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Kawano K, Awano T, Yoshinaga A, Sugiyama J, Sawayama S, Nakagawa S. Paralimibaculum aggregatum gen. nov. sp. nov. and Biformimicrobium ophioploci gen. nov. sp. nov., two novel heterotrophs from brittle star Ophioplocus japonicus. Int J Syst Evol Microbiol 2024; 74:006530. [PMID: 39325648 PMCID: PMC11426391 DOI: 10.1099/ijsem.0.006530] [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: 02/26/2024] [Accepted: 09/12/2024] [Indexed: 09/28/2024] Open
Abstract
Two novel Gram-stain-negative, strictly aerobic, halophilic and non-motile bacterial strains, designated NKW23T and NKW57T, were isolated from a brittle star Ophioplocus japonicus collected from a tidal pool in Wakayama, Japan. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that NKW23T represented a member of the family Paracoccaceae, with Limibaculum halophilum CAU 1123T as its closest relative (94.4% sequence identity). NKW57T was identified as representing a member of the family Microbulbiferaceae, with up to 94.9% sequence identity with its closest relatives. Both strains displayed average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values below the species delimitation threshold against their closest relatives. Additionally, amino acid identity (AAI) values of both strains fell below the genus-defining threshold. Phylogenetic trees based on genome sequences indicated that NKW23T formed a novel lineage, branching deeply prior to the divergence of the genera Limibaculum and Thermohalobaculum, with an evolutionary distance (ED) of 0.31-0.32, indicative of genus-level differentiation. NKW57T similarly formed a distinct lineage separate from the species of the genus Microbulbifer. The major respiratory quinones of NKW23T and NKW57T were ubiquinone-10 (Q-10) and Q-8, respectively. The genomic DNA G+C contents of NKW23T and NKW57T were 71.4 and 58.8%, respectively. On the basis of the physiological and phylogenetic characteristics, it was proposed that these strains should be classified as novel species representing two novel genera: Paralimibaculum aggregatum gen. nov., sp. nov., with strain NKW23T (=JCM 36220T=KCTC 8062T) as the type strain, and Biformimicrobium ophioploci gen. nov., sp. nov., with strain NKW57T (=JCM 36221T=KCTC 8063T) as the type strain.
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Affiliation(s)
- Keisuke Kawano
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tatsuya Awano
- Laboratory of Tree Cell Biology, Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Arata Yoshinaga
- Laboratory of Tree Cell Biology, Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Junji Sugiyama
- Laboratory of Tree Cell Biology, Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka 237-0061, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji-Cho, Okazaki 444-8787, Japan
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Ishaq N, Zhang M, Gao L, Ilan M, Li Z. Microbulbifer spongiae sp. nov., isolated from marine sponge Diacarnus erythraeanus. Int J Syst Evol Microbiol 2024; 74. [PMID: 39325661 DOI: 10.1099/ijsem.0.006521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2024] Open
Abstract
A novel bacterium, designated as MI-GT, was isolated from marine sponge Diacarnus erythraeanus. Cells of strain MI-GT are Gram-stain-negative, aerobic, and rod or coccoid-ovoid in shape. MI-GT is able to grow at 10-40 °C (optimum, 28 °C), with 1.0-8.0% (w/v) NaCl (optimum, 4.0%), and at pH 5.5-9.0 (optimum, pH 8.0). The 16S rRNA gene sequence of strain MI-GT shows 98.35, 97.32 and 97.25% similarity to those of Microbulbifer variabilis Ni-2088T, Microbulbifer maritimus TF-17T and Microbulbifer echini AM134T, respectively. Phylogenetic analysis also exhibits that strain MI-GT falls within a clade comprising members of the genus Microbulbifer (class Gammaproteobacteria). The genome size of strain MI-GT is 4478124 bp with a G+C content of 54.51 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MI-GT and other type strains are 71.61-76.44% (ANIb), 83.27-84.36% (ANIm) and 13.4-18.7% (dDDH), respectively. These values are significantly lower than the recommended threshold values for bacterial species delineation. Percentage of conserved proteins and average amino acid identity values among the genomes of strain MI-GT and other closely related species are 52.04-59.13% and 67.47-77.21%, respectively. The major cellular fatty acids of MI-GT are composed of summed feature 8 (C18 : 1 ω7c or C18 : 1 ω6c), iso-C11 : 0 3-OH, iso-C15 : 0, C16 : 0, and summed feature 9 (C17 : 1 iso ω9c or C16 : 0 10-methyl). The polar lipids of MI-GT mainly consist of phosphatidylethanolamine, phosphatidylglycerol, aminolipid, and two glycolipids. The major respiratory quinone is Q-8. Based on differential phenotypic and phylogenetic data, strain MI-GT is considered to represent a novel species of genus Microbulbifer, for which the name Microbulbifer spongiae sp. nov. is proposed. The type strain is MI-GT (=MCCC 1K07826T=KCTC 8081T).
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Affiliation(s)
- Nabila Ishaq
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Mimi Zhang
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Luyao Gao
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Micha Ilan
- School of Zoology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Zhiyong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
- Yazhou Bay Institute of Deepsea Science and Technology, Shanghai Jiao Tong University, Shanghai, PR China
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Zhong W, Agarwal V. Polymer degrading marine Microbulbifer bacteria: an un(der)utilized source of chemical and biocatalytic novelty. Beilstein J Org Chem 2024; 20:1635-1651. [PMID: 39076296 PMCID: PMC11285056 DOI: 10.3762/bjoc.20.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 07/02/2024] [Indexed: 07/31/2024] Open
Abstract
Microbulbifer is a genus of halophilic bacteria that are commonly detected in the commensal marine microbiomes. These bacteria have been recognized for their ability to degrade polysaccharides and other polymeric materials. Increasingly, Microbulbifer genomes indicate these bacteria to be an untapped reservoir for novel natural product discovery and biosynthetic novelty. In this review, we summarize the distribution of Microbulbifer bacteria, activities of the various polymer degrading enzymes that these bacteria produce, and an up-to-date summary of the natural products that have been isolated from Microbulbifer strains. We argue that these bacteria have been hiding in plain sight, and contemporary efforts into their genome and metabolome mining are going to lead to a proliferation of Microbulbifer-derived natural products in the future. We also describe, where possible, the ecological interactions of these bacteria in marine microbiomes.
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Affiliation(s)
- Weimao Zhong
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Huang Y, Jiang Y, Zhao A, Liu Y, Chen X, Wang F, Liu H, Huang W, Ihsan YN, Jiang M, Jiang Y. Microbulbifer litoralis sp. nov., Isolated from Seashore of Weizhou Island. Curr Microbiol 2024; 81:105. [PMID: 38393402 DOI: 10.1007/s00284-023-03594-5] [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: 02/21/2023] [Accepted: 12/19/2023] [Indexed: 02/25/2024]
Abstract
A bacterium designated GXH0434T was isolated from sea shore samples collected from Weizhou Island, Beihai, Guangxi, China. The organism is motile, strictly aerobic, and possesses a rod-coccus cell cycle in association with the growth phase. It can grow at 15-45 °C (optimum 37 °C), at pH 6.0-11.0 (optimum 6.0), and at 0-20% (w/v) NaCl (optimum 5.0-8.0%). The strain is positive for peroxidase and oxidase activity, negative for Voges-Proskauer test, can hydrolyze Tween 20, Tween 60, Tween 80, casein, and is able to produce siderophore and has the function of nitrogen fixation. Molecular phylogenetic analysis based on 16S rRNA gene sequences indicated that GXH0434T was most closely related to Microbulbifer halophilus KCTC 12848T with the similarity of 97.2%, followed by Microbulbifer chitinilyticus JCM 16148T (97.1%) and Microbulbifer taiwanensis LMG 26125T (96.5%). The digital DNA-DNA hybridization and the average nucleotide identity values between GXH0434T and Microbulbifer halophilus KCTC 12848T were 28.90% and 83.38%, respectively, which were below thresholds of species delineation. The genomic DNA G+C content of the strain was 61.9%. The major fatty acids were iso-C15:0, C16:0, iso-C11:0 3-OH, iso-C11:0 and Summed features 8 (C18:0 ω7c and/or C18:0 ω6c). The major polar lipids detected in GXH0434T were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC). The major respiratory quinone was ubiquinone Q-8. Based on the above polyphasic classification indicated strain GXH0434T represents a novel species of the genus Microbulbifer, for which the name Microbulbifer litoralis sp. nov. is proposed. The type strain is GXH0434T (= MCCC 1K07158T = KCTC 92169T).
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Affiliation(s)
- Ying Huang
- School of Marine Sciences and Biotechnology, Guangxi Key Laboratory of Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning, 530008, People's Republic of China
| | - Yu Jiang
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, People's Republic of China
| | - Aolin Zhao
- School of Marine Sciences and Biotechnology, Guangxi Key Laboratory of Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning, 530008, People's Republic of China
| | - Ying Liu
- School of Chemistry and Chemical Engineering, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Minzu University, Nanning, 530008, People's Republic of China
| | - Xuemei Chen
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Fang Wang
- School of Marine Sciences and Biotechnology, Guangxi Key Laboratory of Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning, 530008, People's Republic of China
| | - Hongcun Liu
- School of Marine Sciences and Biotechnology, Guangxi Key Laboratory of Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning, 530008, People's Republic of China
| | - Wenshan Huang
- Guangxi Lvyounong Biological Technology Co., Ltd, Nanning, 530000, People's Republic of China
| | - Yudi N Ihsan
- Department of Marine Science, Universitas Padjadjaran, Jatinangor, Indonesia
| | - Mingguo Jiang
- School of Marine Sciences and Biotechnology, Guangxi Key Laboratory of Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning, 530008, People's Republic of China.
| | - Yi Jiang
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China.
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Microbulbifer okhotskensis sp. nov., isolated from a deep bottom sediment of the Okhotsk Sea. Arch Microbiol 2022; 204:548. [PMID: 35945400 DOI: 10.1007/s00203-022-03161-9] [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: 04/19/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/02/2022]
Abstract
A Gram-negative, aerobic, non-motile bacterium КMM 9862T was isolated from a deep bottom sediment sample obtained from the Okhotsk Sea, Russia. Based on the 16S rRNA gene and whole genome sequences analyses the novel strain КMM 9862T fell into the genus Microbulbifer (class Gammaproteobacteria) sharing the highest 16S rRNA gene sequence similarities of 97.4% to Microbulbifer echini AM134T and Microbulbifer epialgicus F-104T, 97.3% to Microbulbifer pacificus SPO729T, 97.1% to Microbulbifer variabilis ATCC 700307T, and similarity values of < 97.1% to other recognized Microbulbifer species. The average nucleotide identity and digital DNA-DNA hybridization values between strain КMM 9862T and M. variabilis ATCC 700307T and M. thermotolerans DSM 19189T were 80.34 and 77.72%, and 20.2 and 19.0%, respectively. Strain КMM 9862T contained Q-8 as the predominant ubiquinone and C16:0, C16:1 ω7c, C12:0, and C10:0 3-OH as the major fatty acids. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unidentified aminophospholipid, an unidentified aminolipid, two unidentified phospholipids, phosphatidic acid, and an unidentified lipid. The DNA G+C content of 49.8% was calculated from the genome sequence. On the basis of the phylogenetic evidence and distinctive phenotypic characteristics, the marine bacterium KMM 9862T is proposed to be classified as a novel species Microbulbifer okhotskensis sp. nov. The type strain of the species is strain KMM 9862T (= KACC 22804T).
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Cheng Y, Zhu S, Guo C, Xie F, Jung D, Li S, Zhang W, He S. Microbulbifer hainanensis sp. nov., a moderately halopilic bacterium isolated from mangrove sediment. Antonie van Leeuwenhoek 2021; 114:1033-1042. [PMID: 33844121 DOI: 10.1007/s10482-021-01574-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/01/2021] [Indexed: 11/29/2022]
Abstract
A new bacterium was successfully isolated from a mangrove sediment sample in Haikou City, Hainan Province, China. The organism is a Gram-negative, rod-shaped, non-motile and strictly aerobic bacterium, named NBU-8HK146T. Strain NBU-8HK146T was able to grow at temperatures of 10-40 °C, at salinities of 0-11% (w/v) and at pH 5.5-9.5. Veoges-Proskauer, methyl red reaction and hydrolysis of Tween 20 were negative. Catalase and oxidase activities, H2S production, hydrolysis of starch, casein, Tweens 40, 60 and 80 were positive. The major cellular fatty acids were C16:0, iso-C15:0 and summed feature 9. The major respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and two unidentified glycolipids. According to 16S rRNA gene sequence similarities, strain NBU-8HK146T shared 98.0%, 97.9%, 97.7%, 97.6% and 97.3% similarities to the species with validated name Microbulbifer taiwanensis CC-LN1-12T, Microbulbifer rhizosphaerae Cs16bT, Microbulbifer marinus Y215T, Microbulbifer donghaiensis CN85T and Microbulbifer aggregans CCB-MM1T, respectively. Phylogenetic analyses indicated that strain NBU-8HK146T formed a distinct lineage with strains Microbulbifer taiwanensis CC-LN1-12T and Microbulbifer marinus Y215T. Both digital DNA-DNA hybridization values (19.5-22.7%) and average nucleotide identity values (73.2-78.9%) between strain NBU-8HK146T and related species of genus Microbulbifer were below the species delineation cutoffs. The DNA G+C content was 58.9 mol%. Many proteins involving in the adaption of osmotic stress in the salt environment of mangrove were predicted in genome of strain NBU-8HK146T. From phenotypic, genotypic, phylogenetic and chemotaxonomic characteristics, strain NBU-8HK146T can be regarded as a new Microbulbifer species for which the name Microbulbifer hainanensis. The type strain is NBU-8HK146T (= KCTC 82226T = MCCC 1K04737T).
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Affiliation(s)
- Yuping Cheng
- College of Food and Pharmaceutical Sciences, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315800, People's Republic of China
| | - Suting Zhu
- College of Food and Pharmaceutical Sciences, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315800, People's Republic of China
| | - Chaobo Guo
- College of Food and Pharmaceutical Sciences, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315800, People's Republic of China
| | - Feilu Xie
- College of Food and Pharmaceutical Sciences, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315800, People's Republic of China
| | - Dawoon Jung
- College of Food and Pharmaceutical Sciences, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315800, People's Republic of China
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Weiyan Zhang
- College of Food and Pharmaceutical Sciences, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315800, People's Republic of China.
| | - Shan He
- College of Food and Pharmaceutical Sciences, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315800, People's Republic of China.
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Karim MRU, Harunari E, Oku N, Akasaka K, Igarashi Y. Bulbimidazoles A-C, Antimicrobial and Cytotoxic Alkanoyl Imidazoles from a Marine Gammaproteobacterium Microbulbifer Species. JOURNAL OF NATURAL PRODUCTS 2020; 83:1295-1299. [PMID: 32191468 DOI: 10.1021/acs.jnatprod.0c00082] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Three new alkanoyl imidazoles, designated bulbimidazoles A-C (1-3), were found from the culture extract of the gammaproteobacterium Microbulbifer sp. DC3-6 isolated from a stony coral of the genus Tubastraea. The absolute configuration of the anteiso-methyl substitution in 1 was established to be a mixture of (R)- and (S)-configurations in a ratio of 9:91 by applying the Ohrui-Akasaka method. Compounds 1-3 displayed unique broad-spectrum antimicrobial activity against Gram-positive and -negative bacteria and fungi with MICs ranging from 0.78 to 12.5 μg/mL. They also exhibited cytotoxicity toward P388 murine leukemia cells with IC50 in the micromolar range.
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Affiliation(s)
- Md Rokon Ul Karim
- Biotechnology Research Center, Toyama Prefectural University, Imizu, Toyama 939-0398, Japan
| | - Enjuro Harunari
- Biotechnology Research Center, Toyama Prefectural University, Imizu, Toyama 939-0398, Japan
| | - Naoya Oku
- Biotechnology Research Center, Toyama Prefectural University, Imizu, Toyama 939-0398, Japan
| | - Kazuaki Akasaka
- Shokei Gakuin University, 4-10-1 Yurigaoka, Natori, Miyagi 981-1295, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center, Toyama Prefectural University, Imizu, Toyama 939-0398, Japan
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Sharma AR, Harunari E, Zhou T, Trianto A, Igarashi Y. Isolation and biosynthesis of an unsaturated fatty acid with unusual methylation pattern from a coral-associated bacterium Microbulbifer sp. Beilstein J Org Chem 2019; 15:2327-2332. [PMID: 31666867 PMCID: PMC6808205 DOI: 10.3762/bjoc.15.225] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 09/16/2019] [Indexed: 12/22/2022] Open
Abstract
(2Z,4E)-3-Methyl-2,4-decadienoic acid (1) was identified as a major metabolite from a culture extract of a marine bacterium Microbulbifer which was collected from a stony coral Porites sp. NMR-based spectroscopic analysis revealed that 1 is an unsaturated fatty acid in which a methyl group is located in an uncommon position as a natural product. Feeding experiments of 13C-labeled precursors clarified that ʟ-methionine-derived methylation takes place at the carbon which is derived from the carbonyl carbon of acetate. Compound 1 showed weak growth inhibition against Saccharomyces cerevisiae.
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Affiliation(s)
- Amit Raj Sharma
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Enjuro Harunari
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Tao Zhou
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Agus Trianto
- Faculty of Fisheries and Marine Sciences, Diponegoro University, Tembalang Campus, St. Prof. Soedarto SH., Semarang 50275, Central Java, Indonesia
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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Poduval PB, Noronha JM, Bansal SK, Ghadi SC. Characterization of a new virulent phage ϕMC1 specific to Microbulbifer strain CMC-5. Virus Res 2018; 257:7-13. [DOI: 10.1016/j.virusres.2018.08.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 06/11/2018] [Accepted: 08/28/2018] [Indexed: 11/29/2022]
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Moh TH, Furusawa G, Amirul AAA. Microbulbifer aggregans sp. nov., isolated from estuarine sediment from a mangrove forest. Int J Syst Evol Microbiol 2017; 67:4089-4094. [DOI: 10.1099/ijsem.0.002258] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tsu Horng Moh
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia
| | - Go Furusawa
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia
| | - Abdullah Al-Ashraf Amirul
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
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Moh TH, Lau NS, Furusawa G, Amirul AAA. Complete genome sequence of Microbulbifer sp. CCB-MM1, a halophile isolated from Matang Mangrove Forest, Malaysia. Stand Genomic Sci 2017; 12:36. [PMID: 28694917 PMCID: PMC5501506 DOI: 10.1186/s40793-017-0248-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 06/29/2017] [Indexed: 12/30/2022] Open
Abstract
Microbulbifer sp. CCB-MM1 is a halophile isolated from estuarine sediment of Matang Mangrove Forest, Malaysia. Based on 16S rRNA gene sequence analysis, strain CCB-MM1 is a potentially new species of genus Microbulbifer. Here we describe its features and present its complete genome sequence with annotation. The genome sequence is 3.86 Mb in size with GC content of 58.85%, harbouring 3313 protein coding genes and 92 RNA genes. A total of 71 genes associated with carbohydrate active enzymes were found using dbCAN. Ectoine biosynthetic genes, ectABC operon and ask_ect were detected using antiSMASH 3.0. Cell shape determination genes, mreBCD operon, rodA and rodZ were annotated, congruent with the rod-coccus cell cycle of the strain CCB-MM1. In addition, putative mreBCD operon regulatory gene, bolA was detected, which might be associated with the regulation of rod-coccus cell cycle observed from the strain.
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Affiliation(s)
- Tsu Horng Moh
- Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Penang, Malaysia
| | - Nyok-Sean Lau
- Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Penang, Malaysia
| | - Go Furusawa
- Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Penang, Malaysia
| | - Al-Ashraf Abdullah Amirul
- Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Penang, Malaysia.,School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
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Park S, Yoon SY, Ha MJ, Yoon JH. Microbulbifer aestuariivivens sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2017; 67:1436-1441. [DOI: 10.1099/ijsem.0.001831] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Sun Young Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Min-Ji Ha
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
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Camacho M, del Carmen Montero-Calasanz M, Redondo-Gómez S, Rodríguez-Llorente I, Schumann P, Klenk HP. Microbulbifer rhizosphaerae sp. nov., isolated from the rhizosphere of the halophyte Arthrocnemum macrostachyum. Int J Syst Evol Microbiol 2016; 66:1844-1850. [DOI: 10.1099/ijsem.0.000955] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Maria Camacho
- IFAPA-Instituto de Investigación y Formación Agraria y Pesquera, Centro Las Torres-Tomejil, Ctra. Sevilla-Cazalla de la Sierra, Km 12.2, 41200 Alcalá del Río, Sevilla, Spain
| | - Maria del Carmen Montero-Calasanz
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
- School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Susana Redondo-Gómez
- Facultad de Biología, Universidad de Sevilla. Avda. Reina Mercedes s/n, ., Sevilla, Spain
| | | | - Peter Schumann
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne, NE1 7RU, UK
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14
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Spring S, Scheuner C, Göker M, Klenk HP. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Front Microbiol 2015; 6:281. [PMID: 25914684 PMCID: PMC4391266 DOI: 10.3389/fmicb.2015.00281] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 03/21/2015] [Indexed: 11/13/2022] Open
Abstract
In recent years a large number of isolates were obtained from saline environments that are phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, which were originally identified in seawater samples using cultivation independent methods and are characterized by high seasonal abundances in coastal environments. To date a sound taxonomic framework for the classification of these ecologically important isolates and related species in accordance with their evolutionary relationships is missing. In this study we demonstrate that a reliable allocation of members of the oligotrophic marine gammaproteobacteria (OMG) group and related species to higher taxonomic ranks is possible by phylogenetic analyses of whole proteomes but also of the RNA polymerase beta subunit, whereas phylogenetic reconstructions based on 16S rRNA genes alone resulted in unstable tree topologies with only insignificant bootstrap support. The identified clades could be correlated with distinct phenotypic traits illustrating an adaptation to common environmental factors in their evolutionary history. Genome wide gene-content analyses revealed the existence of two distinct ecological guilds within the analyzed lineage of marine gammaproteobacteria which can be distinguished by their trophic strategies. Based on our results a novel order within the class Gammaproteobacteria is proposed, which is designated Cellvibrionales ord. nov. and comprises the five novel families Cellvibrionaceae fam. nov., Halieaceae fam. nov., Microbulbiferaceae fam. nov., Porticoccaceae fam. nov., and Spongiibacteraceae fam. nov.
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Affiliation(s)
- Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Carmen Scheuner
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Markus Göker
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Hans-Peter Klenk
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany ; School of Biology, Newcastle University Newcastle upon Tyne, UK
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15
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Cheng H, Zhang S, Huo YY, Jiang XW, Zhang XQ, Pan J, Zhu XF, Wu M. Gilvimarinus polysaccharolyticus sp. nov., an agar-digesting bacterium isolated from seaweed, and emended description of the genus Gilvimarinus. Int J Syst Evol Microbiol 2014; 65:562-569. [PMID: 25392347 DOI: 10.1099/ijs.0.065078-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study was carried out on strain YN3(T), which was isolated from a seaweed sample taken from the coast of Weihai, China. The bacterium was Gram-stain-negative, rod-shaped, and could grow at pH 5.0-10.0 and 4-32 °C in the presence of 0-9.0 % (w/v) NaCl. Strain YN3(T) was positive for the hydrolysis of polysaccharides, such as agar, starch and xylan. The predominant respiratory quinone was ubiquinone-8. The major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1ω7c. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and two unidentified glycolipids. The genomic DNA G+C content was 49.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YN3(T) should be assigned to the genus Gilvimarinus. 'Gilvimarinus agarilyticus' KCTC 23325 and Gilvimarinus chinensis QM42(T) had the closest phylogenetic relationship to strain YN3(T), and showed 97.9 % and 95.8 % sequence similarities, respectively. On the basis of phenotypic, chemotaxonomic and genotypic data and DNA-DNA hybridization studies, we propose that strain YN3(T) represents a novel species of the genus Gilvimarinus, for which the name Gilvimarinus polysaccharolyticus sp. nov. is proposed. The type strain is YN3(T) ( = KCTC 32438(T) = JCM 19198(T)). An emended description of the genus Gilvimarinus is also presented.
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Affiliation(s)
- Hong Cheng
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Shun Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Ying-Yi Huo
- Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Xia-Wei Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, PR China
| | - Xin-Qi Zhang
- School of Forestry and Biotechnology, Zhejiang Agriculture & Forestry University, Linan 311300, PR China
| | - Jie Pan
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xu-Fen Zhu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
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16
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Fagervold SK, Urios L, Intertaglia L, Batailler N, Lebaron P, Suzuki MT. Pleionea mediterranea gen. nov., sp. nov., a gammaproteobacterium isolated from coastal seawater. Int J Syst Evol Microbiol 2013; 63:2700-2705. [DOI: 10.1099/ijs.0.045575-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, aerobic, cream-pigmented, non-motile, non-spore-forming straight rod, strain MOLA115T, was isolated from a coastal water sample from the Mediterranean Sea. On the basis of phylogenetic analysis of the 16S rRNA gene sequences, strain MOLA115T was shown to belong to the
Gammaproteobacteria
, adjacent to members of the genera
Marinicella
,
Arenicella
and
Kangiella
, sharing less than 89 % 16S rRNA gene sequence similarity with strains of all recognized species within the
Gammaproteobacteria
. The only isoprenoid quinone was ubiquinone-8. Polar lipids in strain MOLA115T included phosphatidylethanolamine, an aminolipid, phosphatidylglycerol and an aminophospholipid. Fatty acid analysis revealed iso-C15 : 0 and iso-C17 : 1ω9c to be the dominant components. The DNA G+C content was 44.5 mol%. Based upon the phenotypic and phylogenetic data, we propose that strain MOLA115T should be considered to represent a novel species in a new genus, for which the name Pleionea mediterranea gen. nov., sp. nov. is proposed. The type strain of Pleionea mediterranea is MOLA115T ( = CIP 110343T = DSM 25350T).
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Affiliation(s)
- Sonja K. Fagervold
- CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66650, Banyuls/Mer, France
- UPMC Université Paris 6, UMS 2348, UMR 7621, Observatoire Océanologique, F-66650 Banyuls/Mer, France
| | - Laurent Urios
- Université de Pau et des Pays de l’Adour, IPREM UMR 5254, Equipe Environnement et Microbiologie, IBEAS, F-64013 PAU, France
| | - Laurent Intertaglia
- CNRS, UMS 2348, Observatoire Océanologique, F-66650, Banyuls/Mer, France
- UPMC Université Paris 6, UMS 2348, UMR 7621, Observatoire Océanologique, F-66650 Banyuls/Mer, France
| | - Nicole Batailler
- CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66650, Banyuls/Mer, France
- UPMC Université Paris 6, UMS 2348, UMR 7621, Observatoire Océanologique, F-66650 Banyuls/Mer, France
| | - Philippe Lebaron
- CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66650, Banyuls/Mer, France
- UPMC Université Paris 6, UMS 2348, UMR 7621, Observatoire Océanologique, F-66650 Banyuls/Mer, France
| | - Marcelino T. Suzuki
- CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66650, Banyuls/Mer, France
- UPMC Université Paris 6, UMS 2348, UMR 7621, Observatoire Océanologique, F-66650 Banyuls/Mer, France
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17
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Vashist P, Nogi Y, Ghadi SC, Verma P, Shouche YS. Microbulbifer mangrovi sp. nov., a polysaccharide-degrading bacterium isolated from an Indian mangrove. Int J Syst Evol Microbiol 2013; 63:2532-2537. [DOI: 10.1099/ijs.0.042978-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A rod-shaped, Gram-negative, non-motile, aerobic and non-endospore forming bacterium, designated strain DD-13T, was isolated from the mangrove ecosystem of Goa, India. Strain DD-13T degraded polysaccharides such as agar, alginate, chitin, cellulose, laminarin, pectin, pullulan, starch, carrageenan, xylan and β-glucan. The optimum pH and temperature for growth was 7 and 36 °C, respectively. The strain grew optimally in the presence of 3 % NaCl (w/v). The DNA G+C content was 61.4 mol%. The predominant fatty acid of strain DD-13T was iso-C15 : 0. Ubiquinone-8 was detected as the major respiratory lipoquinone. Phylogenetic studies based on 16S rRNA gene sequence analysis demonstrated that strain DD-13T formed a coherent cluster with species of the genus
Microbulbifer
. Strain DD-13T exhibited 16S rRNA gene sequence similarity levels of 98.9–97.1 % with
Microbulbifer hydrolyticus
IRE-31T,
Microbulbifer salipaludis
JCM 11542T,
Microbulbifer agarilyticus
JAMB A3T,
Microbulbifer celer
KCTC 12973T and
Microbulbifer elongatus
DSM 6810T. However, the level of DNA–DNA relatedness between strain DD-13T and the five type strains of these species of the genus
Microbulbifer
were in the range of 26–33 %. Additionally, strain DD-13T demonstrates several phenotypic differences from these type strains of species of the genus
Microbulbifer
. Thus strain DD-13T represents a novel species of the genus
Microbulbifer
, for which the name Microbulbifer mangrovi sp. nov. is proposed with the type strain DD-13T ( = KCTC 23483T = JCM 17729T).
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Affiliation(s)
- Poonam Vashist
- Department of Biotechnology, Goa University, Taleigao Plateau, Goa, India
| | - Yuichi Nogi
- Extremobiosphere Research program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15, Natsushima-cho, Yokosuka 237-0061, Japan
| | - Sanjeev C. Ghadi
- Department of Biotechnology, Goa University, Taleigao Plateau, Goa, India
| | - Pankaj Verma
- Molecular Biology Unit, National Centre for Cell Science, Pune University, Pune, India
| | - Yogesh S. Shouche
- Molecular Biology Unit, National Centre for Cell Science, Pune University, Pune, India
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18
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Jeong SH, Yang SH, Jin HM, Kim JM, Kwon KK, Jeon CO. Microbulbifer gwangyangensis sp. nov. and Microbulbifer pacificus sp. nov., isolated from marine environments. Int J Syst Evol Microbiol 2013; 63:1335-1341. [DOI: 10.1099/ijs.0.042606-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel Gram-stain-negative, chemoheterotrophic and strictly aerobic bacteria, strains GY2T and SPO729T, were isolated from a tidal flat at Gwangyang Bay in Korea and a marine sponge sample from the Pacific Ocean, respectively. The two strains were halotolerant, catalase- and oxidase-positive, and non-motile rods. Optimum temperature and pH for growth of both strains were observed to be 35 °C and pH 7.0–7.5, but optimum salinity for strain SPO729T [2–3 % (w/v)] was slightly higher than that for strain GY2T (1–2 %). The major cellular fatty acids of both strains were C16 : 0, iso-C15 : 0, iso-C17 : 0, iso-C17 : 1ω9c, C18 : 1ω7c, iso-C11 : 0 and iso-C11 : 0 3-OH. The genomic DNA G+C contents of strains GY2T and SPO729T were 55.1 and 57.9 mol%, respectively, and ubiquinone 8 (Q-8) was detected as the sole respiratory quinone from the two strains. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains GY2T and SPO729T formed tight phyletic lineages with members of the genus
Microbulbifer
. Strain GY2T was closely related to
Microbulbifer okinawensis
ABABA23T (98.2 %), strain SPO729T (98.0 %) and
Microbulbifer donghaiensis
CN85T (97.0 %); strain SPO729T was closely related to
M. okinawensis
ABABA23T (98.3 %) and
M. donghaiensis
CN85T (98.2 %). The DNA–DNA relatedness values of strain GY2T with
M. okinawensis
ABABA23T, strain SPO729T and
M. donghaiensis
CN85T were 40.0±2.1 %, 13.1±3.9 % and 16.2±5.8 %, respectively, whereas those of strain SPO729T with
M. okinawensis
ABABA23T and
M. donghaiensis
CN85T were 48.0±4.0 % and 34.6±9.3 %, respectively. On the basis of phenotypic and molecular features, it is concluded that the two strains GY2T and SPO729T represent two novel species of the genus
Microbulbifer
, for which the names Microbulbifer gwangyangensis sp. nov. and Microbulbifer pacificus are proposed; the type strains are GY2T ( = KACC 16189T = JCM 17800T) and SPO729T ( = KCCM 42667T = JCM 14507T), respectively.
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Affiliation(s)
- Sang Hyeon Jeong
- School of Biological Sciences, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Sung-Hyun Yang
- Korea Ocean Research & Development Institute, Ansan-si, Kyunggi-do 426-170, Republic of Korea
| | - Hyun Mi Jin
- School of Biological Sciences, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Jeong Myeong Kim
- School of Biological Sciences, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Kae Kyoung Kwon
- Korea Ocean Research & Development Institute, Ansan-si, Kyunggi-do 426-170, Republic of Korea
| | - Che Ok Jeon
- School of Biological Sciences, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
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