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Yang AI, Kim B, Joe SH, Joe HI, Choe H, Kim KH, Jun MO, Shin NR. Sporosarcina jeotgali sp. nov., Sporosarcina oncorhynchi sp. nov., and Sporosarcina trichiuri sp. nov., Isolated from Jeotgal, a Traditional Korean Fermented Seafood. J Microbiol 2024:10.1007/s12275-024-00106-3. [PMID: 38587589 DOI: 10.1007/s12275-024-00106-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 04/09/2024]
Abstract
Three novel, Gram-stain-positive, obligate aerobic, catalase- and oxidase-positive bacterial strains, designated B2O-1T, T2O-4T, and 0.2-SM1T-5T, were isolated from jeotgal, a traditional Korean fermented seafood. Strains B2O-1T, T2O-4T, and 0.2-SM1T-5T exhibited distinct colony colors, characterized by pink, yellow, and red opaque circular colonies, respectively. Phylogenetic analysis revealed that three strains formed a paraphyletic clade within the genus Sporosarcina and shared < 99.0% similarity with Sporosarcina aquimarina KCTC 3840T and Sporosarcina saromensis KCTC 13119T in their 16S rRNA gene sequences. The three strains exhibiting Orthologous Average Nucleotide Identity values < 79.3% and digital DNA-DNA hybridization values < 23.1% within the genus Sporosarcina affirmed their distinctiveness. Strains B2O-1T, T2O-4T, and 0.2-SM1T-5T contained MK-7 as a sole respiratory menaquinone and A4α type peptidoglycan based on lysine with alanine, glutamic acid, and aspartic acid. The common polar lipids include diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Strain T2O-4T contained one unidentified phospholipid, whereas strain 0.2-SM1T-5T contained two unidentified phospholipids. Cellular fatty acid profiles, with C15:0 anteiso as the major fatty acid, supported the affiliation of the three strains to the genus Sporosarcina. Based on the polyphasic characteristics, strains B2O-1T (= KCTC 43506T = JCM 36032T), T2O-4T (= KCTC 43489T = JCM 36031T), and 0.2-SM1T-5T (= KCTC 43519T = JCM 36034T) represent three novel species within the genus Sporosarcina, named Sporosarcina jeotgali sp. nov., Sporosarcina oncorhynchi sp. nov., and Sporosarcina trichiuri sp. nov., respectively.
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Affiliation(s)
- Ah-In Yang
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
- Department of Biology, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Bora Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Sung-Hong Joe
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
- Department of Microbiology, Chonnam National University Medical School, Hwasun, 58128, Republic of Korea
| | - Hae-In Joe
- Department of Biology, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Hanna Choe
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Ki Hyun Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Min Ok Jun
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Na-Ri Shin
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea.
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Kim B, Yang AI, Joe HI, Kim KH, Choe H, Joe SH, Jun MO, Shin NR. Genomic attributes and characterization of novel exopolysaccharide-producing bacterium Halomonas piscis sp. nov. isolated from jeotgal. Front Microbiol 2023; 14:1303039. [PMID: 38156007 PMCID: PMC10752968 DOI: 10.3389/fmicb.2023.1303039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/01/2023] [Indexed: 12/30/2023] Open
Abstract
Halophilic bacterial strains, designated SG2L-4T, SB1M4, and SB2L-5, were isolated from jeotgal, a traditional Korean fermented food. Cells are Gram-stain-negative, aerobic, non-motile, rod-shaped, catalase-positive, and oxidase-negative. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain SG2L-4T is closely related to Halomonas garicola KACC 18117T with a similarity of 96.2%. The complete genome sequence of strain SG2L-4T was 3,227,066 bp in size, with a genomic G + C content of 63.3 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain SG2L-4T and H. garicola KACC 18117T were 90.5 and 40.7%, respectively. The optimal growth conditions for strain SG2L-4T were temperatures between 30 and 37°C, a pH value of 7, and the presence of 10% (w/v) NaCl. The polar lipids identified included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown phospholipid, an unknown glycolipid, and an unknown polar lipid. The major cellular fatty acids were C16:0, summed features 8 (C18:1ω6c and/or C18:1ω7c), C19:0 cyclo ω8c, and summed features 3 (C16:1ω6c and/or C16:1ω7c). The predominant respiratory quinone was ubiquinone with nine isoprene units (Q-9). Based on the phenotypic, genotypic, and chemotaxonomic results, strain SG2L-4T represents a novel species within the genus Halomonas, for which the name Halomonas piscis sp. nov. is proposed. The type strain is SG2L-4T (=KCTC 92842T = JCM 35929T). Functional annotation of the genome of strain SG2L-4T confirmed the presence of exopolysaccharide synthesis protein (ExoD) and capsular polysaccharide-related genes. Strain SG2L-4T also exhibited positive results in Molisch's test, indicating the presence of extracellular carbohydrates and exopolysaccharides (EPS) production. These findings provide valuable insights into the EPS-producing capabilities of H. piscis sp. nov. isolated from jeotgal, contributing to understanding its potential roles in food and biotechnological applications.
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Affiliation(s)
- Bora Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, Republic of Korea
| | - Ah-In Yang
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, Republic of Korea
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Hae-In Joe
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Ki Hyun Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, Republic of Korea
| | - Hanna Choe
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, Republic of Korea
| | - Sung-Hong Joe
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, Republic of Korea
- Department of Microbiology, Chonnam National University Medical School, Hwasun, Republic of Korea
| | - Min Ok Jun
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, Republic of Korea
| | - Na-Ri Shin
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, Republic of Korea
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Yang AI, Joe HI, Choe H, Kim HS, Eom MK, Li Z, Jun MO, Kim B, Lee JS, Shin NR. Alkalimarinus alittae sp. nov., isolated from gut of marine sandworm ( Alitta virens) and emended description of the genus Alkalimarinus. Int J Syst Evol Microbiol 2023; 73. [PMID: 37681757 DOI: 10.1099/ijsem.0.006029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023] Open
Abstract
A novel, Gram-stain-negative, aerobic, motile, catalase- and oxidase-negative bacterial strain, designated A2M4T, was isolated from the gut contents of a marine sandworm Alitta virens, collected from the eastern coast of the Republic of Korea. Strain A2M4T formed translucent circular colonies and showed rod-shaped cells with peritrichous flagella. Optimal growth of strain A2M4T occurred at 25 °C, pH 7.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain A2M4T was closely related to Alkalimarinus sediminis FA028T, with the highest sequence similarity of 98.9 %. The complete genome sequence of strain A2M4T was 4.25 Mbp in size and the genomic G+C content, calculated from the genome sequence, was 43.2 mol%. A comparison between the genome sequence of strain A2M4T and that of its closest relative, A. sediminis FA028T, showed an average nucleotide identity value of 76.63 % and a digital DNA-DNA hybridization value of 22.2 %. Strain A2M4T contained Q-9 as the sole respiratory isoprenoid quinone and the major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids of strain A2M4T were C14 : 0, C16 : 0 and summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c). Based on its phenotypic, chemotaxonomic and genomic characteristics, strain A2M4T represents a novel species of the genus Alkalimarinus, for which the name Alkalimarinus alittae sp. nov. is proposed. The type is strain A2M4T (=KCTC 92030T=JCM 35924T). The description of the genus Alkalimarinus has also been emended.
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Affiliation(s)
- Ah-In Yang
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Hae-In Joe
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Hanna Choe
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Han Sol Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Mi Kyung Eom
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Zhun Li
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Min Ok Jun
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Bora Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Jung-Sook Lee
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Na-Ri Shin
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
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Siddiqi MZ, Lee JE, Jun MO, Huq MA, Im WT. Isolation and characterization of a novel glycoside hydrolase positive bacterial strain named Terrimonas ginsenosidimutans sp. nov. with ginsenoside-converting activity. Int J Syst Evol Microbiol 2023; 73. [PMID: 37289495 DOI: 10.1099/ijsem.0.005781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023] Open
Abstract
A novel yellow-pigmented catalase- and oxidase-positive bacterial strain (designated NA20T) was isolated from wetland soil and characterized. Results of 16S rRNA and draft genome sequence analysis placed strain NA20T within the genus Terrimonas of the family Chitinophagaceae. Strain NA20T showed ≤97.1 % sequence similarity to members of the genus Terrimonas and the highest sequence similarity was found to Terrimonas lutea DYT (97.1%). The draft genome of strain NA20T had a total length of 7 144 125 base pairs. A total of 5659 genes were identified, of which 5613 were CDS and 46 RNA genes were assigned a putative function. Mining the genomes revealed the presence of 225 carbohydrate genes out of 1334 genes. Strain NA20T contained iso-C15 : 0, iso-C15 : 0 G, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) as major fatty acids. The predominant quinone was MK-7. The major polar lipids were phosphatidylethanolamine, one unknown polar lipid and one unknown aminophospholipid. Additionally, the functional analysis of NA20T showed the conversion of protopanaxatriol-mix type major ginsenosides (Rb1, Rc and Rd) to minor ginsenosides F2 and weak conversion of Rh2 and C-K within 24 h. As a result, the genotypic, phenotypic and taxonomic analyses support the affiliation of NA20T within the genus Terrimonas, for which the name Terrimonas ginsenosidimutans sp. nov. is proposed. The type strain is NA20T (=KACC 22218T=LMG 32198T).
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Affiliation(s)
- Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyong National University, 327 Jungang-ro Anseong-si, Gyonggi-do 17579, Republic of Korea
- AceEMzyme Co., Ltd., Academic Industry Cooperation, 327 Jungang-ro Anseong-si, Gyonggi-do 17579, Republic of Korea
| | - Ji Eun Lee
- HK Ginseng Research Center, Hankyong National University, Anseong 17579, Republic of Korea
| | - Min Ok Jun
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Md Amdadul Huq
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| | - Wan-Taek Im
- Department of Biotechnology, Hankyong National University, 327 Jungang-ro Anseong-si, Gyonggi-do 17579, Republic of Korea
- AceEMzyme Co., Ltd., Academic Industry Cooperation, 327 Jungang-ro Anseong-si, Gyonggi-do 17579, Republic of Korea
- HK Ginseng Research Center, Hankyong National University, Anseong 17579, Republic of Korea
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Choi GM, Liu Q, Liu Q, Jun MO, Choi WJ, Yong Kim S, Wee JH, Im WT. Hanamia caeni gen. nov., sp. nov., a Member of the Family Chitinophagaceae Isolated from Activated Sludge in Korea. Curr Microbiol 2022; 79:134. [PMID: 35294641 DOI: 10.1007/s00284-022-02814-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 02/17/2022] [Indexed: 11/03/2022]
Abstract
A novel Gram-stain-negative, aerobic, yellowish-pigmented, non-motile, rod-shaped bacterial strain, designated strain BO-59T, was isolated from the activated sludge of a wastewater treatment plant in Hanam City, South Korea. Phylogenetic study based on the 16S rRNA gene sequence positioned BO-59T in a distinct lineage in the family Chitinophagaceae, sharing less than 92.8% sequence similarity with members of the closely related genera Ferruginibacter, Flavitalea, Pseudoflavitalea, Flavisolibacter, Niastella, and Terrimonas. Phylogenomic- and genomic relatedness analyses revealed that strain BO-59T is clearly distinguished from other genera in the family Chitinophagaceae by average nucleotide identity < 66.9%) and the genome-to-genome distance (< 29.5%) values. The strain BO-59T contained MK-7 as the predominant quinone, and iso-C15:0, iso-C17:0 3OH, and iso-C15:1 G as major fatty acids (> 10%). The DNA G + C content was 39.1 mol% based on genome sequence analysis. The polar lipids of strain BO-59T were phosphatidylethanolamine, an unidentified aminophospholipid and three unidentified polar lipids. 16S rRNA gene sequence similarity, physiological, and biochemical characteristics indicated that strain BO-59T represents a novel species of a new genus, for which the name Hanamia caeni gen. nov., sp. nov. is proposed. The type strain is BO-59T (= KACC 19646T = LMG 30865 T).
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Affiliation(s)
- Gyu-Min Choi
- Department of Biotechnology, Hankyong National University, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea.,AceEMzyme Co., Ltd., Academic Industry Cooperation, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea
| | - Qingmei Liu
- Department of Biotechnology, Hankyong National University, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea.,AceEMzyme Co., Ltd., Academic Industry Cooperation, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea.,HK Ginseng Research Center, Hankyong National University, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea
| | - Qingzhen Liu
- Department of Biotechnology, Hankyong National University, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea.,AceEMzyme Co., Ltd., Academic Industry Cooperation, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea
| | - Min Ok Jun
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, 56212, Jeollabuk-do, Republic of Korea
| | - Won Jung Choi
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, 56212, Jeollabuk-do, Republic of Korea
| | - Sang Yong Kim
- Department of Food Science & Bio Technology, Shinansan University, Ansan, Republic of Korea
| | - Ji-Hyang Wee
- Department of Food Science & Bio Technology, Shinansan University, Ansan, Republic of Korea
| | - Wan-Taek Im
- Department of Biotechnology, Hankyong National University, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea. .,AceEMzyme Co., Ltd., Academic Industry Cooperation, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea. .,HK Ginseng Research Center, Hankyong National University, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea.
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Koyama H, Iwasa M, Maeno Y, Tsuchimochi T, Isobe I, Yoshimi SN, Jun MO, Matsumoto T, Horii T, Nagao M. Y-chromosomal STR haplotype in the Japanese population. Forensic Sci Int 2001; 124:221-3. [PMID: 11792515 DOI: 10.1016/s0379-0738(01)00572-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Allele and haplotype frequencies of seven Y-chromosome STR loci from samples of 108 unrelated Japanese males living in Aichi Prefecture.
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Affiliation(s)
- H Koyama
- Department of Legal Medicine, Medical School, Nagoya City University Hospital, Kawasumi Mizuho-ku, Nagoya 467-8601, Japan
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