroshi Itoh
- AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda-ku, Japan,Department of Endocrinology, Metabolism and Nephrology, School of Medicine, Keio University, Shinjuku-ku, Japan
| | - Kenji Yamamoto
- Center for Innovative and Joint Research, Wakayama University, Wakayama, Japan
| | - Ikuo Kimura
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Japan,AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda-ku, Japan,Laboratory of Molecular Neurobiology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan,Department of Molecular Neurobiology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan,CONTACT Ikuo Kimura Laboratory of Molecular Neurobiology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501183-8509, Japan
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15
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Alexandri M, Hübner D, Schneider R, Fröhling A, Venus J. Towards efficient production of highly optically pure d-lactic acid from lignocellulosic hydrolysates using newly isolated lactic acid bacteria. N Biotechnol 2022; 72:1-10. [PMID: 35981701 DOI: 10.1016/j.nbt.2022.08.003] [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: 05/24/2022] [Revised: 08/05/2022] [Accepted: 08/11/2022] [Indexed: 12/14/2022]
Abstract
This study presents the production of D-lactic acid with high enantiomeric purity using lignocellulosic hydrolysates from newly isolated lactic acid bacterial (LAB) strains. Six strains, 4 heterofermentative and 2 homofermentative, were investigated for their ability to grow and produce lactic acid on sugar beet pulp (SBP) hydrolysates, containing a mixture of hexose and pentose sugars. Among the strains tested, three were isolates designated as A250, A257 and A15, all of which belonged to the genus Leuconostoc. Only strain A250 could be reliably identified as Leuconostoc pseudomesenteroides based on cluster analysis of Maldi-ToF spectra. All strains produced D-lactic acid in the presence of SBP hydrolysates, but with varying optical purities. The homofermentative strains achieved higher D-lactic acid optical purities, but without assimilating the pentose sugars. Co-cultivation of the homofermentative strain Lactobacillus coryniformis subsp. torquens DSM 20005 together with the heterofermentative isolate A250 led to the production of 21.7 g/L D-lactic acid with 99.3 % optical purity. This strategy enabled the complete sugar utilization of the substrate. Nanofiltration of the SBP hydrolysate enhanced the enantiomeric purity of the D-lactic acid produced from the isolates A250 and A15 by about 5 %. The highest D-lactic acid concentration (40 g/L) was achieved in fed-batch cultures of A250 isolate with nanofiltered SBP, where optical purity was 99.4 %. The results of this study underline the feasibility of a novel isolate as an efficient D-lactic acid producer using lignocellulosic hydrolysates.
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Affiliation(s)
- Maria Alexandri
- Leibniz Institute for Agricultural Engineering and Bioecomomy (ATB), Max-Eyth Allee 100, Potsdam, Germany; Ionian University, Department of Food Science and Technology, Argostoli 28100, Kefalonia, Greece
| | - Dennis Hübner
- Leibniz Institute for Agricultural Engineering and Bioecomomy (ATB), Max-Eyth Allee 100, Potsdam, Germany
| | - Roland Schneider
- Leibniz Institute for Agricultural Engineering and Bioecomomy (ATB), Max-Eyth Allee 100, Potsdam, Germany
| | - Antje Fröhling
- Leibniz Institute for Agricultural Engineering and Bioecomomy (ATB), Max-Eyth Allee 100, Potsdam, Germany
| | - Joachim Venus
- Leibniz Institute for Agricultural Engineering and Bioecomomy (ATB), Max-Eyth Allee 100, Potsdam, Germany.
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16
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Yang X, Hu W, Xiu Z, Ji Y, Guan Y. Interactions between Leu. mesenteroides and L. plantarum in Chinese northeast sauerkraut. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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17
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Yu L, Chen Y, Duan H, Qiao N, Wang G, Zhao J, Zhai Q, Tian F, Chen W. Latilactobacillus sakei: a candidate probiotic with a key role in food fermentations and health promotion. Crit Rev Food Sci Nutr 2022; 64:978-995. [PMID: 35997270 DOI: 10.1080/10408398.2022.2111402] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Latilactobacillus sakei is used extensively in industrial production and food fermentations. The species is primarily derived from fermented meat and vegetable products and is also found in human feces. Genomics and metabolomics have revealed unique metabolic pathways in L. sakei and molecular mechanisms underlying its competitive advantages in different habitats, which are mostly attributed to its flexible carbohydrate metabolism, cold tolerance, acid and salt tolerance, ability to cope with oxygen changes, and heme uptake. In recent years, probiotic effects of L. sakei and its metabolites have been identified, including the ability to effectively alleviate metabolic syndrome, inflammatory bowel disease, and atopic dermatitis. This review summarizes the genomic and metabolic characteristics of L. sakei and its metabolites and describes their applications, laying a foundation for their expanded use across the food and healthcare industries.
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Affiliation(s)
- Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China
| | - Ying Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hui Duan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
| | - Nanzhen Qiao
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Gang Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
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18
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Zhai Y, Wei C. Open pangenome of Lactococcus lactis generated by a combination of metagenome-assembled genomes and isolate genomes. Front Microbiol 2022; 13:948138. [PMID: 36081802 PMCID: PMC9445621 DOI: 10.3389/fmicb.2022.948138] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022] Open
Abstract
Lactococcus lactis (L. lactis) is a well isolated and cultured lactic acid bacterium, but if utilizing the isolate genomes alone, the genome-based analysis of this taxon would be incomplete, because there are still uncultured strains in some ecological niches. In this study, we recovered 93 high-quality metagenome-assembled genomes (MAGs) of L. lactis from food and human gut metagenomes with a culture-independent method. We then constructed a unified genome catalog of L. lactis by integrating these MAGs with 70 publicly available isolated genomes. Having this comprehensive resource, we assessed the genomic diversity and phylogenetic relationships to further explore the genetic and functional properties of L. lactis. An open pangenome of L. lactis was generated using our genome catalog, consisting of 13,066 genes in total, from which 5,448 genes were not identified in the isolate genomes. The core genome-based phylogenetic analysis showed that L. lactis strains we collected were separated into two main subclades corresponding to two subspecies, with some uncultured phylogenetic lineages discovered. The species disparity was also indicated in PCA analysis based on accessory genes of our pangenome. These various analyzes shed further light on unexpectedly high diversity within the taxon at both genome and gene levels and gave clues about its population structure and evolution. Lactococcus lactis has a long history of safe use in food fermentations and is considered as one of the important probiotic microorganisms. Obtaining the complete genetic information of L. lactis is important to the food and health industry. However, it can naturally inhabit many environments other than dairy products, including drain water and human gut samples. Here we presented an open pan-genome of L. lactis constructed from 163 high-quality genomes obtained from various environments, including MAGs recovered from environmental metagenomes and isolate genomes. This study expanded the genetic information of L. lactis about one third, including more than 5,000 novel genes found in uncultured strains. This more complete gene repertoire of L. lactis is crucial to further understanding the genetic and functional properties. These properties may be harnessed to impart additional value to dairy fermentation or other industries.
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Insights into genome evolution, pan-genome, and phylogenetic implication through mitochondrial genome sequence of Naegleria fowleri species. Sci Rep 2022; 12:13152. [PMID: 35909191 PMCID: PMC9339544 DOI: 10.1038/s41598-022-17006-4] [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: 08/04/2021] [Accepted: 07/19/2022] [Indexed: 11/09/2022] Open
Abstract
In the current study, we have systematically analysed the mitochondrial DNA (mtDNA) sequence of Naegleria fowleri (N. fowleri) isolate AY27, isolated from Karachi, Pakistan. The N. fowleri isolate AY27 has a circular mtDNA (49,541 bp), which harbours 69 genes (46 protein-coding genes, 21 tRNAs and 2 rRNAs). The pan-genome analysis of N. fowleri species showed a Bpan value of 0.137048, which implies that the pan-genome is open. KEGG classified core, accessory and unique gene clusters for human disease, metabolism, environmental information processing, genetic information processing and organismal system. Similarly, COG characterization of protein showed that core and accessory genes are involved in metabolism, information storages and processing, and cellular processes and signaling. The Naegleria species (n = 6) formed a total of 47 gene clusters; 42 single-copy gene clusters and 5 orthologous gene clusters. It was noted that 100% genes of Naegleria species were present in the orthogroups. We identified 44 single nucleotide polymorphisms (SNP) in the N. fowleri isolate AY27 mtDNA using N. fowleri strain V511 as a reference. Whole mtDNA phylogenetic tree analysis showed that N. fowleri isolates AY27 is closely related to N. fowleri (Accession no. JX174181.1). The ANI (Average Nucleotide Identity) values presented a much clear grouping of the Naegleria species compared to the whole mtDNA based phylogenetic analysis. The current study gives a comprehensive understanding of mtDNA architecture as well as a comparison of Naegleria species (N. fowleri and N. gruberi species) at the mitochondrial genome sequence level.
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20
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Lu H, Huang C, Yu K, Liu Z. Effects of mixed inoculation of Leuconostoc citreum and Lactobacillus plantarum on suansun (Sour bamboo shoot) fermentation. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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21
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Pan-Genomic and Transcriptomic Analyses of Marine Pseudoalteromonas agarivorans Hao 2018 Revealed Its Genomic and Metabolic Features. Mar Drugs 2022; 20:md20040248. [PMID: 35447921 PMCID: PMC9027991 DOI: 10.3390/md20040248] [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: 03/05/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 02/06/2023] Open
Abstract
The genomic and carbohydrate metabolic features of Pseudoalteromonas agarivorans Hao 2018 (P. agarivorans Hao 2018) were investigated through pan-genomic and transcriptomic analyses, and key enzyme genes that may encode the process involved in its extracellular polysaccharide synthesis were screened. The pan-genome of the P. agarivorans strains consists of a core-genome containing 2331 genes, an accessory-genome containing 956 genes, and a unique-genome containing 1519 genes. Clusters of Orthologous Groups analyses showed that P. agarivorans harbors strain-specifically diverse metabolisms, probably representing high evolutionary genome changes. The Kyoto Encyclopedia of Genes and Genomes and reconstructed carbohydrate metabolic pathways displayed that P. agarivorans strains can utilize a variety of carbohydrates, such as d-glucose, d-fructose, and d-lactose. Analyses of differentially expressed genes showed that compared with the stationary phase (24 h), strain P. agarivorans Hao 2018 had upregulated expression of genes related to the synthesis of extracellular polysaccharides in the logarithmic growth phase (2 h), and that the expression of these genes affected extracellular polysaccharide transport, nucleotide sugar synthesis, and glycosyltransferase synthesis. This is the first investigation of the genomic and metabolic features of P. agarivorans through pan-genomic and transcriptomic analyses, and these intriguing discoveries provide the possibility to produce novel marine drug lead compounds with high biological activity.
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22
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Hsp60 gene as a reliable target for taxonomical identification and discrimination of Leuconostoc species of dairy origin. Int Dairy J 2022. [DOI: 10.1016/j.idairyj.2021.105227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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23
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A Comparative Genomic and Safety Assessment of Six Lactiplantibacillus plantarum subsp. argentoratensis Strains Isolated from Spontaneously Fermented Greek Wheat Sourdoughs for Potential Biotechnological Application. Int J Mol Sci 2022; 23:ijms23052487. [PMID: 35269627 PMCID: PMC8910486 DOI: 10.3390/ijms23052487] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 02/05/2023] Open
Abstract
The comparative genome analysis of six Lactiplantibacillus plantarum subsp. argentoratensis strains previously isolated from spontaneously fermented Greek wheat sourdoughs is presented. Genomic attributes related to food safety have been studied according to the European Food Safety Authority (EFSA) suggestions for the use of lactic acid bacteria (LAB) in the production of foods. Bioinformatic analysis revealed a complete set of genes for maltose, sucrose, glucose, and fructose fermentation; conversion of fructose to mannitol; folate and riboflavin biosynthesis; acetoin production; conversion of citrate to oxaloacetate; and the ability to produce antimicrobial compounds (plantaricins). Pathogenic factors were absent but some antibiotic resistance genes were detected. CRISPR and cas genes were present as well as various mobile genetic elements (MGEs) such as plasmids, prophages, and insertion sequences. The production of biogenic amines by these strains was not possible due to the absence of key genes in their genome except lysine decarboxylase associated with cadaverine; however, potential degradation of these substances was identified due to the presence of a blue copper oxidase precursor and a multicopper oxidase protein family. Finally, comparative genomics and pan-genome analysis showed genetic differences between the strains (e.g., variable pln locus), and it facilitated the identification of various phenotypic and probiotic-related properties.
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Anastasiou R, Kazou M, Georgalaki M, Aktypis A, Zoumpopoulou G, Tsakalidou E. Omics Approaches to Assess Flavor Development in Cheese. Foods 2022; 11:188. [PMID: 35053920 PMCID: PMC8775153 DOI: 10.3390/foods11020188] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/03/2022] [Accepted: 01/09/2022] [Indexed: 12/27/2022] Open
Abstract
Cheese is characterized by a rich and complex microbiota that plays a vital role during both production and ripening, contributing significantly to the safety, quality, and sensory characteristics of the final product. In this context, it is vital to explore the microbiota composition and understand its dynamics and evolution during cheese manufacturing and ripening. Application of high-throughput DNA sequencing technologies have facilitated the more accurate identification of the cheese microbiome, detailed study of its potential functionality, and its contribution to the development of specific organoleptic properties. These technologies include amplicon sequencing, whole-metagenome shotgun sequencing, metatranscriptomics, and, most recently, metabolomics. In recent years, however, the application of multiple meta-omics approaches along with data integration analysis, which was enabled by advanced computational and bioinformatics tools, paved the way to better comprehension of the cheese ripening process, revealing significant associations between the cheese microbiota and metabolites, as well as their impact on cheese flavor and quality.
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Affiliation(s)
- Rania Anastasiou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece; (M.K.); (M.G.); (A.A.); (G.Z.); (E.T.)
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Comparative Genomic Analysis of Stenotrophomonas maltophilia Strain W18 Reveals Its Adaptative Genomic Features for Degrading Polycyclic Aromatic Hydrocarbons. Microbiol Spectr 2021; 9:e0142021. [PMID: 34817285 PMCID: PMC8612148 DOI: 10.1128/spectrum.01420-21] [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] [Indexed: 11/20/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are hazardous pollutants that are ubiquitous in the environment. Numerous bacteria have evolved to have degrading genes or pathways to degrade PAHs. Stenotrophomonas maltophilia strain W18 was found to be able to degrade PAHs. Including 43 other complete genome sequences of S. maltophilia strains, we performed a comparative genomic analysis of 44 S. maltophilia strains by running OrthoFinder. A KEGG pathway enrichment analysis of environmental and clinical isolates of S. maltophilia revealed that environmental isolates tended to enhance gene functions such as "energy metabolism," "amino acid metabolism," "xenobiotic biodegradation and metabolism," and "folding, sorting, and degradation." The pangenome of the 44 S. maltophilia strains was open, while the core genome was estimated to reach a steady plateau. Based on gene annotations, we inferred that most of the degradation potential came from the core genome of S. maltophilia, while character genes and accessory genes also contributed to the degradation ability of S. maltophilia W18. The genes expression level of core genes, character genes and accessory genes were proved by RT-qPCR experiment, and accessory genes encoding alcohol dehydrogenase were upregulated most compared with genes with similar functions. We performed a credible comparative genomic analysis of S. maltophilia strains. S. maltophilia W18 was set as a model PAH-degrading bacterium of this species in this study, which would provide guidance for understanding and predicting the degradation mechanisms of other PAH-degrading S. maltophilia strains lacking complete genome data or waiting to be determined. IMPORTANCE This study provided the latest comparative genomic analysis on Stenotrophomonas maltophilia strains and focused on analyzing their genomic features that allow them to adapt to natural environments. In this study, we set S. maltophilia W18 as a typical PAH-degrading strain of this species. By discussing the genomic adaptative features of degrading PAH, we can predict genomic adaptative features of other S. maltophilia PAH-degrading strains since the core function of this species is stable. The gene functions of how S. maltophilia environmental isolates are enhanced for adaptation to various natural environments compared with clinical isolates have been revealed. Combined with a pangenome analysis and RT-qPCR results, we have proved that core genes, character genes, and accessory genes are all involved in PAH degradation. Accessory genes encoding alcohol dehydrogenase were upregulated most compared with core and character genes with similar functions, which suggests that PAH metabolization potential might be enhanced by horizontal gene transfer.
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Capacity of soybean carbohydrate metabolism in Leuconostoc mesenteroides, Lactococcus lactis and Streptococcus thermophilus. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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27
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Zeng J, Huang W, Tian X, Hu X, Wu Z. Brewer’s spent grain fermentation improves its soluble sugar and protein as well as enzymatic activities using Bacillus velezensis. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.10.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Effects of the main ingredients of the fermented food, kimchi, on bacterial composition and metabolite profile. Food Res Int 2021; 149:110668. [PMID: 34600670 DOI: 10.1016/j.foodres.2021.110668] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/05/2021] [Accepted: 08/24/2021] [Indexed: 12/26/2022]
Abstract
Kimchi is a fermented food prepared via spontaneous fermentation by lactic acid bacteria originating from raw ingredients. To investigate the effect of these ingredients on food fermentation, four types of food that differed only in their main raw ingredients (kimchi cabbage, green onion, leaf mustard, and young radish) were evaluated. The major microorganisms were Leuconostoc gelidum, Weissella kandleri, and Lactobacillus sakei groups. The distribution of these species depended on the sample type. All three species were primarily distributed in the food prepared from kimchi cabbage and young radish; however, the Lac. sakei group was hardly found in the food prepared using green onion and leaf mustard. Metabolite analysis results showed that the free sugar, organic acid, ethanol, and amino acid profiles differed with the sample type. This study indicates that the main ingredients could be an important factor in determining the composition of the microbial community and the metabolite composition.
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Park JM, Han YM, Oh JY, Lee DY, Choi SH, Hahm KB. Transcriptome profiling implicated in beneficiary actions of kimchi extracts against Helicobacter pylori infection. J Clin Biochem Nutr 2021; 69:171-187. [PMID: 34616109 PMCID: PMC8482382 DOI: 10.3164/jcbn.20-116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/15/2020] [Indexed: 12/12/2022] Open
Abstract
Dietary intervention to prevent Helicobacter pylori (H. pylori)-gastric cancer might be ideal because of no risk of bacterial resistance, safety, and rejuvenating action of atrophic gastritis. We have published data about the potential of fermented kimchi as nutritional approach for H. pylori. Hence recent advances in RNAseq analysis lead us to investigate the transcriptome analysis to explain these beneficiary actions of kimchi. gastric cells were infected with either H. pylori or H. pylori plus kimchi. 943 genes were identified as significantly increased or decreased genes according to H. pylori infection and 68 genes as significantly changed between H. pylori infection and H. pylori plus kimchi (p<0.05). Gene classification and Medline database showed DLL4, FGF18, PTPRN, SLC7A11, CHAC1, FGF21, ASAN, CTH, and CREBRF were identified as significantly increased after H. pylori, but significantly decreased with kimchi and NEO1, CLDN8, KLRG1, and IGFBP1 were identified as significantly decreased after H. pylori, but increased with kimchi. After KEGG and STRING-GO analysis, oxidative stress, ER stress, cell adhesion, and apoptosis genes were up-regulated with H. pylori infection but down-regulated with kimchi, whereas tissue regeneration, cellular anti-oxidative response, and anti-inflammation genes were reversely regulated with kimchi (p<0.01). Conclusively, transcriptomes of H. pylori plus kimchi showed significant biological actions.
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Affiliation(s)
- Jong Min Park
- Daejeon University School of Oriental Medicine, Daejeon, 34520, Korea
| | - Young Min Han
- Seoul Center, Korea Basic Science Institute, Seoul, 02456, Korea
| | - Ji Young Oh
- CJ Food Research Center, Suwon, 16471, Korea
| | | | | | - Ki Baik Hahm
- CHA Cancer Preventive Research Center, CHA Bio Complex, Pangyo, 13497, Korea
- Medpacto Research Institute, Medpacto, Seoul, 06668, Korea
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Genetic Diversity of Leuconostoc mesenteroides Isolates from Traditional Montenegrin Brine Cheese. Microorganisms 2021; 9:microorganisms9081612. [PMID: 34442691 PMCID: PMC8401054 DOI: 10.3390/microorganisms9081612] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 11/17/2022] Open
Abstract
In many dairy products, Leuconostoc spp. is a natural part of non-starter lactic acid bacteria (NSLAB) accounting for flavor development. However, data on the genomic diversity of Leuconostoc spp. isolates obtained from cheese are still scarce. The focus of this study was the genomic characterization of Leuconostoc spp. obtained from different traditional Montenegrin brine cheeses with the aim to explore their diversity and provide genetic information as a basis for the selection of strains for future cheese production. In 2019, sixteen Leuconostoc spp. isolates were obtained from white brine cheeses from nine different producers located in three municipalities in the northern region of Montenegro. All isolates were identified as Ln. mesenteroides. Classical multilocus sequence tying (MLST) and core genome (cg) MLST revealed a high diversity of the Montenegrin Ln. mesenteroides cheese isolates. All isolates carried genes of the bacteriocin biosynthetic gene clusters, eight out of 16 strains carried the citCDEFG operon, 14 carried butA, and all 16 isolates carried alsS and ilv, genes involved in forming important aromas and flavor compounds. Safety evaluation indicated that isolates carried no pathogenic factors and no virulence factors. In conclusion, Ln. mesenteroides isolates from Montenegrin traditional cheeses displayed a high genetic diversity and were unrelated to strains deposited in GenBank.
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Gustaw K, Niedźwiedź I, Rachwał K, Polak-Berecka M. New Insight into Bacterial Interaction with the Matrix of Plant-Based Fermented Foods. Foods 2021; 10:1603. [PMID: 34359473 PMCID: PMC8304663 DOI: 10.3390/foods10071603] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/24/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022] Open
Abstract
Microorganisms have been harnessed to process raw plants into fermented foods. The adaptation to a variety of plant environments has resulted in a nearly inseparable association between the bacterial species and the plant with a characteristic chemical profile. Lactic acid bacteria, which are known for their ability to adapt to nutrient-rich niches, have altered their genomes to dominate specific habitats through gene loss or gain. Molecular biology approaches provide a deep insight into the evolutionary process in many bacteria and their adaptation to colonize the plant matrix. Knowledge of the adaptive characteristics of microorganisms facilitates an efficient use thereof in fermentation to achieve desired final product properties. With their ability to acidify the environment and degrade plant compounds enzymatically, bacteria can modify the textural and organoleptic properties of the product and increase the bioavailability of plant matrix components. This article describes selected microorganisms and their competitive survival and adaptation in fermented fruit and vegetable environments. Beneficial changes in the plant matrix caused by microbial activity and their beneficial potential for human health are discussed as well.
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Affiliation(s)
| | | | - Kamila Rachwał
- Department of Biotechnology, Microbiology and Human Nutrition, Faculty of Food Science and Biotechnology, University of Life Sciences in Lublin, 8 Skromna Street, 20-704 Lublin, Poland; (K.G.); (I.N.); (M.P.-B.)
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ODFM, an omics data resource from microorganisms associated with fermented foods. Sci Data 2021; 8:113. [PMID: 33879798 PMCID: PMC8058077 DOI: 10.1038/s41597-021-00895-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 03/23/2021] [Indexed: 11/08/2022] Open
Abstract
ODFM is a data management system that integrates comprehensive omics information for microorganisms associated with various fermented foods, additive ingredients, and seasonings (e.g. kimchi, Korean fermented vegetables, fermented seafood, solar salt, soybean paste, vinegar, beer, cheese, sake, and yogurt). The ODFM archives genome, metagenome, metataxonome, and (meta)transcriptome sequences of fermented food-associated bacteria, archaea, eukaryotic microorganisms, and viruses; 131 bacterial, 38 archaeal, and 28 eukaryotic genomes are now available to users. The ODFM provides both the Basic Local Alignment Search Tool search-based local alignment function as well as average nucleotide identity-based genetic relatedness measurement, enabling gene diversity and taxonomic analyses of an input query against the database. Genome sequences and annotation results of microorganisms are directly downloadable, and the microbial strains registered in the archive library will be available from our culture collection of fermented food-associated microorganisms. The ODFM is a comprehensive database that covers the genomes of an entire microbiome within a specific food ecosystem, providing basic information to evaluate microbial isolates as candidate fermentation starters for fermented food production.
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33
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García Arteaga V, Leffler S, Muranyi I, Eisner P, Schweiggert-Weisz U. Sensory profile, functional properties and molecular weight distribution of fermented pea protein isolate. Curr Res Food Sci 2020; 4:1-10. [PMID: 33385169 PMCID: PMC7771043 DOI: 10.1016/j.crfs.2020.12.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 12/05/2020] [Accepted: 12/09/2020] [Indexed: 11/30/2022] Open
Abstract
Pea protein isolate (PPI, from Pisum sativum L.) was fermented with six different lactic acid bacteria strains for 24 h and 48 h. The fermented samples were analyzed regarding their retronasal aroma and taste, their protein solubility, emulsifying and foaming capacity. Changes in the molecular weight distribution were analyzed to monitor potential effects of fermentation on the main allergenic protein fractions of PPI. After 24-h fermentation, PPI's characteristic aroma attributes and bitter taste decreased for all fermented PPI. However, after 48-h fermentation, cheesy aroma, and acid and salty tastes were increased. The PPI fermented with L. plantarum showed the most neutral taste and the panel's highest preference; instead, fermentation with L. fermentum led to a fecal aroma and was the least preferred. The protein solubility and emulsifying capacity decreased after PPI fermentation, while foaming capacity remained constant in comparison to the untreated PPI. The electrophoretic results showed a reduction in the intensity of the allergenic protein fractions; however, these changes might be attributed to the reduced protein solubility rather than to a high proteolytic effect of the strains. Fermentation of PPI for 24 h and 48 h might not be a suitable method for the production of highly functional pea proteins. Further modification methods have to be investigated in the future.
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Affiliation(s)
- Verónica García Arteaga
- Fraunhofer Institute for Process Engineering and Packaging IVV, Germany
- Center of Life and Food Sciences Weihenstephan, Technical University of Munich, Germany
| | - Sophia Leffler
- Fraunhofer Institute for Process Engineering and Packaging IVV, Germany
| | - Isabel Muranyi
- Fraunhofer Institute for Process Engineering and Packaging IVV, Germany
| | - Peter Eisner
- Fraunhofer Institute for Process Engineering and Packaging IVV, Germany
- ZIEL - Institute for Food & Health, Technical University of Munich, Germany
- Steinbeis-Hochschule, School of Technology and Engineering, Germany
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34
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Kaushal G, Singh SP. Comparative genome analysis provides shreds of molecular evidence for reclassification of Leuconostoc mesenteroides MTCC 10508 as a strain of Leu. suionicum. Genomics 2020; 112:4023-4031. [DOI: 10.1016/j.ygeno.2020.06.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 06/01/2020] [Accepted: 06/22/2020] [Indexed: 01/01/2023]
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35
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Effects of combining two lactic acid bacteria as a starter culture on model kimchi fermentation. Food Res Int 2020; 136:109591. [DOI: 10.1016/j.foodres.2020.109591] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/26/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023]
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36
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Unraveling microbial fermentation features in kimchi: from classical to meta-omics approaches. Appl Microbiol Biotechnol 2020; 104:7731-7744. [PMID: 32749526 DOI: 10.1007/s00253-020-10804-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/22/2020] [Accepted: 07/30/2020] [Indexed: 12/31/2022]
Abstract
Kimchi is a traditional Korean fermented food prepared via spontaneous fermentation by various microorganisms originating from vegetables such as kimchi cabbage, radishes, and garlic. Recent advances in meta-omics approaches that integrate metataxonomics, metagenomics, metatranscriptomics, and metabolomics have contributed to explaining and understanding food fermentation processes. Kimchi microbial communities are composed of majorly lactic acid bacteria such as Leuconostoc, Lactobacillus, and Weissella and fewer eukaryotic microorganisms and kimchi fermentation are accomplished by complex microbial metabolisms to produce diverse metabolites such as lactate, acetate, CO2, ethanol, mannitol, amino acids, formate, malate, diacetyl, acetoin, and 2, 3-butanediol, which determine taste, quality, health benefit, and safety of fermented kimchi products. Therefore, in the future, kimchi researches should be systematically performed using the meta-omics approaches to understand complex microbial metabolisms during kimchi fermentation. KEY POINTS: • Spontaneous fermentation by raw material microbes gives kimchi its unique flavor. • The kimchi microbiome is altered by environmental factors and raw materials. • Through the multi-omics approaches, it is possible to accurately analyze the diversity and metabolic characteristics of kimchi microbiome and discover potential functionalities.
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37
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Mun SY, Chang HC. Characterization of Weissella koreensis SK Isolated from Kimchi Fermented at Low Temperature (around 0 °C) Based on Complete Genome Sequence and Corresponding Phenotype. Microorganisms 2020; 8:E1147. [PMID: 32751267 PMCID: PMC7464874 DOI: 10.3390/microorganisms8081147] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/21/2020] [Accepted: 07/28/2020] [Indexed: 01/12/2023] Open
Abstract
This study identified lactic acid bacteria (LAB) that play a major role in kimchi fermented at low temperature, and investigated the safety and functionality of the LAB via biologic and genomic analyses for its potential use as a starter culture or probiotic. Fifty LAB were isolated from 45 kimchi samples fermented at -1.5~0 °C for 2~3 months. Weissella koreensis strains were determined as the dominant LAB in all kimchi samples. One strain, W. koreensis SK, was selected and its phenotypic and genomic features characterized. The complete genome of W. koreensis SK contains one circular chromosome and plasmid. W. koreensis SK grew well under mesophilic and psychrophilic conditions. W. koreensis SK was found to ferment several carbohydrates and utilize an alternative carbon source, the amino acid arginine, to obtain energy. Supplementation with arginine improved cell growth and resulted in high production of ornithine. The arginine deiminase pathway of W. koreensis SK was encoded in a cluster of four genes (arcA-arcB-arcD-arcC). No virulence traits were identified in the genomic and phenotypic analyses. The results indicate that W. koreensis SK may be a promising starter culture for fermented vegetables or fruits at low temperature as well as a probiotic candidate.
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Affiliation(s)
| | - Hae Choon Chang
- Department of Food and Nutrition, Kimchi Research Center, Chosun University, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Korea;
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38
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Kim MJ, Lee HW, Kim JY, Kang SE, Roh SW, Hong SW, Yoo SR, Kim TW. Impact of fermentation conditions on the diversity of white colony-forming yeast and analysis of metabolite changes by white colony-forming yeast in kimchi. Food Res Int 2020; 136:109315. [PMID: 32846523 DOI: 10.1016/j.foodres.2020.109315] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/17/2020] [Accepted: 05/13/2020] [Indexed: 12/28/2022]
Abstract
The presence of white colony-forming yeast (WCFY) on kimchi surfaces indicates a reduction in kimchi quality. This study aimed to investigate the effect of different fermentation temperatures (4, 10, and 20 °C) and packaging conditions (open or closed) on WCFY diversity, and the changes of metabolite by the difference of WCFY diversity. Community analysis using high-throughput DNA sequencing revealed that Kazachstania servazzii and K. barnettii were most prevalent in kimchi fermented under closed packaging condition at 4, 10, and 20 °C. In open packaging condition, four species of Candida sake, K. servazzii, K. barnettii, and Tausonia pullulans were the predominant yeast species at 4 °C, and four species of C. sake, K. servazzii, K. barnettii, and Debaryomyces hancenii were predominantly detected at 10 °C. The diversity of the WCFY community was higher under the open rather than the closed packaging condition. However, at all fermentation temperatures, non-volatile metabolite production by the different WCFY communities did not significantly differ between open and closed packaging conditions, whereas glycerol levels in kimchi samples harboring WCFY increased relative to the control (0 day). These results indicate that fermentation temperature and air exposure can alter WCFY diversity on kimchi surface, however, non-volatile metabolite profiles in kimchi soup are not significantly affected by the difference of WCFY diversity caused by packaging conditions. This study furthers the current understanding of the growth of undesirable WCFY in kimchi.
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Affiliation(s)
- Mi-Ju Kim
- Research and Development of Division, World Institute of Kimchi, Gwangju 61755 Republic of Korea
| | - Hae-Won Lee
- Research and Development of Division, World Institute of Kimchi, Gwangju 61755 Republic of Korea
| | - Joon Yong Kim
- Research and Development of Division, World Institute of Kimchi, Gwangju 61755 Republic of Korea
| | - Seong Eun Kang
- Research and Development of Division, World Institute of Kimchi, Gwangju 61755 Republic of Korea
| | - Seong Woon Roh
- Research and Development of Division, World Institute of Kimchi, Gwangju 61755 Republic of Korea
| | - Sung Wook Hong
- Research and Development of Division, World Institute of Kimchi, Gwangju 61755 Republic of Korea
| | - Seung Ran Yoo
- Research and Development of Division, World Institute of Kimchi, Gwangju 61755 Republic of Korea
| | - Tae-Woon Kim
- Research and Development of Division, World Institute of Kimchi, Gwangju 61755 Republic of Korea.
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Ricciardi A, Storti LV, Zotta T, Felis GE, Parente E. Analysis of rpoB polymorphism and PCR-based approaches for the identification of Leuconostoc mesenteroides at the species and subspecies level. Int J Food Microbiol 2020; 318:108474. [PMID: 31841785 DOI: 10.1016/j.ijfoodmicro.2019.108474] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 11/21/2019] [Accepted: 12/07/2019] [Indexed: 10/25/2022]
Abstract
Leuconostoc mesenteroides includes the subsp. cremoris, subsp. dextranicum, subsp. mesenteroides and subsp. jonggajibkimchii, but the identification at the subspecies level using current phenotypic and/or genotypic methods is still difficult. In this study, a polyphasic approach based on the analysis of rpoB gene polymorphism, Multiplex-PCR and phenotypic tests was optimised and used to identify a collection of Leuc. mesenteroides strains at the species and subspecies levels. The annotation of published Leuc. mesenteroides genomes was also revised. A polymorphic region of rpoB gene was effective in separating Leuc. mesenteroides strains at the species (rpoB-species-specific-PCR) and subspecies (phylogenetic comparison) levels. Multiplex-PCR discriminated the subsp. mesenteroides from subsp. cremoris, but strains of uncertain attribution were found among subsp. dextranicum and subsp. jonggajibkimchii. Most of phenotypic features were not suitable for subspecies discrimination. Our assays may provide a rapid and reliable identification of subsp. mesenteroides and subsp. cremoris strains in fermented foods. The discrimination of subsp. dextranicum and subsp. jonggajibkimchii suffered from several limitations (e.g. low number of available strains and genomes, phenotypic profile close to subsp. mesenteroides, discrepancy between genotypic and phenotypic traits) and further investigations are needed to clarify their delineation and taxonomical position.
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Affiliation(s)
- Annamaria Ricciardi
- Scuola di Scienze Agrarie, Alimentari, Forestali ed Ambientali (SAFE), Università degli Studi della Basilicata, 85100 Potenza, Italy
| | - Livia V Storti
- Scuola di Scienze Agrarie, Alimentari, Forestali ed Ambientali (SAFE), Università degli Studi della Basilicata, 85100 Potenza, Italy
| | - Teresa Zotta
- Istituto di Scienze dell'Alimentazione-CNR, 83100 Avellino, Italy.
| | - Giovanna E Felis
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37100 Verona, Italy
| | - Eugenio Parente
- Dipartimento di Scienze, Università degli Studi della Basilicata, 85100 Potenza, Italy
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Abstract
Numerous traditional low-alcohol fermented beverages produced from fruit or vegetables are described around the world. Fruit and vegetables and lactic fermented products both present nutritional benefits, which give reasons for the recent expansion of non-dairy lactic fermented juices on the market. In addition, fruit and vegetable juices are new carriers for probiotic bacteria. Specific phenotypic traits of lactic acid bacteria (LAB) are required so that LAB can effectively grow in fruit or vegetable juices, increase their safety and improve their sensory and nutritional quality. From the diversity of microbiota of spontaneous fermentations, autochthonous starters can be selected, and their higher performance than allochthonous LAB was demonstrated. Achieving long-term storage and constant high quality of these beverages requires additional processing steps, such as heat treatment. Alternatives to conventional treatments are investigated as they can better preserve nutritional properties, extract bioactive compounds and promote the growth and metabolism of LAB. Specific processing approaches were shown to increase probiotic viability of fruit and vegetable juices. More knowledge on the metabolic activity of lactic acid bacterium consortium in fruit or vegetable juices has become a bottleneck for the understanding and the prediction of changes in bioactive compounds for functional beverages development. Hopefully, the recent developments of metabolomics and methods to describe enzymatic machinery can result in the reconstruction of fermentative pathways.
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Tracking of Intentionally Inoculated Lactic Acid Bacteria Strains in Yogurt and Probiotic Powder. Microorganisms 2019; 8:microorganisms8010005. [PMID: 31861385 PMCID: PMC7022703 DOI: 10.3390/microorganisms8010005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 12/20/2022] Open
Abstract
The present work aimed at tracking intentionally inoculated lactic acid bacteria (LAB) strains in yogurt and probiotic powder. Leuconostoc (Leu.) mesenteroides (11251), Lactobacillus (L.) brevis (B151), and Lactobacillus plantarum (LB41K) strains were tracked in yogurt, and L. plantarum (LB41P) was tracked in a commercial probiotic powder. The yogurt was intentionally inoculated with the selected bacterial strains. Two types of yogurt with known and unknown bacterial pools were utilized. The standard 16S rRNA gene sequencing was used to evaluate the initial screening. The molecular typing tools, random amplified polymorphic DNA (RAPD), repetitive element palindromic PCR (rep-PCR), and comparative gene sequence analysis of selected housekeeping loci were used to track the inoculated dubious strains. Out of 30 random selections for each inoculation, the developed method identified seven (11251), nine (B151), and five (LB41K) colonies in the yogurt. The validation was performed by identifying 7 colonies (LB41P) out of 30 in the probiotic powder. The DNA banding profiles and the gene sequence alignments led to the identification of the correct inoculated strains. Overall, the study summarizes the use of molecular tools to identify the deliberately inoculated LAB strains. In conclusion, the proposed polyphasic approach effectively tracked the intentionally inoculated strains: Leu. mesenteroides, L. brevis, and L. plantarum (LB41K) in yogurt and L. plantarum (LB41P) in probiotic powder. The study demonstrates how to track industrially relevant misused LAB strains in marketable food products.
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Investigation of genomic characteristics and carbohydrates' metabolic activity of Lactococcus lactis subsp. lactis during ripening of a Swiss-type cheese. Food Microbiol 2019; 87:103392. [PMID: 31948633 DOI: 10.1016/j.fm.2019.103392] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 10/04/2019] [Accepted: 11/20/2019] [Indexed: 01/08/2023]
Abstract
Genetic diversity and metabolic properties of Lactococcus lactis subsp. lactis were explored using phylogenetic, pan-genomic and metatranscriptomic analysis. The genomes, used in the current study, were available and downloaded from the GenBank which were primarily related with microorganisms isolated from dairy products and secondarily from other foodstuffs. To study the genetic diversity of the microorganism, various bioinformatics tools were employed such as average nucleotide identity, digital DNA-DNA hybridization, phylogenetic analysis, clusters of orthologous groups analysis, KEGG orthology analysis and pan-genomic analysis. The results showed that Lc. lactis subsp. lactis strains cannot be sufficiently separated into phylogenetic lineages based on the 16S rRNA gene sequences and core genome-based phylogenetic analysis was more appropriate. Pan-genomic analysis of the strains indicated that the core, accessory and unique genome comprised of 1036, 3146 and 1296 genes, respectively. Considering the results of pan-genomic and KEGG orthology analyses, the metabolic network of Lc. lactis subsp. lactis was rebuild regarding its carbohydrates' metabolic capabilities. Based on the metatranscriptomic data during the ripening of the Swiss-type Maasdam cheese at 20 °C and 5 °C, it was shown that the microorganism performed mixed acid fermentation producing lactate, formate, acetate, ethanol and 2,3-butanediol. Mixed acid fermentation was more pronounced at higher ripening temperatures. At lower ripening temperatures, the genes involved in mixed acid fermentation were repressed while lactate production remained unaffected resembling to a homolactic fermentation. Comparative genomics and metatranscriptomic analysis are powerful tools to gain knowledge on the genomic diversity of the lactic acid bacteria used as starter cultures as well as on the metabolic activities occurring in fermented dairy products.
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Genomic and metabolic features of Lactobacillus sakei as revealed by its pan-genome and the metatranscriptome of kimchi fermentation. Food Microbiol 2019; 86:103341. [PMID: 31703875 DOI: 10.1016/j.fm.2019.103341] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/08/2019] [Accepted: 09/20/2019] [Indexed: 12/20/2022]
Abstract
The genomic and metabolic features of Lactobacillus sakei were investigated using its pan-genome and by analyzing the metatranscriptome of kimchi fermentation. In the genome-based relatedness analysis, the strains were divided into the Lb. sakei ssp. sakei and Lb. sakei ssp. carnosus lineage groups. Genomic and metabolic pathway analysis revealed that all Lb. sakei strains have the capability of producing d/l-lactate, ethanol, acetate, CO2, formate, l-malate, diacetyl, acetoin, and 2,3-butanediol from d-glucose, d-fructose, d-galactose, sucrose, d-lactose, l-arabinose, cellobiose, d-mannose, d-gluconate, and d-ribose through homolactic and heterolactic fermentation, whereas their capability of d-maltose, d-xylose, l-xylulose, d-galacturonate, and d-glucuronate metabolism is strain-specific. All strains carry genes for the biosynthesis of folate and thiamine, whereas genes for biogenic amine and toxin production, hemolysis, and antibiotic resistance were not identified. The metatranscriptomic analysis showed that the expression of Lb. sakei transcripts involved in carbohydrate metabolism increased as kimchi fermentation progressed, suggesting that Lb. sakei is more competitive during late fermentation stage. Homolactic fermentation pathway was highly expressed and generally constant during kimchi fermentation, whereas expression of heterolactic fermentation pathway increased gradually as fermentation progressed. l-Lactate dehydrogenase was more highly expressed than d-lactate dehydrogenase, suggesting that l-lactate is the major lactate metabolized by Lb. sakei.
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Complete Genome Sequence of Leuconostoc kimchii Strain NKJ218, Isolated from Homemade Kimchi. Microbiol Resour Announc 2019; 8:8/27/e00367-19. [PMID: 31270190 PMCID: PMC6606904 DOI: 10.1128/mra.00367-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Leuconostoc kimchii strain NKJ218 was isolated from homemade kimchi in South Korea. The whole genome was sequenced using the PacBio RS II and Illumina NovoSeq 6000 platforms. Here, we report a genome sequence of strain NKJ218, which consists of a 1.9-Mbp chromosome and three plasmid contigs. A total of 2,005 coding sequences (CDS) were predicted, including 1,881 protein-coding sequences.
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Park SC, Lee K, Kim YO, Won S, Chun J. Large-Scale Genomics Reveals the Genetic Characteristics of Seven Species and Importance of Phylogenetic Distance for Estimating Pan-Genome Size. Front Microbiol 2019; 10:834. [PMID: 31068915 PMCID: PMC6491781 DOI: 10.3389/fmicb.2019.00834] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 04/01/2019] [Indexed: 11/13/2022] Open
Abstract
For more than a decade, pan-genome analysis has been applied as an effective method for explaining the genetic contents variation of prokaryotic species. However, genomic characteristics and detailed structures of gene pools have not been fully clarified, because most studies have used a small number of genomes. Here, we constructed pan-genomes of seven species in order to elucidate variations in the genetic contents of >27,000 genomes belonging to Streptococcus pneumoniae, Staphylococcus aureus subsp. aureus, Salmonella enterica subsp. enterica, Escherichia coli and Shigella spp., Mycobacterium tuberculosis complex, Pseudomonas aeruginosa, and Acinetobacter baumannii. This work showed the pan-genomes of all seven species has open property. Additionally, systematic evaluation of the characteristics of their pan-genome revealed that phylogenetic distance provided valuable information for estimating the parameters for pan-genome size among several models including Heaps' law. Our results provide a better understanding of the species and a solution to minimize sampling biases associated with genome-sequencing preferences for pathogenic strains.
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Affiliation(s)
- Sang-Cheol Park
- Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Kihyun Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
| | - Yeong Ouk Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Sungho Won
- Institute of Health and Environment, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea.,Department of Public Health Sciences, Seoul National University, Seoul, South Korea
| | - Jongsik Chun
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea.,Department of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
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Chun BH, Han DM, Kim KH, Jeong SE, Park D, Jeon CO. Genomic and metabolic features of Tetragenococcus halophilus as revealed by pan-genome and transcriptome analyses. Food Microbiol 2019; 83:36-47. [PMID: 31202417 DOI: 10.1016/j.fm.2019.04.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/14/2019] [Accepted: 04/20/2019] [Indexed: 01/10/2023]
Abstract
The genomic and metabolic diversity and features of Tetragenococcus halophilus, a moderately halophilic lactic acid bacterium, were investigated by pan-genome, transcriptome, and metabolite analyses. Phylogenetic analyses based on the 16S rRNA gene and genome sequences of 15 T. halophilus strains revealed their phylogenetic distinctness from other Tetragenococcus species. Pan-genome analysis of the T. halophilus strains showed that their carbohydrate metabolic capabilities were diverse and strain dependent. Aside from one histidine decarboxylase gene in one strain, no decarboxylase gene associated with biogenic amine production was identified from the genomes. However, T. halophilus DSM 20339T produced tyramine without a biogenic amine-producing decarboxylase gene, suggesting the presence of an unidentified tyramine-producing gene. Our reconstruction of the metabolic pathways of these strains showed that T. halophilus harbors a facultative lactic acid fermentation pathway to produce l-lactate, ethanol, acetate, and CO2 from various carbohydrates. The transcriptomic analysis of strain DSM 20339T suggested that T. halophilus may produce more acetate via the heterolactic pathway (including d-ribose metabolism) at high salt conditions. Although genes associated with the metabolism of glycine betaine, proline, glutamate, glutamine, choline, and citrulline were identified from the T. halophilus genomes, the transcriptome and metabolite analyses suggested that glycine betaine was the main compatible solute responding to high salt concentration and that citrulline may play an important role in the coping mechanism against high salinity-induced osmotic stresses. Our results will provide a better understanding of the genome and metabolic features of T. halophilus, which has implications for the food fermentation industry.
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Affiliation(s)
- Byung Hee Chun
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Dong Min Han
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Sang Eun Jeong
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Dongbin Park
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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Kim JW, Choi BH, Jung JH, Yuan X, Kim JM, Lee PC. Genome resequencing and analysis of d-lactic acid fermentation ability of Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Chun BH, Kim KH, Jeong SE, Jeon CO. Genomic and metabolic features of the Bacillus amyloliquefaciens group- B. amyloliquefaciens, B. velezensis, and B. siamensis- revealed by pan-genome analysis. Food Microbiol 2018; 77:146-157. [PMID: 30297045 DOI: 10.1016/j.fm.2018.09.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 07/31/2018] [Accepted: 09/01/2018] [Indexed: 10/28/2022]
Abstract
The genomic and metabolic features of the Bacillus amyloliquefaciens group comprising B. amyloliquefaciens, B. velezensis, and B. siamensis were investigated through a pan-genome analysis combined with an experimental verification of some of the functions identified. All B. amyloliquefaciens group genomes were retrieved from GenBank and their phylogenetic relatedness was subsequently investigated. Genome comparisons of B. amyloliquefaciens, B. siamensis, and B. velezensis showed that their genomic and metabolic features were similar; however species-specific features were also identified. Energy metabolism-related genes are more enriched in B. amyloliquefaciens, whereas secondary metabolite biosynthesis-related genes are enriched in B. velezensis. Compared to B. amyloliquefaciens and B. siamensis, B. velezensis harbors more genes in its core-genome which are involved in the biosynthesis of antimicrobial compounds, as well as genes involved in d-galacturonate and d-fructuronate metabolism. B. amyloliquefaciens, B. siamensis, and B. velezensis all harbor a xanthine oxidase gene cluster (xoABCDE) in their core-genomes that is involved in metabolizing xanthine and uric acid to glycine and oxalureate. A reconstruction of B. amyloliquefaciens group metabolic pathways using their individual pan-genomes revealed that the B. amyloliquefaciens group strains have the ability to metabolize diverse carbon sources aerobically, or anaerobically, and can produce various metabolites such as lactate, ethanol, acetate, CO2, xylitol, diacetyl, acetoin, and 2,3-butanediol. This study therefore provides insights into the genomic and metabolic features of the B. amyloliquefaciens group.
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Affiliation(s)
- Byung Hee Chun
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Sang Eun Jeong
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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Jia B, Pu ZJ, Tang K, Jia X, Kim KH, Liu X, Jeon CO. Catalytic, Computational, and Evolutionary Analysis of the d-Lactate Dehydrogenases Responsible for d-Lactic Acid Production in Lactic Acid Bacteria. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:8371-8381. [PMID: 30008205 DOI: 10.1021/acs.jafc.8b02454] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
d-Lactate dehydrogenase (d-LDH) catalyzes the reversible reaction pyruvate + NADH + H+ ↔ lactate + NAD+, which is a principal step in the production of d-lactate in lactic acid bacteria. In this study, we identified and characterized the major d-LDH (d-LDH1) from three d-LDHs in Leuconostoc mesenteroides, which has been extensively used in food processing. A molecular simulation study of d-LDH1 showed that the conformation changes during substrate binding. During catalysis, Tyr101 and Arg235 bind the substrates by hydrogen bonds and His296 acts as a general acid/base for proton transfer. These residues are also highly conserved and have coevolved. Point mutations proved that the substrate binding sites and catalytic site are crucial for enzyme activity. Network and phylogenetic analyses indicated that d-LDH1 and the homologues are widely distributed but are most abundant in bacteria and fungi. This study expands the understanding of the functions, catalytic mechanism, and evolution of d-LDH.
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Affiliation(s)
- Baolei Jia
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering , Qilu University of Technology (Shandong Academy of Sciences) , Jinan 250353 , China
- Department of Life Science , Chung-Ang University , Seoul 06974 , Republic of Korea
| | - Zhong Ji Pu
- School of Life Science and Biotechnology , Dalian University of Technology , Dalian 116024 , China
| | - Ke Tang
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering , Qilu University of Technology (Shandong Academy of Sciences) , Jinan 250353 , China
| | - Xiaomeng Jia
- Department of Life Science , Chung-Ang University , Seoul 06974 , Republic of Korea
| | - Kyung Hyun Kim
- Department of Life Science , Chung-Ang University , Seoul 06974 , Republic of Korea
| | - Xinli Liu
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering , Qilu University of Technology (Shandong Academy of Sciences) , Jinan 250353 , China
| | - Che Ok Jeon
- Department of Life Science , Chung-Ang University , Seoul 06974 , Republic of Korea
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Kim KH, Jia X, Jia B, Jeon CO. Identification and Characterization of l-Malate Dehydrogenases and the l-Lactate-Biosynthetic Pathway in Leuconostoc mesenteroides ATCC 8293. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:8086-8093. [PMID: 29998731 DOI: 10.1021/acs.jafc.8b02649] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
One putative l-lactate dehydrogenase gene (l- ldh) and three putative d- ldh genes from Leuconostoc mesenteroides ATCC 8293 were overexpressed, and their enzymatic properties were investigated. Only one gene showed d-LDH activity, catalyzing pyruvate and d-lactate interconversion, whereas the other genes displayed l- and d-malate dehydrogenase (MDH) activity, catalyzing oxaloacetate and l- and d-malate interconversion, suggesting that strain ATCC 8293 may not harbor an l- ldh gene. Putative phosphoenolpyruvate carboxylase (PEPC)- and malolactic enzyme (MLE)-encoding genes were identified from strain ATCC 8293, and sequence analysis showed that they could exhibit PEPC and MLE activities, respectively. l-Lactate production and transcriptional expression of the mle gene in this strain were highly increased in the presence of l-malate. We propose that in strain ATCC 8293, which lacks an l- ldh gene, l-lactate is produced through sequential enzymatic conversions from phosphoenolpyruvate to oxaloacetate, then l-malate, and finally l-lactate by PEPC, l-MDH, and MLE, respectively.
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Affiliation(s)
- Kyung Hyun Kim
- Department of Life Science , Chung-Ang University , 84, HeukSeok-Ro , Seoul 06974 , Republic of Korea
| | - Xiaomeng Jia
- Department of Life Science , Chung-Ang University , 84, HeukSeok-Ro , Seoul 06974 , Republic of Korea
| | - Baolei Jia
- Department of Life Science , Chung-Ang University , 84, HeukSeok-Ro , Seoul 06974 , Republic of Korea
| | - Che Ok Jeon
- Department of Life Science , Chung-Ang University , 84, HeukSeok-Ro , Seoul 06974 , Republic of Korea
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