1
|
Sawabe T, Umeki Y, Natarajan RK, Jiang C, Thompson F, Mino S. Unexpected Diversity in Gene Clusters Encoding Formate Hydrogenlyase Complex Machinery in Vibrionaceae Correlated to Fermentative Hydrogen Production. Curr Microbiol 2025; 82:208. [PMID: 40131504 DOI: 10.1007/s00284-025-04176-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2024] [Accepted: 03/04/2025] [Indexed: 03/27/2025]
Abstract
An entire Hyf-type formate hydrogenlyase comple (Hyf-FHL) gene cluster was first discovered in a marine Vibrio species, Vibrio tritonius isolated from the digestive tract of the sea hare Aplysia kurodai [1]. The bacterium is also the first marine bacterium in which hydrogen production ability exceeds that of Escherichia coli under saline conditions [Sawabe et al. in Front Microbiol 4:414, 2013;Matsumura et al. in Int J Hydrog Energy 39:7270-7277, 2014;]. However, we were still unable to answer the evolutionary question as to why only minor groups of vibrios could maintain the FHL gene clusters and hydrogen (gas) production ability. Here, we set up comparative genomics and fermentative hydrogen production profiling using all 16 currently known Vibrionaceae species, which maintain FHL gene clusters and/or gas production, including 12 Vibrio and 4 Photobacterium species. Whole-genome comparison using complete genome sequences revealed unexpected diversity of FHL gene clusters, at least, with two new types of FHL gene clusters. Additional fermentative hydrogen profiling and structure modeling of FHLs showed formate detoxification as a part of formate and pH homeostasis could be one of the selective pressures in the evolution of FHL gene clusters responsible for high hydrogen production in vibrios.
Collapse
Affiliation(s)
- Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan.
| | - Yuito Umeki
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Ramesh Kumar Natarajan
- National Institute for Interdisciplinary Science and Technology (CSIR), Thiruvananthapuram, Kerala, India
| | - Chunqi Jiang
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Fabiano Thompson
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan.
| |
Collapse
|
2
|
Bae CI, Gwak YS, Eom SJ, Lee S, Kim MJ. Effects of storage temperature on the diversity of white colony-forming yeast and correlations between bacterial and yeast communities in salted kimchi cabbage. Food Sci Biotechnol 2025; 34:1001-1014. [PMID: 39974852 PMCID: PMC11833002 DOI: 10.1007/s10068-024-01739-1] [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: 07/21/2024] [Revised: 10/06/2024] [Accepted: 10/11/2024] [Indexed: 02/21/2025] Open
Abstract
In this study, we investigated the impact of different temperatures (10 °C, 4 °C, and - 1 °C) on salted kimchi cabbage. The diversity of white colony forming yeast (WCFY) on kimchi cabbage was assessed. The culture-dependent method revealed Candida as the predominant yeast, whereas the culture-independent method showed variations in the WCFY community based on storage temperatures. Meanwhile, the bacterial communities of salted kimchi cabbage were analyzed at different temperatures, with Latilactobacillus being the most abundant after WCFY observation. Other major LAB involved in kimchi fermentation were also observed at all temperatures. Additionally, the yeast communities revealed that Kazachstania, Candida, and Mrakia showed the highest relative abundance at 10 °C, 4 °C, and - 1 °C, respectively, as the storage period increased. Furthermore, correlation analysis showed that Candida had significant negative correlations between Levilactobacillus, Lactiplantibacillus, and Latilactobacillus. These findings suggest that the microbial community at different storage temperatures can affect the quality and safety of kimchi cabbage. Supplementary Information The online version contains supplementary material available at 10.1007/s10068-024-01739-1.
Collapse
Affiliation(s)
- Chan-Il Bae
- Institute of Life Sciences & Resources and Department of Food Science & Biotechnology, Kyung Hee University, Yongin, 17104 Republic of Korea
| | - Yoon-Soo Gwak
- Institute of Life Sciences & Resources and Department of Food Science & Biotechnology, Kyung Hee University, Yongin, 17104 Republic of Korea
| | - Su-Jeong Eom
- Institute of Life Sciences & Resources and Department of Food Science & Biotechnology, Kyung Hee University, Yongin, 17104 Republic of Korea
| | - Shinyoung Lee
- Institute of Life Sciences & Resources and Department of Food Science & Biotechnology, Kyung Hee University, Yongin, 17104 Republic of Korea
| | - Mi-Ju Kim
- Institute of Life Sciences & Resources and Department of Food Science & Biotechnology, Kyung Hee University, Yongin, 17104 Republic of Korea
| |
Collapse
|
3
|
Xiong S, Xu X, Zhang L, Du T, Huang T, Huang J, Ren H, Xiong T, Xie M. Integrated metatranscriptomics and metabolomics reveal microbial succession and flavor formation mechanisms during the spontaneous fermentation of Laotan Suancai. Food Res Int 2024; 177:113865. [PMID: 38225131 DOI: 10.1016/j.foodres.2023.113865] [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: 09/23/2023] [Revised: 12/04/2023] [Accepted: 12/14/2023] [Indexed: 01/17/2024]
Abstract
Laotan Suancai, a Chinese traditional fermented vegetable, possesses a unique flavor that depends on the fermentative microbiota. However, the drivers of microbial succession and the correlation between flavor and active microbiota remain unclear. A total of 21 characteristic flavor metabolites were identified in Laotan Suancai by metabolomics, including 8 sulfides, 6 terpenes, 3 organic acids, 2 isothiocyanates, 1 ester, and 1 pyrazine. Metatranscriptome analysis revealed variations in the active microbiota at different stages of fermentation, and further analysis indicated that organic acids were the primary drivers of microbial succession. Additionally, we reconstructed the metabolic network responsible for the formation of characteristic flavor compounds and identified Companilactobacillus alimentarius, Weissella cibaria, Lactiplantibacillus plantarum, and Loigolactobacillus coryniformis as the core functional microbes involved in flavor development. This study contributed to profoundly understanding the relationship between the active microbiota and flavor quality formation, as well as the targeted selection of starters with flavor regulation abilities.
Collapse
Affiliation(s)
- Shijin Xiong
- State Key Laboratory of Food Science & Resources, Nanchang University, Jiangxi 330047, PR China; School of Food Science & Technology, Nanchang University, Jiangxi 330006, PR China
| | - Xiaoyan Xu
- State Key Laboratory of Food Science & Resources, Nanchang University, Jiangxi 330047, PR China; School of Food Science & Technology, Nanchang University, Jiangxi 330006, PR China
| | - Linli Zhang
- State Key Laboratory of Food Science & Resources, Nanchang University, Jiangxi 330047, PR China; School of Food Science & Technology, Nanchang University, Jiangxi 330006, PR China
| | - Tonghao Du
- State Key Laboratory of Food Science & Resources, Nanchang University, Jiangxi 330047, PR China; School of Food Science & Technology, Nanchang University, Jiangxi 330006, PR China
| | - Tao Huang
- State Key Laboratory of Food Science & Resources, Nanchang University, Jiangxi 330047, PR China; School of Food Science & Technology, Nanchang University, Jiangxi 330006, PR China; International Institute of Food Innovation, Nanchang University, Jiangxi, 330200, PR China
| | - Jinqing Huang
- Institute of Agricultural Products Processing, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi 330200, PR China
| | - Hongbing Ren
- Yunnan Key Laboratory of Fermented Vegetables, Honghe, Yunnan, 661100, PR China
| | - Tao Xiong
- State Key Laboratory of Food Science & Resources, Nanchang University, Jiangxi 330047, PR China; School of Food Science & Technology, Nanchang University, Jiangxi 330006, PR China.
| | - Mingyong Xie
- State Key Laboratory of Food Science & Resources, Nanchang University, Jiangxi 330047, PR China; School of Food Science & Technology, Nanchang University, Jiangxi 330006, PR China
| |
Collapse
|
4
|
Enciso-Ibarra J, Roque A, Bolán-Mejia C, Enciso-Ibarra K, González-Castillo A, Gomez-Gil B. Vibrio eleionomae sp. nov., isolated from shrimp ( Penaeus vannamei) pond water. Int J Syst Evol Microbiol 2023; 73. [PMID: 37167075 DOI: 10.1099/ijsem.0.005866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
A novel Vibrio strain (CAIM 722T=SW9T=DSM 24596T) was isolated in 2003 from water of a shrimp (Penaeus vannamei) culture pond located in Los Mochis, Sinaloa, Mexico, and taxonomically characterized using a polyphasic approach. The 16S rRNA gene sequence clustered within those of the genus Vibrio, showing high similarity to the type strains of the Porteresiae clade. Multilocus sequence analysis using eight housekeeping genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, topA and 16S rRNA) and phylogenetic analysis with 139 single-copy genes showed that the strain forms an independent branch. Whole genome sequencing and genomic analyses (average nucleotide identity, OrthoANI, average amino acid identity and in silico DNA-DNA hybridization) produced values well below the thresholds for species delineation with all methods tested. In addition, a phenotypic characterization was performed to support the description and differentiation of the novel strain from related taxa. The results obtained demonstrate that the strain represent a novel species, for which the name Vibrio eleionomae sp. nov. is proposed.
Collapse
Affiliation(s)
| | - Ana Roque
- Institut de Recerca i Tecnologia Agroalimentaries, Centre d'Aquicultura, Crta: Poble Nou, Km 5,5. La Ràpita, 43540, Spain
| | - Carmen Bolán-Mejia
- CIAD, A.C., Mazatlán Unit for Aquaculture, AP. 711 Mazatlán, Sinaloa 82000, Mexico
| | - Karen Enciso-Ibarra
- CIAD, A.C., Mazatlán Unit for Aquaculture, AP. 711 Mazatlán, Sinaloa 82000, Mexico
| | - Adrián González-Castillo
- Universidad Politécnica de Sinaloa, Programa Académico de Ingeniería en Biotecnología, Carretera Municipal Libre Km.3 Mazatlán-Higueras, Mazatlán, Sinaloa 82199, Mexico
| | - Bruno Gomez-Gil
- CIAD, A.C., Mazatlán Unit for Aquaculture, AP. 711 Mazatlán, Sinaloa 82000, Mexico
| |
Collapse
|
5
|
Weigert S, Perez‐Garcia P, Gisdon FJ, Gagsteiger A, Schweinshaut K, Ullmann GM, Chow J, Streit WR, Höcker B. Investigation of the halophilic PET hydrolase PET6 from Vibrio gazogenes. Protein Sci 2022; 31:e4500. [PMID: 36336469 PMCID: PMC9679969 DOI: 10.1002/pro.4500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/21/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
The handling of plastic waste and the associated ubiquitous occurrence of microplastic poses one of the biggest challenges of our time. Recent investigations of plastic degrading enzymes have opened new prospects for biological microplastic decomposition as well as recycling applications. For polyethylene terephthalate, in particular, several natural and engineered enzymes are known to have such promising properties. From a previous study that identified new PETase candidates by homology search, we chose the candidate PET6 from the globally distributed, halophilic organism Vibrio gazogenes for further investigation. By mapping the occurrence of Vibrios containing PET6 homologs we demonstrated their ubiquitous prevalence in the pangenome of several Vibrio strains. The biochemical characterization of PET6 showed that PET6 has a comparatively lower activity than other enzymes but also revealed a superior turnover at very high salt concentrations. The crystal structure of PET6 provides structural insights into this adaptation to saline environments. By grafting only a few beneficial mutations from other PET degrading enzymes onto PET6, we increased the activity up to three-fold, demonstrating the evolutionary potential of the enzyme. MD simulations of the variant helped rationalize the mutational effects of those mutants and elucidate the interaction of the enzyme with a PET substrate. With tremendous amounts of plastic waste in the Ocean and the prevalence of Vibrio gazogenes in marine biofilms and estuarine marshes, our findings suggest that Vibrio and the PET6 enzyme are worthy subjects to study the PET degradation in marine environments.
Collapse
Affiliation(s)
| | - Pablo Perez‐Garcia
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
| | | | | | | | | | - Jennifer Chow
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
| | - Wolfgang R. Streit
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
| | - Birte Höcker
- Department of BiochemistryUniversity of BayreuthBayreuthGermany
| |
Collapse
|
6
|
Vibrio salinus sp. nov., a marine nitrogen-fixing bacterium isolated from the lagoon sediment of an islet inside an atoll in the western Pacific Ocean. Antonie Van Leeuwenhoek 2022; 115:1203-1214. [PMID: 35908088 DOI: 10.1007/s10482-022-01768-y] [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: 12/24/2021] [Accepted: 07/17/2022] [Indexed: 10/16/2022]
Abstract
A marine, facultatively anaerobic, nitrogen-fixing bacterium, designated strain DNF-1T, was isolated from the lagoon sediment of Dongsha Island, Taiwan. Cells grown in broth cultures were Gram-negative rods that were motile by means of monotrichous flagella. Cells grown on plate medium produced prosthecae and vesicle-like structures. NaCl was required and optimal growth occurred at about 2-3% NaCl, 25-30 °C and pH 7-8. The strain grew aerobically and was capable of anaerobic growth by fermenting D-glucose or other carbohydrates as substrate. Both the aerobic and anaerobic growth could be achieved with NH4Cl as a sole nitrogen source. When N2 served as the sole nitrogen source only anaerobic growth was observed. Major cellular fatty acids were C14:0, C16:0 and C16:1 ω7c, while major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 42.2 mol% based on the genomic DNA data. Phylogenetic analyses based on 16S rRNA genes and the housekeeping genes, gapA, pyrH, recA and gyrB, revealed that the strain formed a distinct lineage at species level in the genus Vibrio of the family Vibrionaceae. These results and those from genomic, chemotaxonomic and physiological studies strongly support the assignment of a novel Vibrio species. The name Vibrio salinus sp. nov. is proposed for the novel species, with DNF-1T (= BCRC 81209T = JCM 33626T) as the type strain. This newly proposed species represents the second example of the genus Vibrio that has been demonstrated to be capable of anaerobic growth by fixing N2 as the sole nitrogen source.
Collapse
|
7
|
Kahraman-Ilıkkan Ö, Bağdat EŞ. Metataxonomic sequencing to assess microbial safety of Turkish white cheeses. Braz J Microbiol 2022; 53:969-976. [PMID: 35277850 PMCID: PMC9151932 DOI: 10.1007/s42770-022-00730-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/04/2022] [Indexed: 02/01/2023] Open
Abstract
High-throughput sequencing has provided a way to monitor the large diversity of microorganisms in fermented foods that have complex microbiota. Up to date, many kinds of cheese have been characterized with the metataxonomic approach, but the safety of unpacked Turkish white cheeses, which are widely consumed in Turkey, has not been assessed. In this study, fifteen unpacked white cheeses sold in public bazaars in Ankara province have been collected and subjected to microbial enumeration as well as physicochemical analysis. Five white cheeses, which have relatively the highest foodborne pathogens, out of fifteen white cheeses, have been analyzed by next-generation sequencing and metataxonomic analysis. According to the results, abundant families were Lactobacillaceae, Oceanospirillaceae, Enterococcaceae, Pseudomonadaceae, and Vibrionaceae. Staphylococcus aureus, E. coli, and Salmonella, which are indicators of bad hygiene and sanitation conditions, were found in cheeses. In conclusion, culture-independent methods such as metataxonomic can be important to evaluate the safety of foods.
Collapse
Affiliation(s)
- Özge Kahraman-Ilıkkan
- Food Quality Control and Analysis Program, Kahramankazan Vocational School, Başkent University, 06980, Ankara, Turkey.
| | - Elif Şeyma Bağdat
- Food Technology Program, Kahramankazan Vocational School, Başkent University, 06980, Ankara, Turkey
| |
Collapse
|
8
|
Huang WS, Wang LT, Chen JS, Chen YT, Wei STS, Chiang YR, Wang PL, Lee TH, Lin ST, Huang L, Shieh WY. Vibrio nitrifigilis sp. nov., a marine nitrogen-fixing bacterium isolated from the lagoon sediment of an islet inside an atoll. Antonie van Leeuwenhoek 2021; 114:933-945. [PMID: 33864545 DOI: 10.1007/s10482-021-01567-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/01/2021] [Indexed: 10/21/2022]
Abstract
A nitrogen-fixing isolate of facultatively anaerobic, marine bacterium, designated strain NFV-1T, was recovered from the lagoon sediment of Dongsha Island, Taiwan. It was a Gram-negative rod which exhibited motility with monotrichous flagellation in broth cultures. The strain required NaCl for growth and grew optimally at about 25-35 °C, 3% NaCl and pH 7-8. It grew aerobically and could achieve anaerobic growth by fermenting D-glucose or other carbohydrates as substrates. NH4Cl could serve as a sole nitrogen source for growth aerobically and anaerobically, whereas growth with N2 as the sole nitrogen source was observed only under anaerobic conditions. Cellular fatty acids were predominated by C16:1 ω7c, C16:0, and C18:1 ω7c. The major polar lipids consisted of phosphatidylethanolamine and phosphatidylserine. Strain NFV-1T had a DNA G + C content of 42.5 mol%, as evaluated according to the chromosomal DNA sequencing data. Analyses of sequence similarities and phylogeny based on the 16S rRNA genes, together with the housekeeping genes, gyrB, ftsZ, mreB, topA and gapA, indicated that the strain formed a distinct species-level lineage in the genus Vibrio of the family Vibrionaceae. These phylogenetic data and those from genomic and phenotypic characterisations support the establishment of a novel Vibrio species, for which the name Vibrio nitrifigilis sp. nov. (type strain NFV-1T = BCRC 81211T = JCM 33628T) is proposed.
Collapse
Affiliation(s)
- Wei-Sheng Huang
- Institute of Oceanography, National Taiwan University, P.O. Box 23-13, Taipei, 10617, Taiwan
| | - Li-Ting Wang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd., Hsinchu, 30062, Taiwan
| | - Jwo-Sheng Chen
- College of Health Care, China Medical University, No. 91, Shyue-Shyh Rd, Taichung, Taiwan
| | - Yen-Ting Chen
- Institute of Oceanography, National Taiwan University, P.O. Box 23-13, Taipei, 10617, Taiwan
| | | | - Yin-Ru Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Pei-Ling Wang
- Institute of Oceanography, National Taiwan University, P.O. Box 23-13, Taipei, 10617, Taiwan
| | - Tzong-Huei Lee
- Institute of Fisheries Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Shih-Ting Lin
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd., Hsinchu, 30062, Taiwan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd., Hsinchu, 30062, Taiwan
| | - Wung Yang Shieh
- Institute of Oceanography, National Taiwan University, P.O. Box 23-13, Taipei, 10617, Taiwan.
| |
Collapse
|
9
|
Li B, Li Y, Liu R, Xue C, Zhu X, Tian X, Wang X, Liang J, Zheng Y, Zhang XH. Vibrio ouci sp. nov. and Vibrio aquaticus sp. nov., two marine bacteria isolated from the East China Sea. Int J Syst Evol Microbiol 2020; 70:172-179. [DOI: 10.1099/ijsem.0.003732] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Bei Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Yuying Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Ronghua Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Chunxu Xue
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiaoyu Zhu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiaorong Tian
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiaolei Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Jinchang Liang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Yanfen Zheng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiao-Hua Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| |
Collapse
|