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Park Y, Ten LN, Lee YK, Jung HY, Kim MK. Larkinella humicola sp. nov., a gamma radiation-resistant bacterium isolated from soil. Arch Microbiol 2022; 204:182. [PMID: 35179646 DOI: 10.1007/s00203-022-02790-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 01/16/2022] [Accepted: 02/01/2022] [Indexed: 11/02/2022]
Abstract
A Gram-negative, short rod-shaped, and pink-pigmented bacterial strain, designated MA1T, was isolated from a soil sample from Gijang-gun, Busan in Republic of Korea. The 16S rRNA gene sequence analysis showed that strain MA1T belonged to the genus Larkinella and was closely related to "Larkinella punicea" (97.5% similarity), Larkinella rosea 15J16-1T3AT (96.5%), and Larkinella knui 15J6-3T6T (96.2%). Polar lipid profile of strain MA1T contained phosphatidylethanolamine, two unidentified aminolipids, and three unidentified lipids. Menaquinone-7 was the only quinone and the main fatty acids were C16:1 ω5c (36.7%), iso-C15:0 (30.0%), iso-C17:0 3-OH (7.7%), and summed feature 3 (C16:1 ω6c and/or C16:1 ω7c and/or iso-C15:0 2-OH) (7.3%). The genomic DNA G + C content was 52.3 mol% based on the whole-genome analysis. Strain MA1T exhibited a relatively low level of ANI and in silico DDH values with "Larkinella punicea" (91.9 and 47.1%, respectively), Larkinella rosea (79.7 and 23.3%), and Larkinella knui (81.9 and 25.7%). Based on its phenotypic properties and phylogenetic distinctiveness, strain MA1T should be classified in the genus Larkinella as a representative of a novel species, for which the name Larkinella humicola sp. nov. is proposed. The type strain is MA1T (= KCTC 72629T = NBRC 114191T).
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Affiliation(s)
- Yuna Park
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 01797, Republic of Korea
| | - Leonid N Ten
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Young Koung Lee
- Institute of Plasma Technology, Korea Institute of Fusion Energy, 37 Dongjangsan-ro, Gunsan, Jeollabuk, 54004, Republic of Korea
| | - Hee-Young Jung
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea. .,Institute of Plant Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Myung Kyum Kim
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 01797, Republic of Korea.
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Kang H, Cha I, Kim H, Joh K. Spirosoma telluris sp. nov. and Spirosoma arboris sp. nov. isolated from soil and tree bark, respectively. Int J Syst Evol Microbiol 2020; 70:5355-5362. [DOI: 10.1099/ijsem.0.004418] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Two novel strains (HMF3257T and HMF4905T), isolated from freshwater and bark samples, were investigated to determine their relationships within and between species of the genus
Spirosoma
by using a polyphasic approach. They were aerobic, Gram-stain-negative, non-motile and rod-shaped bacteria. The major fatty acids (>10%) in both strains were identified as summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c) and C16 : 1
ω5c, while strains HMF3257T and HMF4905T contained a moderately high amount of C16 : 0 and iso-C15 : 0, respectively. The predominant respiratory quinone was MK-7 for both strains. In addition to phosphatidylethanolamine and one unidentified glycolipid, the polar lipid profile of strain HMF3257T consisted of three unidentified aminophospholipids, one unidentified aminolipid and two unidentified polar lipids, and that of strain HMF4905T consisted of one unidentified aminophospholipid, two unidentified aminolipids and three unidentified polar lipids. The DNA G+C contents of strains HMF3257T and HMF4905T were 47.2 and 46.4 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains HMF3257T and HMF4905T are closely related to
Spirosoma migulaei
15J9-8T (97.0 % sequence similarity), while sharing 97.4 % sequence similarity with each other. The average nucleotide identity value between strains HMF3257T and HMF4905T was 81.1 %, and the digital DNA–DNA hybridization value between these two strains was 24.4 %. Based on the above data, strains HMF3257T and HMF4905T represent two novel members within the genus
Spirosoma
, for which the names Spirosoma telluris sp. nov. and Spirosoma arboris sp. nov. are proposed, respectively. The type strain of S. telluris is HMF3257T (=KCTC 62463T=NBRC 112670T) and type strain of S. arboris is HMF4905T (=KCTC 72779T=NBRC 114270T).
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Affiliation(s)
- Heeyoung Kang
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Inseong Cha
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Haneul Kim
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Kiseong Joh
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
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Kang MS, Srinivasan S. Complete genome sequence of Methylobacterium sp. 17Sr1-43, a radiation-resistant bacterium. Mol Cell Toxicol 2018. [DOI: 10.1007/s13273-018-0050-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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5
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Complete genome sequence of Nibribacter radioresistens DG15C, a radiation resistant bacterium. Mol Cell Toxicol 2018. [DOI: 10.1007/s13273-018-0035-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Complete genome sequence of Spirosoma pulveris JSH 5-14T, a bacterium isolated from a dust sample. Mol Cell Toxicol 2017. [DOI: 10.1007/s13273-017-0041-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Kim EB, Kang MS, Joo ES, Jeon SH, Jeong SW, Lim SY, Jung HY, Srinivasan S, Kim MK. Deinococcus ruber sp. nov., a radiation-resistant bacterium isolated from soil. Int J Syst Evol Microbiol 2017; 67:72-76. [DOI: 10.1099/ijsem.0.001567] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Eun Bit Kim
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 139-774, Republic of Korea
| | - Myung Suk Kang
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 404-107, Republic of Korea
| | - Eun Sun Joo
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 139-774, Republic of Korea
| | - Seon Hwa Jeon
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 139-774, Republic of Korea
| | - Sun Wook Jeong
- Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
| | - Sang Yong Lim
- Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
| | - Hee Young Jung
- Institute of Plant Medicine, Kyungpook National University, Daegu 702-701, Republic of Korea
- College of Agricultural and Life Sciences, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 139-774, Republic of Korea
| | - Myung Kyum Kim
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 139-774, Republic of Korea
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Jeon SH, Kang MS, Joo ES, Kim EB, Lim S, Jeong SW, Jung HY, Srinivasan S, Kim MK. Deinococcus persicinus sp. nov., a radiation-resistant bacterium from soil. Int J Syst Evol Microbiol 2016; 66:5077-5082. [DOI: 10.1099/ijsem.0.001473] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Seon Hwa Jeon
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 139-774, Republic of Korea
| | - Myung-Suk Kang
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 404-107, Republic of Korea
| | - Eun Sun Joo
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 139-774, Republic of Korea
| | - Eun Bit Kim
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 139-774, Republic of Korea
| | - Sangyong Lim
- Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
| | - Sun-wook Jeong
- Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
| | - Hee-Young Jung
- College of Agricultural and Life Sciences, Kyungpook National University, Daegu 702-701, Republic of Korea
- Institute of Plant Medicine, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 139-774, Republic of Korea
| | - Myung Kyum Kim
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 139-774, Republic of Korea
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Choi SG, Jeon SH, Lee JB, Joo ES, Lim S, Jung HY, Kim MK. Deinococcus rubellus sp. nov., bacteria isolated from the muscle of antarctic fish. J Microbiol 2016; 54:796-801. [PMID: 27888462 DOI: 10.1007/s12275-016-6390-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 08/31/2016] [Accepted: 09/21/2016] [Indexed: 11/28/2022]
Abstract
Two new bacterial strains designated as Ant6T and Ant18 were isolated from the muscle of a fish which had been caught in the Antarctic Ocean. Both strains are Gram-stain-positive, catalase positive, oxidase negative, aerobic, and coccoid bacteria. Phylogenetic analysis based on the 16S rRNA gene sequences of strains Ant6T and Ant18 revealed that the strains Ant6T and Ant18 belong to the genus Deinococcus in the family Deinococcaceae in the class Deinococci. The highest degrees of sequence similarities of strains Ant6T and Ant18 were found with Deinococcus alpinitundrae LMG 24283T by 96.4% and 96.8%, respectively. Strain Ant6T exhibited a high level of DNA- DNA hybridization values with strain Ant18 (82 ± 0.6%). Chemotaxonomic data revealed that the predominant fatty acids were C17: 0 cyclo, 16:0, and feature 3 (C16:1 ω6c/ω7c) for both strains. A complex polar lipid profile consisted of major amounts of unknown phosphoglycolipids (PGL) and unknown aminophospholipid (APL). Based on the phylogenetic, phenotypic, and chemotaxonomic data, strains Ant6T (=KEMB 9004-169T =JCM 31434T) and Ant18 (=KEMB 9004-170) should be classified as a new species, for which the name Deinococcus rubellus sp. nov. is proposed.
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Affiliation(s)
- Seok-Gwan Choi
- Distant-water Fisheries Resources Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Seon Hwa Jeon
- Department of Bio and Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 01797, Republic of Korea
| | - Jae-Bong Lee
- Distant-water Fisheries Resources Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Eun Sun Joo
- Department of Bio and Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 01797, Republic of Korea
| | - Sangyong Lim
- Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 34057, Republic of Korea
| | - Hee-Young Jung
- College of Agricultural and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea.,Institute of Plant Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Myung Kyum Kim
- Department of Bio and Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 01797, Republic of Korea.
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Sun Joo E, Jin Lee J, Kang MS, Lim S, Jeong SW, Bit Kim E, Hwa Jeon S, Srinivasan S, Kyum Kim M. Deinococcus actinosclerus sp. nov., a novel bacterium isolated from soil of a rocky hillside. Int J Syst Evol Microbiol 2016; 66:1003-1008. [DOI: 10.1099/ijsem.0.000825] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Eun Sun Joo
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul 139-774, Korea
| | - Jae Jin Lee
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul 139-774, Korea
| | - Myung-Suk Kang
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 404-107, Republic of Korea
| | - Sangyong Lim
- Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
| | - Sun-wook Jeong
- Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
| | - Eun Bit Kim
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul 139-774, Korea
| | - Seon Hwa Jeon
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul 139-774, Korea
| | - Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul 139-774, Korea
| | - Myung Kyum Kim
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul 139-774, Korea
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Hymenobacter rubidus sp. nov., bacterium isolated from a soil. Antonie van Leeuwenhoek 2016; 109:457-66. [DOI: 10.1007/s10482-016-0652-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 01/13/2016] [Indexed: 01/28/2023]
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12
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Joo ES, Cha S, Kim MK, Jheong W, Seo T, Srinivasan S. Flavisolibacter swuensis sp. nov. isolated from soil. J Microbiol 2015; 53:442-7. [PMID: 26115992 DOI: 10.1007/s12275-015-5241-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/12/2015] [Accepted: 06/12/2015] [Indexed: 10/23/2022]
Abstract
A Gram-staining-negative, non-motile, non-spore-forming, and rod-shaped bacterium designated as strain SR2-4-2(T) was isolated from soil in South Korea. Phylogenetic analysis based on 16S rRNA gene sequence of strain SR2-4-2(T) revealed that it belonged to the genus of Flavisolibacter, family of Chitinophagaceae, and class of Sphingobacteriia. It shared sequence similarities with Flavisolibacter ginsengisoli Gsoil 643(T) (96.4%), Flavisolibacter ginsengiterrae Gsoil 492(T) (96.3%), and Flavisolibacter rigui 02SUJ3(T) (93.0%). Chemotaxonomic data revealed that its predominant fatty acids were iso-C15:0 (26.4%) and iso-C17:0 3OH (10.7%). Its major polar lipid was phosphatidylethanolamine (PE) and its predominant respiratory quinone was MK-7. The G+C content of genomic DNA of the strain SR2-4-2(T) DNA was 45.0%. Based on the phylogenetic, chemotaxonomic, and phenotypic data, the strain SR2-4-2(T) (=JCM 19974(T) =KEMB 9004-156(T)) is classified as a type strain of a novel species for which the name of Flavisolibacter swuensis sp. nov. is proposed.
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Affiliation(s)
- Eun Sun Joo
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 139-774, Republic of Korea
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