Journal of Microbiology

Journal Articles

Integrated proteomic and metabolomic analyses reveal significant changes in chloroplasts and mitochondria of pepper (Capsicum annuum L.) during Sclerotium rolfsii infection: Hongdong Liao , Xiangyu Wen , Xuelei Deng , Yonghong Wu , Jianping Xu , Xin Li , Shudong Zhou , Xuefeng Li , Chunhui Zhu , Feng Luo , Yanqing Ma , Jingyuan Zheng; J. Microbiol. 2022;60(5):511-525. Published online March 31, 2022; DOI: https://doi.org/10.1007/s12275-022-1603-4

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Infection by Sclerotium rolfsii will cause serious disease and lead to significant economic losses in chili pepper. In this study, the response of pepper during S. rolfsii infection was explored by electron microscopy, physiological determination and integrated proteome and metabolome analyses. Our results showed that the stomata of pepper stems were important portals for S. rolfsii infection. The plant cell morphology was significantly changed at the time of the fungal hyphae just contacting (T1) or surrounding (T2) the pepper. The chlorophyll, carotenoid, and MDA contents and the activities of POD, SOD, and CAT were markedly upregulated at T1 and T2. Approximately 4129 proteins and 823 metabolites were clearly identified in proteome and metabolome analyses, respectively. A change in 396 proteins and 54 metabolites in pepper stem tissues was observed at T1 compared with 438 proteins and 53 metabolites at T2. The proteins and metabolites related to photosynthesis and antioxidant systems in chloroplasts and mitochondria were disproportionally affected by S. rolfsii infection, impacting carbohydrate and amino acid metabolism. This study provided new insights into the response mechanism in pepper stems during S. rolfsii infection, which can guide future work on fungal disease resistance breeding in pepper.

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Multifaceted chemical and bioactive features of Ag@TiO2 and Ag@SeO2 core/shell nanoparticles biosynthesized using Beta vulgaris L. extract
Khaled M. Elattar, Fatimah O. Al-Otibi, Mohammed S. El-Hersh, Attia A. Attia, Noha M. Eldadamony, Ashraf Elsayed, Farid Menaa, WesamEldin I.A. Saber
Heliyon.2024; 10(7): e28359. CrossRef
Fighting for Survival at the Stomatal Gate
Maeli Melotto, Brianna Fochs, Zachariah Jaramillo, Olivier Rodrigues
Annual Review of Plant Biology .2024; 75(1): 551. CrossRef
Zinc and Boron Soil Applications Affect Athelia rolfsii Stress Response in Sugar Beet (Beta vulgaris L.) Plants
Tamalika Bhadra, Chandan Kumar Mahapatra, Md. Hosenuzzaman, Dipali Rani Gupta, Abeer Hashem, Graciela Dolores Avila-Quezada, Elsayed Fathi Abd_Allah, Md. Anamul Hoque, Swapan Kumar Paul
Plants.2023; 12(19): 3509. CrossRef
Genetic Regulation, Environmental Cues, and Extraction Methods for Higher Yield of Secondary Metabolites in Capsicum
Khushbu Islam, Abdul Rawoof, Ajay Kumar, John Momo, Ilyas Ahmed, Meenakshi Dubey, Nirala Ramchiary
Journal of Agricultural and Food Chemistry.2023; 71(24): 9213. CrossRef
Integrated pathological, proteomic and metabolomic analyses reveal significant changes of Eriocheir sinensis hepatopancreatic in response to the microsporidian Hepatospora eriocheir infection
Libo Hou, Mengdi Wang, Hao Li, Lei Zhu, Xianghui Kong, Wei Gu, Keran Bi, Jie Du, Qingguo Meng
Aquaculture.2023; 577: 739994. CrossRef

Mucilaginibacter limnophilus sp. nov., isolated from a lake: Shih-Yi Sheu , Yi-Ru Xie , Wen-Ming Chen; J. Microbiol. 2019;57(11):967-975. Published online August 28, 2019; DOI: https://doi.org/10.1007/s12275-019-9146-z

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A polyphasic taxonomy approach was used to characterize strain YBJ-36T, isolated from a freshwater lake in Taiwan. Phylogenetic analyses, based on 16S rRNA gene sequences and coding sequences of an up-to-date bacterial core gene set (92 protein clusters), indicated that strain YBJ-36T formed a phylogenetic lineage in the genus Mucilaginibacter. 16S rRNA gene sequence similarity indicated that strain YBJ-36T is closely related to species within the genus Mucilaginibacter (93.8–97.8% sequence similarity) and is most similar to Mucilaginibacter fluminis TTM-2T (97.8%), followed by Mucilaginibacter roseus TTM-1T (97.2%). Microbiological analyses demonstrated that strain YBJ-36T is Gram-negative, aerobic, non-motile, rod-shaped, surrounded by a thick capsule, and forms pink-colored colonies. Strain YBJ-36T grew between 20–40°C (optimal range, 35–37°C), pH 5.5–7.0 (optimal pH of 6) and 0–2% NaCl (optimal concentration, 0.5%). The predominant fatty acids of strain YBJ-36T are iso-C15:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), the major polar lipid is phosphatidylethanolamine, the major polyamine is homospermidine, and the major isoprenoid quinone is MK-7. The draft genome is approximately 4.63 Mb in size with a G+C content of 42.8 mol%. Strain YBJ-36T exhibited less than 35% DNA-DNA relatedness with Mucilaginibacter fluminis TTM-2T and Mucilaginibacter roseus TTM-1T. Based on phenotypic and genotypic properties and phylogenetic inference, strain YBJ-36T should be classified in a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter limnophilus sp. nov. is proposed. The type strain is YBJ-36T (= BCRC 81056T = KCTC 52811T = LMG 30058T).

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Complete genomes of Mucilaginibacter sabulilitoris SNA2 and Mucilaginibacter sp. cycad4: microbes with the potential for plant growth promotion
Ann M. Hirsch, Ethan Humm, Liudmilla Rubbi, Giorgia Del Vecchio, Sung Min Ha, Matteo Pellegrini, Robert P. Gunsalus, Leighton Pritchard
Microbiology Resource Announcements.2024;[Epub] CrossRef
Mucilaginibacter sp. Strain Metal(loid) and Antibiotic Resistance Isolated from Estuarine Soil Contaminated Mine Tailing from the Fundão Dam
Ana L. S. Vasconcelos, Fernando Dini Andreote, Thaiane Defalco, Endrews Delbaje, Leticia Barrientos, Armando C. F. Dias, Fabricio Angelo Gabriel, Angelo F. Bernardino, Kattia Núñez-Montero
Genes.2022; 13(2): 174. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(3): 1443. CrossRef
Reclassification of genus Izhakiella into the family Erwiniaceae based on phylogenetic and genomic analyses
Lingmin Jiang, Dexin Wang, Ji-Sun Kim, Ju Huck Lee, Dae-Hyuk Kim, Suk Weon Kim, Jiyoung Lee
International Journal of Systematic and Evolutionary Microbiology .2020; 70(5): 3541. CrossRef

Hymenobacter jeollabukensis sp. nov., isolated from soil: Leonid N. Ten , Young Eun Han , Kyeung Il Park , In-Kyu Kang , Jeung-Sul Han , Hee-Young Jung; J. Microbiol. 2018;56(7):500-506. Published online June 28, 2018; DOI: https://doi.org/10.1007/s12275-018-8085-4

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Abstract

A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterial strain, designated 1-3-3-8T, was isolated from soil and characterized taxonomically using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain 1-3-3-8T belongs to the family Cytophagaceae of phylum Bacteroidetes and is most closely related to Hymenobacter paludis KBP-30T (96.8% similarity), Hymenobacter ocellatus Myx2105T (96.8%), Hymenobacter coalescens WW84T (95.6%), and Hymenobacter deserti ZLB-3T (95.4%). The G + C content of the genomic DNA of strain 1-3-3-8T was 63.6 mol%. The isolate contained C15:0 iso (28.4%), summed feature 4 (C17:1 anteiso B/C17:1 iso I; 18.9%), and C15:0 anteiso (17.6%) as major fatty acids, MK-7 as the predominant respiratory quinone, and sym-homospermidine as the predominant polyamine. The major polar lipids were phosphatidylethanolamine and an unidentified lipid. The phenotypic and chemotaxonomic data supported the affiliation of strain 1-3-3-8T with the genus Hymenobacter. The DNA-DNA relatedness between strain 1-3-3-8T and H. paludis KCTC 32237T and H. ocellatus DSM 11117T were 24.5 and 27.4% respectively, clearly showing that the isolate is not related to them at the species level. Overall, the novel strain could be differentiated from its phylogenetic neighbors on the basis of several phenotypic, genotypic, and chemotaxonomic features. Therefore, strain 1-3-3-8T represents a novel species of the genus Hymenobacter, for which the name Hymenobacter jeollabukensis sp. nov. has been proposed. The type strain is 1-3-3-8T (= KCTC 52741T = JCM 32192T).

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Isolation and characterization of two new species, Hymenobacter mellowenesis sp. nov. and Hymenobacter aranciens sp. nov., from soil
Seonjae Kim, Sathiyaraj Srinivasan, Myung Kyum Kim
Archives of Microbiology.2024;[Epub] CrossRef
Hymenobacter canadensis sp. nov., isolated from freshwater of the pond in Cambridge Bay, Canada
Woohyun Kim, Seonghan Jang, Namyi Chae, Mincheol Kim, Jung-Yong Yeh, Sanghee Kim, Yung Mi Lee
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Compositional Data Analysis of 16S rRNA Gene Sequencing Results from Hospital Airborne Microbiome Samples
Maria Rita Perrone, Salvatore Romano, Giuseppe De Maria, Paolo Tundo, Anna Rita Bruno, Luigi Tagliaferro, Michele Maffia, Mattia Fragola
International Journal of Environmental Research and Public Health.2022; 19(16): 10107. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology.2019; 69(1): 5. CrossRef
Hymenobacter oligotrophus sp. nov., isolated from a contaminated agar plate
Yingchao Geng, Yumin Zhang, Jin Tian, Jia Liu, Kun Qin, Yao Huang, Ziyan Wei, Fang Peng
Antonie van Leeuwenhoek.2019; 112(10): 1533. CrossRef
Hymenobacter edaphi sp. nov., isolated from abandoned arsenic-contaminated farmland soil
Li Nie, Xia Fan, Dongfang Xiang, Shuijiao Liao, Gejiao Wang
International Journal of Systematic and Evolutionary Microbiology.2019; 69(9): 2921. CrossRef

Characterization of Flavobacterium aquimarinum sp. nov., a halotolerant bacterium isolated from seawater: Sylvia Kristyanto , Tuan Manh Nguyen , Dhiraj Kumar Chaudhary , Sang-Seob Lee , Jaisoo Kim; J. Microbiol. 2018;56(5):317-323. Published online May 2, 2018; DOI: https://doi.org/10.1007/s12275-018-7454-3

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Abstract

A novel, aerobic, Gram-stain-negative, non-motile, non-spore forming, rod-shaped bacterium, designated strain Dol 15-39T, was isolated from a seawater sample near Geoje Island in the South Sea, Republic of Korea. The strain was found to be oxidase-negative and catalase-positive. The isolate was observed to grow at temperatures from 4 to 37°C, at salinities of up to 7%, and at pH levels from 6 to 9; moreover, it was not able to degrade starch, DNA, esculin, or tyrosine. Phylogenetic analysis based on 16S rRNA gene sequences showed that Dol 15-39T was most closely related to Flavobacterium jumunjinense HME7102T with a sequence similarity of 97.3%. However, the levels of DNA-DNA relatedness between Dol 15-39T and the most closely related species were much lower than 70%, confirming that they represented distinct genomic species. The genomic DNA G + C content of Dol 15-39T was calculated to be 32.6 mol%. MK-6 was the predominant respiratory quinine, while iso-C15:0 (25.0%), iso- C15:1 G (17.0%), and iso-C17:0 3-OH (10.4%) were the major cellular fatty acids. Phosphatidylethanolamine was identified as a major polar lipid, while various unidentified aminolipids and polar lipids were also detected. Based on polyphasic taxonomic data, Dol 15-39T represents a novel species of the genus Flavobacterium, for which the name F. aquimarinum sp. nov. is proposed. The type strain is accessible under the culture collection numbers (KEMB 9005-617T = JCM 31930T).

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Flavobacterium adhaerens sp. nov. and Flavobacterium maritimum sp. nov., two novel flavobacteria isolated from the Pearl River Estuary
Zi-Qi Peng, Jia-Ling Li, Zi-Wen Yang, Pan-Deng Wang, Dan-Yuan Guo, Xiao-Qing Luo, Qi-Qi Deng, Qi Li, Ting-Ting She, Wen-Jun Li
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Flavobacterium frigoritolerans sp. nov. and Flavobacterium shii sp. nov., isolated from glaciers on the Tibetan Plateau
Lei-Lei Yang, Hong-Can Liu, Yu-Hua Xin, Qing Liu
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Identification of Flavobacterium algoritolerans sp. nov. and Flavobacterium yafengii sp. nov., two novel members of the genus Flavobacterium
Ce-Ce Yin, Lei-Lei Yang, Yu-Hua Xin, Jian Ye, Qing Liu
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Ten Novel Species Belonging to the Genus Flavobacterium, Isolated from Freshwater Environments: F. praedii sp. nov., F. marginilacus sp. nov., F. aestivum sp. nov., F. flavigenum sp. nov., F. luteolum sp. nov., F. gelatinilyticum sp. nov., F. aquiphilum s
Hyunyoung Jo, Miri S. Park, Yeonjung Lim, Ilnam Kang, Jang-Cheon Cho
Journal of Microbiology.2023; 61(5): 495. CrossRef
Description of Flavobacterium cyclinae sp. nov. and Flavobacterium channae sp. nov., isolated from the intestines of Cyclina sinensis (Corb shell) and Channa argus (Northern snakehead)
Seomin Kang, Jae-Yun Lee, Jeong Eun Han, Yun-Seok Jeong, Do-Hun Gim, Jin-Woo Bae
Journal of Microbiology.2022; 60(9): 890. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology.2018; 68(9): 2707. CrossRef

Hymenobacter terrigena sp. nov., isolated from soil: Jeong-Eun Ohn , Leonid N. Ten , Kyeung Il Park , Byung-Oh Kim , Jeung-Sul Han , Hee-Young Jung; J. Microbiol. 2018;56(4):231-237. Published online April 2, 2018; DOI: https://doi.org/10.1007/s12275-018-8029-z

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Abstract

A Gram-stain-negative, non-motile, non-spore-forming, rodshaped, aerobic bacterial strain, designated S1-2-2-5T, was isolated from the Jeollabuk-do province, Republic of Korea, and was characterized taxonomically using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain S1-2-2-5T belonged to the family Cytophagaceae in phylum Bacteroidetes, and was most closely related to Hymenobacter terrae DG7AT (98.2%), Hymenobacter rubidus DG7BT (98.0%), Hymenobacter soli PB17T (97.7%), Hymenobacter daeguensis 16F3Y-2T (97.2%) and Hymenobacter saemangeumensis GSR0100T (97.0%). The G + C content of the genomic DNA of strain S1-2-2-5T was 59.4 mol%. The detection of menaquinone MK-7 as the predominant respiratory quinone, a fatty acid profile with summed feature 3 (C16:1 ω7c/C16:1 ω6c; 32.0%), C15:0 iso (19.0%), and C15:0 anteiso (15.0%) as the major components, and a polar lipid profile with phosphatidylethanolamine as the major component supported the affiliation of strain S1-2-2-5T to the genus Hymenobacter. The DNA-DNA relatedness between strain S1-2-2-5T and H. terrae KCTC 32554T, H. rubidus KCTC 32553T, H. soli KCTC 12607T, H. daeguensis KCTC 52537T, and H. saemangeumensis KACC 16452T were 49.5, 48.2, 34.1, 28.1, and 31.8% respectively, clearly showing that the isolate is not related to them at the species level. Strain S1-2-2-5T could be clearly differentiated from its closest neighbors on the basis of its phenotypic, genotypic and chemotaxonomic features. Therefore, strain S1-2-2-5T represents a novel species of the genus Hymenobacter, for which the name Hymenobacter terrigena sp. nov. is proposed. The type strain is S1-2-2-5T (= KCTC 52737T = JCM 32195T).

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Isolation and characterization of two new species, Hymenobacter mellowenesis sp. nov. and Hymenobacter aranciens sp. nov., from soil
Seonjae Kim, Sathiyaraj Srinivasan, Myung Kyum Kim
Archives of Microbiology.2024;[Epub] CrossRef
Hymenobacter canadensis sp. nov., isolated from freshwater of the pond in Cambridge Bay, Canada
Woohyun Kim, Seonghan Jang, Namyi Chae, Mincheol Kim, Jung-Yong Yeh, Sanghee Kim, Yung Mi Lee
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Hymenobacter cyanobacteriorum sp. nov., isolated from a freshwater reservoir during the cyanobacterial bloom period
Ve Van Le, So-Ra Ko, Mingyeong Kang, Hee-Mock Oh, Chi-Yong Ahn
Archives of Microbiology.2022;[Epub] CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology.2018; 68(9): 2707. CrossRef

Spirosoma pomorum sp. nov., isolated from apple orchard soil: Weilan Li , Seung-Yeol Lee , In-Kyu Kang , Leonid N. Ten , Hee-Young Jung; J. Microbiol. 2018;56(2):90-96. Published online February 2, 2018; DOI: https://doi.org/10.1007/s12275-018-7430-y

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Abstract

A Gram-negative, motile, rod-shaped, aerobic bacterial strain, designated S7-2-11T, was isolated from apple orchard soil from Gyeongsangnam-do Province, Republic of Korea, and was characterized taxonomically using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain S7-2- 11T belongs to the family Cytophagaceae in phylum Bacteroidetes, and is closely related to Spirosoma luteolum 16F6ET (94.2% identity), Spirosoma knui 15J8-12T (92.7%), and Spirosoma linguale DSM 74T (91.0%). The G + C content of the genomic DNA of strain S7-2-11T was 49.8 mol%. Strain S7-2-11T contained summed feature 3 (C16:1 ω7c/C16:1 ω6c; 35.1%), C16:1 ω5c (22.4%), C15:0 iso (13.9%), and C17:0 iso 3-OH (10.6%) as major cellular fatty acids, and MK-7 as the predominant respiratory quinone. The main polar lipids were phosphatidylethanolamine, an unidentified aminophospholipid, and two unidentified polar lipids. Phenotypic and chemotaxonomic data supported the affiliation of strain S7-2-11T with the genus Spirosoma. The results of physiological and biochemical tests showed the genotypic and phenotypic differentiation of the isolate from recognized Spirosoma species. On the basis of its phenotypic properties, genotypic distinctiveness, and chemotaxonomic features, strain S7-2-11T represents a novel species of the genus Spirosoma, for which the name Spirosoma pomorum sp. nov. is proposed. The type strain is S7-2-11T (= KCTC 52726T = JCM 32130T).

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Chloroxylenol positively affects the aerobic sequencing batch reactor performance and reshapes microbial communities and antibiotic resistance genes
Qiao Ma, Hanqing Pan, Da Li, Jingwei Wang
Journal of Water Process Engineering.2024; 57: 104642. CrossRef
Isolation of Spirosoma foliorum sp. nov. from the fallen leaf of Acer palmatum by a novel cultivation technique
Ho Le Han, Dian Alfian Nurcahyanto, Neak Muhammad, Yong-Jae Lee, Tra T. H. Nguyen, Song-Gun Kim, Sook Sin Chan, Kuan Shiong Khoo, Kit Wayne Chew, Pau Loke Show, Thi Ngoc Thu Tran, Thi Dong Phuong Nguyen, Chen Yaw Chiu
Scientific Reports.2023;[Epub] CrossRef
Spirosoma rhododendri sp. nov., isolated from a flower of royal azalea (Rhododendron schlippenbachii)
Miyoung Won, Seung-Beom Hong, Byeong-Hak Han, Soon-Wo Kwon
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Barks from avocado trees of different geographic locations have consistent microbial communities
Eneas Aguirre-von-Wobeser, Alexandro Alonso-Sánchez, Alfonso Méndez-Bravo, Luis Alberto Villanueva Espino, Frédérique Reverchon
Archives of Microbiology.2021; 203(7): 4593. CrossRef
Spirosoma endbachense sp. nov., isolated from a natural salt meadow
Julian Rojas, Binoy Ambika Manirajan, Stefan Ratering, Christian Suarez, Rita Geissler-Plaum, Sylvia Schnell
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef
Draft Genome Sequences of Spirosoma agri KCTC 52727 and Spirosoma terrae KCTC 52035
Julian Rojas, Binoy Ambika Manirajan, Stefan Ratering, Christian Suarez, Sylvia Schnell, David Rasko
Microbiology Resource Announcements.2020;[Epub] CrossRef
Spirosoma telluris sp. nov. and Spirosoma arboris sp. nov. isolated from soil and tree bark, respectively
Heeyoung Kang, Inseong Cha, Haneul Kim, Kiseong Joh
International Journal of Systematic and Evolutionary Microbiology .2020; 70(10): 5355. CrossRef
Spirosoma sordidisoli sp. nov., a propanil-degrading bacterium isolated from a herbicide-contaminated soil
Long Zhang, Xi-Yi Zhou, Xiao-Jing Su, Qiang Hu, Jian-Dong Jiang
Antonie van Leeuwenhoek.2019; 112(10): 1523. CrossRef
Spirosoma utsteinense sp. nov. isolated from Antarctic ice-free soils from the Utsteinen region, East Antarctica
Guillaume Tahon, Liesbeth Lebbe, Anne Willems
International Journal of Systematic and Evolutionary Microbiology .2019;[Epub] CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2018; 68(7): 2130. CrossRef

Larkinella roseus sp. nov., a species of the family Cytophagaceae isolated from beach soil: Jae-Bong Lee , Sumin Hong , Seung-Yeol Lee , Su-Jin Park , Kyeung Il Park , Seok-Gwan Choi , Myung Kyum Kim , Leonid N. Ten , Hee-Young Jung; J. Microbiol. 2018;56(1):30-35. Published online January 4, 2018; DOI: https://doi.org/10.1007/s12275-018-7476-x

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Abstract

The taxonomic position of bacterial strain, designated 15J16- 1T3AT, recovered from a soil sample was established using a polyphasic approach. Phylogenic analysis based on the 16S rRNA gene sequence showed that strain 15J16-1T3AT belonged to the family Cytophagaceae, phylum Bacteroidetes, and was most closely related to ‘Larkinella harenae’ 15J9-9 (95.9% similarity), Larkinella ripae 15J11-11T (95.6%), Larkinella bovis M2TB15T (94.7%), Larkinella arboricola Z0532T (93.9%), and Larkinella insperata LMG 22510T (93.5%). Cells were rod-shaped, Gram-stain-negative, aerobic, and nonmotile. The isolate grew on NA, R2A, TSA, but not on LB agar. The strain was able to grow at temperature range from 10°C to 30°C with an optimum at 25°C and pH 6–8. Menaquinone MK-7 was the predominant respiratory quinone. The major cellular fatty acids comprised C16:1 ω5c (48.6%) and C15:0 iso (24.1%). Phosphatidylethanolamine, phosphatidylserine, and an unidentified lipid were the major polar lipids. The G + C content of the genomic DNA was 49.5 mol%. Strain 15J16-1T3AT could be distinguished from its closest phylogenetic neighbors based on its phenotypic, genotypic, and chemotaxonomic features. Therefore, the isolate is considered to represent a novel species in the genus Larkinella, for which the name Larkinella roseus sp. nov. is proposed. The type strain is 15J16-1T3AT (= KCTC 52004T = JCM 31991T).

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Larkinella humicola sp. nov., a gamma radiation-resistant bacterium isolated from soil
Yuna Park, Leonid N. Ten, Young Koung Lee, Hee‑Young Jung, Myung Kyum Kim
Archives of Microbiology.2022;[Epub] CrossRef
Larkinella punicea sp. nov., isolated from manganese mine soil
Zijie Zhou, Lin Zhu, Yixuan Dong, Xian Xia, Shijuan Wu, Gejiao Wang
Archives of Microbiology.2020; 202(9): 2517. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology.2018; 68(5): 1411. CrossRef
Hymenobacter segetis sp. nov., isolated from soil
Leonid N. Ten, Soo Jeong Lim, Byung-Oh Kim, In-Kyu Kang, Hee-Young Jung
Archives of Microbiology.2018; 200(8): 1167. CrossRef

Spirosoma migulaei sp. nov., isolated from soil: Joseph Okiria , Leonid N. Ten , Su-Jin Park , Seung-Yeol Lee , Dong Hoon Lee , In-Kyu Kang , Dae Sung Lee , Hee-Young Jung; J. Microbiol. 2017;55(12):927-932. Published online December 7, 2017; DOI: https://doi.org/10.1007/s12275-017-7377-4

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Abstract

A Gram-stain-negative, non-motile, non-spore-forming, rodshaped, aerobic bacterium, designated 15J9-8T, was isolated from soil on Jeju Island, Republic of Korea. The isolate was able to grow between 10 and 30°C, pH 6.5–8.5, and in presence of 0–1% (w/v) NaCl. The results of comparative 16S rRNA gene sequence analysis indicated that strain 15J9-8T represented a member of the family Cytophagaceae, phylum Bacteroidetes, and was most closely related to Spirosoma aerophilum 5516J-17T (96.1% similarity), Spirosoma pulveris JSH5-14T (95.6%), and Spirosoma linguale DSM 74T (95.2%). The G + C content of the genomic DNA of the isolate was 47.0 mol%. Strain 15J9-8T contained summed feature 3 (C16:1 ω7c/C16:1 ω6c), C16:1 ω5c, and iso-C15:0 as the major fatty acids, phosphatidylethanolamine and an unidentified aminophospholipid as the main polar lipids, and menaquinone MK-7 as the predominant respiratory quinone. On the basis of its phenotypic and genotypic properties, and phylogenetic distinctiveness, strain 15J9-8T should be classified as a representative of a novel species of the genus Spirosoma, for which the name Spirosoma migulaei sp. nov. is proposed. The type strain is 15J9-8T (=KCTC 52028T =JCM 31996T).

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Isolation of Spirosoma foliorum sp. nov. from the fallen leaf of Acer palmatum by a novel cultivation technique
Ho Le Han, Dian Alfian Nurcahyanto, Neak Muhammad, Yong-Jae Lee, Tra T. H. Nguyen, Song-Gun Kim, Sook Sin Chan, Kuan Shiong Khoo, Kit Wayne Chew, Pau Loke Show, Thi Ngoc Thu Tran, Thi Dong Phuong Nguyen, Chen Yaw Chiu
Scientific Reports.2023;[Epub] CrossRef
Spirosoma rhododendri sp. nov., isolated from a flower of royal azalea (Rhododendron schlippenbachii)
Miyoung Won, Seung-Beom Hong, Byeong-Hak Han, Soon-Wo Kwon
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Fibrivirga algicola gen. nov., sp. nov., an algicidal bacterium isolated from a freshwater river
Sanghwa Park, Ja Young Cho, Dong-Hyun Jung, Seok Won Jang, Jung Hye Eom, Seung Won Nam, Dae Ryul Kwon, Jaewon Ryu, Keug Tae Kim
Antonie van Leeuwenhoek.2022; 115(7): 899. CrossRef
Spirosoma telluris sp. nov. and Spirosoma arboris sp. nov. isolated from soil and tree bark, respectively
Heeyoung Kang, Inseong Cha, Haneul Kim, Kiseong Joh
International Journal of Systematic and Evolutionary Microbiology .2020; 70(10): 5355. CrossRef
Complete Genome Sequence of Spirosoma sp. Strain KCTC 42546, Isolated from a Reservoir in South Korea
Pokchut Kusolkumbot, Song-Gun Kim, Chatrudee Suwannachart, Kenneth M. Stedman
Microbiology Resource Announcements.2020;[Epub] CrossRef
Spirosoma sordidisoli sp. nov., a propanil-degrading bacterium isolated from a herbicide-contaminated soil
Long Zhang, Xi-Yi Zhou, Xiao-Jing Su, Qiang Hu, Jian-Dong Jiang
Antonie van Leeuwenhoek.2019; 112(10): 1523. CrossRef
Spirosoma utsteinense sp. nov. isolated from Antarctic ice-free soils from the Utsteinen region, East Antarctica
Guillaume Tahon, Liesbeth Lebbe, Anne Willems
International Journal of Systematic and Evolutionary Microbiology .2019;[Epub] CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology.2018; 68(5): 1411. CrossRef

Spirosoma flavus sp. nov., a novel bacterium from soil of Jeju Island: Nabil Elderiny , Seung-Yeol Lee , Sangkyu Park , In-Kyu Kang , Myung Kyum Kim , Dae Sung Lee , Leonid N. Ten , Hee-Young Jung; J. Microbiol. 2017;55(11):850-855. Published online October 27, 2017; DOI: https://doi.org/10.1007/s12275-017-7360-0

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Abstract

A novel, Gram-staining negative, yellow pigmented bacterial strain, designated 15J11-2T, was isolated from soil sample on Jeju Island, Republic of Korea. The strain was subjected to a taxonomic study using a polyphasic approach. The strain was able to grow at temperature range from 10°C to 30°C, pH 7–8, and in presence of 0–1% (w/v) NaCl. Comparative 16S rRNA gene sequence analysis showed that strain 15J11-2T belongs to the genus Spirosoma and levels of 16S rRNA gene sequence similarity ranged from 91.5% to 89.8%. The genomic DNA G + C content of strain 15J11-2T was 46.0 mol%. The isolate contained phosphatidylethanolamine and an unidentified aminophospholipid as the main polar lipids, menaquinone MK-7 as the predominant respiratory quinone, and summed feature 3 (C16:1 ω6c/C16:1 ω7c; 39.4%), C16:1 ω5c (27.1%), and C16:0 (13.0%) as the major fatty acids, which supported the affiliation of strain 15J11-2T to the genus Spirosoma. The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 15J11-2T from recognized Spirosoma species. On the basis of its phenotypic properties, genotypic distinctiveness, chemotaxonomic features, strain 15J11-2T represents a novel species of the genus Spirosoma, for which the name Spirosoma flavus sp. nov. is proposed. The type strain is 15J11-2T (= KCTC 52026T = JCM 31998T).

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Spirosoma profusum sp. nov., and Spirosoma validum sp. nov., radiation-resistant bacteria isolated from soil in South Korea
Yuna Park, Soohyun Maeng, Tuvshinzaya Damdintogtokh, Jing Zhang, Min-Kyu Kim, Sathiyaraj Srinivasan, Myung Kyum Kim
Antonie van Leeuwenhoek.2021; 114(7): 1155. CrossRef

Spirosoma daeguensis sp. nov., isolated from beach soil: Nabil Elderiny , Leonid N. Ten , Jae-Jin Lee , Seung-Yeol Lee , Sangkyu Park , Young-Je Cho , Myung Kyum Kim , Hee-Young Jung; J. Microbiol. 2017;55(9):678-683. Published online September 2, 2017; DOI: https://doi.org/10.1007/s12275-017-7211-z

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Abstract

A Gram-stain-negative, non-motile, non-spore-forming, rodshaped, aerobic bacterium, designated 15J9-6T, was isolated from beach soil on Jeju Island, South Korea. Strain 15J9-6T, grew at 10–30°C (optimum growth at 25°C) and pH 7–8 (optimum growth at pH 7) on R2A, NA, and TSA agar. Phylogenetically, the strain was closely related to members of the genus Spirosoma (92.3–90.1% 16S rRNA gene sequence similarities) and showed highest sequence similarity to Spirosoma panaciterrae DSM 21099T (92.3%). The G+C content of the genomic DNA of strain 15J9-6T was 45.7 mol%. The strain contained phosphatidylethanolamine, two unidentified aminophospholipids, an unidentified phospholipid, and an unidentified lipid as the major polar lipids; menaquinone MK-7 as the predominant respiratory quinone and summed feature 3 (C16:1 ω6c/C16:1 ω7c; 30.1%), C16:1 ω5c (23.1%), iso C15:0 (13.3%), and C16:0 (8.4%) as the major fatty acids which supported the affiliation of strain 15J9-6T to the genus Spirosoma. The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 15J9-6T from recognized Spirosoma species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain 15J9-6T represents a novel species of the genus Spirosoma, for which the name Spirosoma daeguensis sp. nov. is proposed. The type strain is 15J9-6T (=KCTC 52036T =JCM 31995T)

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Spirosoma rhododendri sp. nov., isolated from a flower of royal azalea (Rhododendron schlippenbachii)
Miyoung Won, Seung-Beom Hong, Byeong-Hak Han, Soon-Wo Kwon
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Spirosoma utsteinense sp. nov. isolated from Antarctic ice-free soils from the Utsteinen region, East Antarctica
Guillaume Tahon, Liesbeth Lebbe, Anne Willems
International Journal of Systematic and Evolutionary Microbiology .2019;[Epub] CrossRef
Spirosoma humi sp. nov., Isolated from Soil in South Korea
Li Weilan, Jae-Jin Lee, Seung-Yeol Lee, Sangkyu Park, Leonid N. Ten, Hee-Young Jung
Current Microbiology.2018; 75(3): 328. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2017; 67(11): 4291. CrossRef

Hymenobacter daeguensis sp. nov. isolated from river water: Leonid N. Ten , Yeon-Hee Lee , Jae-Jin Lee , Su-Jin Park , Seung-Yeol Lee , Sangkyu Park , Dae Sung Lee , In-Kyu Kang , Hee-Young Jung; J. Microbiol. 2017;55(4):253-259. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6524-2

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Abstract

A Gram-stain-negative, non-motile, non-spore-forming, rod- shaped, aerobic bacterial strain, designated 16F3Y-2T, was isolated from the Han River, South Korea, and was charac-terized taxonomically using a polyphasic approach. Compa-rative 16S rRNA gene sequence analysis showed that strain 16F3Y-2T belonged to the family Cytophagaceae in the phy-lum Bacteroidetes and was most closely related to ‘Hymeno-bacter terrae’ DG7A (98.01%), H. soli PB17T (97.26%), H. glaciei VUG-A130T (96.78%), H. antarcticus VUG-A42aaT (96.72%), H. ruber PB156T (96.61%), and H. saemangeumensis GSR0100T (95.77%). The G+C content of the genomic DNA of strain 16F3Y-2T was 62.9 mol%. The isolate contained MK-7 as the predominant respiratory quinone, and summed fea-ture 3 (C16:1 ω7c/C16:1 ω6c; 35.5%), C15:0 iso (16.9%), C16:1 ω5c (10.9%), and C15:0 anteiso (9.9%) as major fatty acids. The ma-jor polar lipid was phosphatidylethanolamine. Phenotypic and chemotaxonomic data supported the affiliation of strain 16F3Y-2T with the genus Hymenobacter. However, strain 16F3Y-2T exhibited relatively low levels of DNA-DNA related-ness with 'H. terrae' KCTC 32554 (44.1%) and H. soli KCTC 12607T (24.3%), clearly indicating that the isolate constitutes a new genospecies. Strain 16F3Y-2T could be differentiated from its phylogenetic neighbors on the basis of several phe-notypic, genotypic, and chemotaxonomic features. Therefore, strain 16F3Y-2T represents a novel species in the genus Hy-menobacter, for which the name Hymenobacter daeguensis sp. nov. is proposed. The type strain is 16F3Y-2T (=KCTC 52537T =JCM 31654T).

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Hymenobacter pomorum sp. nov., Isolated from Apple Orchard Soil
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Hymenobacter jeollabukensis sp. nov., isolated from soil
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Soo-Jeong Lim, Leonid N. Ten, Byung-Oh Kim, In-Kyu Kang, Hee-Young Jung
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Hymenobacter rufus sp. nov., a bacterium isolated from soil
Jeong-Eun Ohn, Leonid N. Ten, Byung-Oh Kim, Young-Je Cho, Hee-Young Jung
International Journal of Systematic and Evolutionary Microbiology.2018; 68(9): 2983. CrossRef
Description of Hymenobacter daejeonensis sp. nov., isolated from grass soil, based on multilocus sequence analysis of the 16S rRNA gene, gyrB and tuf genes
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Hymenobacter agri sp. nov., a novel bacterium isolated from soil
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Hymenobacter terrigena sp. nov., isolated from soil
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Sunxiuqinia dokdonensis sp. nov., Isolated from Deep Sub-Seafloor Sediment: Dong-Ho Chang , Jae-Bong Lee , Geun-Hye Lee , Moon-Soo Rhee , Haewon Lee , Kyung Sook Bae , Doo-Sang Park , Byoung-Chan Kim; J. Microbiol. 2013;51(6):741-746. Published online December 19, 2013; DOI: https://doi.org/10.1007/s12275-013-3492-z

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Abstract

A novel facultatively anaerobic strain DH1T was isolated from deep sub-seafloor sediment at a depth of 900 m below the seafloor off Seo-do (the west part of Dokdo Island) in the East Sea of the Republic of Korea. The new strain was characterized using polyphasic approaches. The isolate was Gram-stain-negative, motile by gliding, non-spore-forming rods, oxidase-negative, and catalase-positive; and formed colonies of orange-red color. The NaCl range for growth was 0.5–7.0% (w/v) and no growth was observed in the absence of NaCl. The isolate grew optimally at 30°C, with 2% (w/v) NaCl and at pH 7. The cell-wall hydrolysates contained ribose as a major sugar. The DNA G+C content was 40.8 mol%. The closest related strains are Sunxiuqinia faeciviva JAM-BA0302T and Sunxiuqinia elliptica DQHS-4T (97.9 and 96.3% sequence similarity, respectively). The level of DNADNA relatedness between strain DH1T and S. faeciviva JAMBA0302T was around 41% (but only 6% between DH1T and S. elliptica DQHS-4T). The major cellular fatty acids of the isolate were contained iso-C15:0 (25.9%), anteiso-C15:0 (16.7%), and summed feature 9 (comprising C16:0 3-OH and/or unknown fatty acid of dimethylacetal ECL 17.157; 13.2%). The predominant menaquinone was MK-7. On the basis of polyphasic evidence from this study, the isolate was considered to represent a novel species of the genus Sunxiuqinia, for which the name Sunxiuqinia dokdonensis sp. nov. is proposed; the type strain is DH1T (=KCTC 32503T =CGMCC 1.12676T =JCM 19380T).

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Whole-genome sequence of Sunxiuqinia dokdonensis DH1 T , isolated from deep sub-seafloor sediment in Dokdo Island
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Wen-Jie Wu, Qian-Qian Liu, Guan-Jun Chen, Zong-Jun Du
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Flavobacterium aquaticum sp. nov., a Member of the Bacteroidetes Isolated from a Freshwater Reservoir: Siwon Lee , Jungnam Lee , Tae-Young Ahn; J. Microbiol. 2013;51(3):283-288. Published online April 26, 2013; DOI: https://doi.org/10.1007/s12275-013-2293-8

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Abstract: A novel bacterial strain, designated ARSA-111T, was isolated from a freshwater reservoir in Cheonan, Korea. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the isolate belonged to the genus Flavobacterium of phylum Bacteroidetes. The 16S rRNA gene sequence of strain ARSA-111T showed a high degree of sequence similarity to those of Flavobacteium cheonanense KACC 14972T (97.3%), F. aquatile JCM 20475T (97.1%), and other type strains of the genus Flavobacterium (＜97.0%). The phylogenetic tree and network analysis (i.e. median-joining) based on 16S rRNA gene sequences showed that strain ARSA-111T is most closely related to F. aquatile JCM 20475T. DNA-DNA hybridization experiment revealed ＜70% of genomic relatedness among strain ARSA-111T, F. aquatile JCM 20475T and F. cheonanense KACC 14972T. The isolate had iso-C15:1, iso-C15:0, and iso-C15:0 3-OH as predominant cellular fatty acids and MK-6 as a predominant menaquinone. The genomic DNA G+C content of the isolate was 35.6 mol%. On the basis of these data, strain ARSA-111T is considered to be a novel species of the genus Flavobacterium, for which the name Flavobacterium aquaticum sp. nov. is proposed. The type strain is strain ARSA-111T (=KACC 14973T =KCTC 23185T = JCM 17070T).

NOTE] Pedobacter jeongneungensis sp. nov., Isolated from Forest Soil: Jaejoon Jung , Woojun Park; J. Microbiol. 2012;50(4):660-664. Published online July 21, 2012; DOI: https://doi.org/10.1007/s12275-012-1629-0

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Abstract

Strain BH45T was isolated from forest soil of Mt. Bukhan in Jeongneung, Seoul, Korea. The Gram-staining-negative strain BH45T grows at 4–30°C (optimum of 25–30°C) and between pH 5–8 (optimum of pH 6–8). Its major cellular fatty acids are C18:3 ω6c (6,9,12) and C10:0. The G+C content of genomic DNA was 40.2 mol%. The major respiratory quinone system in strain BH45T is menaquinone-7. Phylogenetic analysis based on 16S rRNA gene sequences indicates that strain BH45T is closely related to the genus Pedobacter. Sequence similarities with P. terrae KCTC 12762T, P. suwonensis KACC 11317T, P. soli KACC 14939T, P. alluvionis DSM 19624T, P. roseus KCCM 42272T, P. yonginense KCTC 22721T were 97.5, 97.1, 97.0, 97.0, 97.0, and 96.0%, respectively. DNA-DNA hybridization results distinguish strain BH45T from two Pedobacter species with high 16S rRNA gene sequence similarities. According to the phenotypic and molecular data, the strain BH45T clearly represents a novel species within the genus Pedobacter; thus, the name Pedobacter jeongneungensis sp. nov. is proposed for this strain. The type strain is BH45T (=KACC 15514T =JCM 17626T).

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Minkyung Kim, Wonjae Kim, Woojun Park
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Pedobacter vanadiisoli sp. nov., isolated from soil of a vanadium mine
Zhiyong Wang, Yuanqing Tan, Ding Xu, Gejiao Wang, Jihong Yuan, Shixue Zheng
International Journal of Systematic and Evolutionary Microbiology.2016; 66(12): 5112. CrossRef

Flavobacterium koreense sp. nov., Flavobacterium chungnamense sp. nov., and Flavobacterium cheonanense sp. nov., Isolated from a Freshwater Reservoir: Siwon Lee , Hang-Yeon Weon , Soo-Jin Kim , Tae-Young Ahn; J. Microbiol. 2011;49(3):387-392. Published online June 30, 2011; DOI: https://doi.org/10.1007/s12275-011-0382-0

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Abstract: Taxonomic studies were performed on three strains isolated from Cheonho reservoir in Cheonan, Korea. The isolates were Gram-negative, aerobic, rod-shaped, non-motile, catalase-positive, and oxidase-positive. Colonies on solid media were cream-yellow, smooth, shiny, and circular. Phylogenetic analysis of the 16S rRNA gene sequences revealed that these strains belong to the genus Flavobacterium. The strains shared 98.6-99.4% sequence similarity with each other and showed less than 97% similarity with members of the genus Flavobacterium with validly published names. The DNA-DNA hybridization results confirmed the separate genomic status of strains ARSA-42T, ARSA-103T, and ARSA-108T. The isolates contained menaquinone-6 as the predominant menaquinone and iso-C15:0, iso-C15:0 3-OH, iso-C15:1 G, and iso-C16:0 3-OH as the major fatty acids. The genomic DNA G+C content of the isolates were 31.4-33.2 mol%. According to the phenotypic and genotypic data, these organisms are classified as representative of three novel species in the genus Flavobacterium, and the name Flavobacterium koreense sp. nov. (strain ARSA-42T =KCTC 23182T =JCM 17066T =KACC 14969T), Flavobacterium chungnamense sp. nov. (strain ARSA-103T =KCTC 23183T =JCM 17068T =KACC 14971T), and Flavobacterium cheonanense sp. nov. (strain ARSA-108T =KCTC 23184T =JCM 17069T =KACC 14972T) are proposed.

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