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Peng ZQ, Li JL, Yang ZW, Wang PD, Guo DY, Luo XQ, Deng QQ, Li Q, She TT, Li WJ. Flavobacterium adhaerens sp. nov. and Flavobacterium maritimum sp. nov., two novel flavobacteria isolated from the Pearl River Estuary. Int J Syst Evol Microbiol 2024; 74. [PMID: 39041928 DOI: 10.1099/ijsem.0.006471] [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: 07/24/2024] Open
Abstract
Two strains, designated as SYSU M80004T and SYSU M80005T, were isolated from water sampled in the Pearl River Estuary, Guangzhou, Guangdong, PR China. The strains were Gram-stain-negative and aerobic. Strain SYSU M80004T could grow at pH 6.0-8.0 (optimum, pH 7.0), 22-30 °C (optimum, 28 °C) and in the presence of 0-1 % NaCl (w/v; optimum 0 %). Strain SYSU M80005T could grow at pH 6.0-8.0 (optimum, pH 7.0), 4-37 °C (optimum, 28 °C) and in the presence of 0-1 % NaCl (w/v; optimum 0%). Both strains contained MK-6 as the predominant menaquinone. C16 : 0 and iso-C15 : 0 were identified as the major fatty acids (>10 %) of strain SYSU M80004T while strain SYSU M80005T contained iso-C15 : 0 and iso-C17 : 0 3-OH as major fatty acids. Phosphatidylethanolamine was present as the major polar lipid in both strains. The average nucleotide identity and digital DNA-DNA hybridization values between these two strains and their closest relatives were 73.5-79.3 % and 19.6-23.2 %, respectively. Phylogenetic analysis based on the 16S rRNA gene and genomic sequences indicated they belonged to the genus Flavobacterium. Therefore, on the basis of phenotypic, physiological, chemotaxonomic and genomic evidence, two novel species, Flavobacterium adhaerens sp. nov. (type strain=SYSU M80004T=CDMCC 1.4522T=KCTC 102268T) and Flavobacterium maritimum sp. nov. (type strain=SYSU M80005T=CGMCC 1.4523T= KCTC 102269T) are proposed.
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Affiliation(s)
- Zi-Qi Peng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Jia-Ling Li
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, Guangdong, PR China
| | - Zi-Wen Yang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Pan-Deng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Dan-Yuan Guo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Xiao-Qing Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Qi-Qi Deng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Qi Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Ting-Ting She
- School of Biology and Food Engineering, Guangdong University of Education, Guangzhou 510303, Guangdong, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
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Wu N, Liu L, Jiang X, Yuan Y, Mao D, Shao J, He J, Shen Q. Flavobacterium sedimenticola sp. nov., isolated from sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 38054484 DOI: 10.1099/ijsem.0.006180] [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: 12/07/2023] Open
Abstract
A novel yellow-pigmented bacterial strain, designated YZ-48T, was isolated from the sediment of the Yangtze River, PR China. Cells were Gram-stain-negative, non-motile, rod-shaped, strictly aerobic, catalase-positive and oxidase-positive. The strain grew optimally on R2A medium at 37 °C, pH 7.0 and with 1.0 % (w/v) NaCl. Strain YZ-48T showed the closest 16S rRNA gene sequence similarity to Flavobacterium solisilvae SE-s27T (96.4 %) and F. dankookense DSM 25687T (96.2 %). The phylogenetic trees based on 16S rRNA gene sequences showed that strain YZ-48T belonged to the genus Flavobacterium but formed a distinct phylogenetic lineage. The obtained average nucleotide identity and digital DNA-DNA hybridization values between YZ-48T and the two closest strains were 75.0 and 74.5 % and 19.6 and 19.0 %, respectively. The sole respiratory quinone was MK-6. The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids and three unidentified polar lipids. The major cellular fatty acids were iso-C16 : 0, iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and iso-C16 : 0 3-OH. The DNA G+C content was 40.2 mol%. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic data, strain YZ-48T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium sedimenticola sp. nov. is proposed, with strain YZ-48T (=KCTC 82329T=CCTC AB 2023061T=MCCC 1K08804T) as the type strain.
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Affiliation(s)
- Ningning Wu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Le Liu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
| | - Xueting Jiang
- Biological Experiment Center, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Ye Yuan
- Department of Microbiology, College of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, PR China
| | - Dongmei Mao
- Biological Experiment Center, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Jiahui Shao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
| | - Qirong Shen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
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Lin SY, Hameed A, Tsai CF, Young CC. Description of Flavobacterium agricola sp. nov., an auxin producing bacterium isolated from paddy field. Antonie Van Leeuwenhoek 2023; 116:1345-1357. [PMID: 37837564 DOI: 10.1007/s10482-023-01891-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 09/25/2023] [Indexed: 10/16/2023]
Abstract
An auxin-producing bacterial strain, CC-SYL302T, was isolated from paddy soil in Taiwan and identified using a polyphasic taxonomic approach. The cells were observed to be aerobic, non-motile, non-spore-forming rods, and tested positive for catalase and oxidase. Produced carotenoid but flexirubin-type pigments were absent. Optimal growth of strain CC-SYL302T was observed at 25 °C, pH 7.0, and with 2% (w/v) NaCl present. Based on analysis of 16S rRNA gene sequences, it was determined that strain CC-SYL302T belongs to the genus Flavobacterium of the Flavobacteriaceae family. The closest known relatives of this strain are F. tangerinum YIM 102701-2 T (with 93.3% similarity) and F. cucumis R2A45-3 T (with 93.1% similarity). Digital DNA-DNA hybridization (dDDH) values were calculated to assess the genetic distance between strain CC-SYL302T and its closest relatives, with mean values of 21.3% for F. tangerinum and 20.4% for F. cucumis. Strain CC-SYL302T exhibited the highest orthologous average nucleotide identity (OrthoANI) values with members of the Flavobacterium genus, ranging from 67.2 to 72.1% (n = 22). The dominating cellular fatty acids (> 5%) included iso-C14:0, iso-C15:0, iso-C16:0, iso-C15:0 3-OH, iso-C17:0 3-OH, C16:1 ω6c/C16:1 ω7c and C16:0 10-methyl/iso-C17:1 ω9c. The polar lipid profile consisted of phosphatidylethanolamine, an unidentified aminolipid, an unidentified aminophospholipid, and nine unidentified polar lipids. The genome (2.7 Mb) contained 33.6% GC content, and the major polyamines were putrescine and sym-homospermidine. Strain CC-SYL302T exhibits distinct phylogenetic, phenotypic, and chemotaxonomic characteristics, as well as unique results in comparative analysis of 16S rRNA gene sequence, OrthoANI, dDDH, and phylogenomic placement. Therefore, it is proposed that this strain represents a new species of the Flavobacterium genus, for which the name Flavobacterium agricola sp. nov. is proposed. The type strain is CC-SYL302T (= BCRC 81320 T = JCM 34764 T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, Xing Da Rd., Taichung City, 40227, Taiwan
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya University, Mangalore, Karnataka, India
| | - Chia-Fang Tsai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, Xing Da Rd., Taichung City, 40227, Taiwan
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, Xing Da Rd., Taichung City, 40227, Taiwan.
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan.
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Duman M, Altun S, Saticioglu IB, Romalde JL. A review of bacterial disease outbreaks in rainbow trout (Oncorhynchus mykiss) reported from 2010 to 2022. JOURNAL OF FISH DISEASES 2023. [PMID: 37965781 DOI: 10.1111/jfd.13886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023]
Abstract
Outbreaks of bacterial infections in aquaculture have emerged as significant threats to the sustainable production of rainbow trout (Oncorhynchus mykiss) worldwide. Understanding the dynamics of these outbreaks and the bacteria involved is crucial for implementing effective management strategies. This comprehensive review presents an update on outbreaks of bacteria isolated from rainbow trout reported between 2010 and 2022. A systematic literature survey was conducted to identify relevant studies reporting bacterial outbreaks in rainbow trout during the specified time frame. More than 150 published studies in PubMed, Web of Science, Scopus, Google Scholar and relevant databases met the inclusion criteria, encompassing diverse geographical regions and aquaculture systems. The main bacterial pathogens implicated in the outbreaks belong to both gram-negative, namely Chryseobacterium, Citrobacter, Deefgea Flavobacterium, Janthinobacterium, Plesiomonas, Pseudomonas, Shewanella, and gram-positive genera, including Lactococcus and Weissella, and comprise 36 new emerging species that are presented by means of pathogenicity and disturbance worldwide. We highlight the main characteristics of species to shed light on potential challenges in treatment strategies. Moreover, we investigate the role of various risk factors in the outbreaks, such as environmental conditions, fish density, water quality, and stressors that potentially cause outbreaks of these species. Insights into the temporal and spatial patterns of bacterial outbreaks in rainbow trout aquaculture are provided. Furthermore, the implications of these findings for developing sustainable and targeted disease prevention and control measures are discussed. The presented study serves as a comprehensive update on the state of bacterial outbreaks in rainbow trout aquaculture, emphasizing the importance of continued surveillance and research to sustain the health and productivity of this economically valuable species.
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Affiliation(s)
- Muhammed Duman
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Soner Altun
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Izzet Burcin Saticioglu
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Jesús L Romalde
- Cross-disciplinary Research Center in Environmental Technologies (CRETUS), Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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Yin CC, Yang LL, Xin YH, Ye J, Liu Q. Identification of Flavobacterium algoritolerans sp. nov. and Flavobacterium yafengii sp. nov., two novel members of the genus Flavobacterium. Int J Syst Evol Microbiol 2023; 73. [PMID: 37796242 DOI: 10.1099/ijsem.0.006072] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023] Open
Abstract
Six psychrotolerant, Gram-stain-negative, aerobic bacterial strains, designated as LB1P51T, LB2P87T, LB2P84, LB3P48, LB3R18 and XS2P67, were isolated from glaciers on the Tibetan Plateau, PR China. The results of 16S rRNA gene analysis confirmed their classification within the genus Flavobacterium. Strain LB2P87T displayed the highest sequence similarity to Flavobacterium sinopsychrotolerans 0533T (98.18 %), while strain LB1P51T exhibited the highest sequence similarity to Flavobacterium glaciei CGMCC 1.5380T (98.15 %). Strains LB2P87T and LB1P51T had genome sizes of 3.8 and 3.9 Mb, respectively, with DNA G+C contents of 34.2 and 34.1 %, respectively. Pairwise average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) calculations revealed that these strains represented two distinct species within the genus Flavobacterium. The results of phylogenomic analysis using 606 core genes indicated that the six strains formed a distinct clade and were most closely related to F. glaciei CGMCC 1.5380T. The ANI and dDDH values between the two species and other members of the genus Flavobacterium were below 90.3 and 40.1 %, respectively. Genome relatedness, the results of phylogenomic analysis and phenotypic characteristics collectively support the proposal of two novel species of the genus Flavobacterium: Flavobacterium algoritolerans sp. nov. (LB1P51T = CGMCC 1.11237T = NBRC 114813T) and Flavobacterium yafengii sp. nov. (LB2P87T = CGMCC 1.11249T = NBRC 114814T).
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Affiliation(s)
- Ce-Ce Yin
- Hebei University, BaoDing, Hebei province, 071002, PR China
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Lei-Lei Yang
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Hua Xin
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jian Ye
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Qing Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Kim YS, Hwang EM, Jeong CM, Cha CJ. Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov., Isolated from Freshwater and Soil. J Microbiol 2023; 61:891-901. [PMID: 37851309 DOI: 10.1007/s12275-023-00081-1] [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: 06/28/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 10/19/2023]
Abstract
Two novel bacterial strains CJ74T and CJ75T belonging to the genus Flavobacterium were isolated from freshwater of Han River and ginseng soil, South Korea, respectively. Strain CJ74T was Gram-stain-negative, aerobic, rod-shaped, non-motile, and non-flagellated, and did not produce flexirubin-type pigments. Strain CJ75T was Gram-stain-negative, aerobic, rod-shaped, motile by gliding, and non-flagellated, and produced flexirubin-type pigments. Both strains were shown to grow optimally at 30 °C in the absence of NaCl on R2A medium. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains CJ74T and CJ75T belonged to the genus Flavobacterium and were most closely related to Flavobacterium niveum TAPW14T and Flavobacterium foetidum CJ42T with 96.17% and 97.29% 16S rRNA sequence similarities, respectively. Genomic analyses including the reconstruction of phylogenomic tree, average nucleotide identity, and digital DNA-DNA hybridization suggested that they were novel species of the genus Flavobacterium. Both strains contained menaquinone 6 (MK-6) as the primary respiratory quinone and phosphatidylethanolamine as a major polar lipid. The predominant fatty acids of both strains were iso-C15:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). Based on the polyphasic taxonomic study, strains CJ74T and CJ75T represent novel species of the genus Flavobacterium, for which names Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov. are proposed, respectively. The type strains are CJ74T (=KACC 19819T =JCM 32889T) and CJ75T (=KACC 23149T =JCM 36132T).
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Affiliation(s)
- Yong-Seok Kim
- Department or Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Eun-Mi Hwang
- Department or Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Chang-Myeong Jeong
- Department or Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Chang-Jun Cha
- Department or Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea.
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Jo H, Park MS, Lim Y, Kang I, Cho JC. 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 sp. nov., F. limnophilum sp. nov., F. lacustre sp. nov., and F. eburneipallidum sp. nov. J Microbiol 2023:10.1007/s12275-023-00054-4. [PMID: 37219690 DOI: 10.1007/s12275-023-00054-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/24/2023]
Abstract
Eleven bacterial strains were isolated from freshwater environments and identified as Flavobacterium based on 16S rRNA gene sequence analyses. Complete genome sequences of the 11 strains ranged from 3.45 to 5.83 Mb with G + C contents of 33.41-37.31%. The average nucleotide identity (ANI) values showed that strains IMCC34515T and IMCC34518 belonged to the same species, while the other nine strains represented each separate species. The ANI values between the strains and their closest Flavobacterium species exhibited ≤ 91.76%, indicating they represent each novel species. All strains had similar characteristics such as being Gram-stain-negative, rod-shaped, and contained iso-C15:0 as the predominant fatty acid, menaquinone-6 as the respiratory quinone, and phosphatidylethanolamine and aminolipids as major polar lipids. Genomic, phylogenetic, and phenotypic characterization confirmed that the 11 strains were distinct from previously recognized Flavobacterium species. Therefore, Flavobacterium praedii sp. nov. (IMCC34515T = KACC 22282 T = NBRC 114937 T), Flavobacterium marginilacus sp. nov. (IMCC34673T = KACC 22284 T = NBRC 114940 T), Flavobacterium aestivum sp. nov. (IMCC34774T = KACC 22285 T = NBRC 114941 T), Flavobacterium flavigenum sp. nov. (IMCC34775T = KACC 22286 T = NBRC 114942 T), Flavobacterium luteolum sp. nov. (IMCC34776T = KACC 22287 T = NBRC 114943 T), Flavobacterium gelatinilyticum sp. nov. (IMCC34777T = KACC 22288 T = NBRC 114944 T), Flavobacterium aquiphilum sp. nov. (IMCC34779T = KACC 22289 T = NBRC 114945 T), Flavobacterium limnophilum sp. nov. (IMCC36791T = KACC 22290 T = NBRC 114947 T), Flavobacterium lacustre sp. nov. (IMCC36792T = KACC 22291 T = NBRC 114948 T), and Flavobacterium eburneipallidum sp. nov. (IMCC36793T = KACC 22292 T = NBRC 114949 T) are proposed as novel species.
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Affiliation(s)
- Hyunyoung Jo
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Miri S Park
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Yeonjung Lim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Ilnam Kang
- Center for Molecular and Cell Biology, Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea.
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Li S, Mao S, Mu W, Guo B, Li C, Zhu Q, Hou X, Zhao Y, Wei S, Liu H, Liu A. Flavobacterium potami sp. nov., a multi-metal resistance genes harbouring bacterium isolated from shallow river silt. Antonie Van Leeuwenhoek 2023; 116:265-280. [PMID: 36574165 DOI: 10.1007/s10482-022-01802-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/19/2022] [Indexed: 12/29/2022]
Abstract
Environmental pollution by heavy metals is becoming an increasing problem and has become a matter of great concern due to the adverse effects worldwide. In this study, we report a novel strain of multi-metal resistant bacteria. A Gram-stain-negative, strictly aerobic, non-motile, yellow, rod-shaped strain 17AT, was isolated from the shallow silt of Fuyang River located in Longdian town, Hengshui city, Hebei province, China. Strain 17AT grew at 20-35 °C (optimum, 30 °C), pH 5-10 (optimum, pH 7) and 0-2% (w/v) NaCl (optimum, 1%). Phylogenetic analyses of 16S rRNA gene sequences showed that strain 17AT was closely related to members of the genus Flavobacterium, and had the highest 16S rRNA gene sequence similarity with 'Flavobacterium panacis' DCY106T (97.5%), followed by Flavobacterium johnsoniae subsp. johnsoniae UW101T (97.3%), Flavobacterium cutihirudinis E89T (97.2%), Flavobacterium limi THG-AG6.4T (97.2%), Flavobacterium hibisci THG-HG1.4T (97.2%) and Flavobacterium johnsoniae subsp. aurantiacum DSM 6792T (97.1%). The genome size of strain 17AT was 5.4 Mb and the DNA G + C content was 34.0%. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values among strain 17AT and reference strains were in the ranges of 79.8-86.1%, 24.1-31.4% and 80.5-88.6%, respectively, lower than the threshold values for species delineation. Strain 17AT contained iso-C15:0 and C16:0 3-OH as the predominant fatty acids (≥ 10%). The main isoprenoid quinone of strain 17AT was identified as MK-6. The polar lipids consisted of phosphatidylethanolamine, three unidentified aminolipids, two unidentified aminophospholipids and six unidentified lipids. Comparative genomics analysis between strain 17AT and its reference type strains revealed that there are a number of metal-resistant genes in strain 17AT, which are located in 15 gene clusters responsible for the copper homeostasis, cobalt-zinc-cadmium resistance, copper resistance, and arsenic/antimony resistance, with the copper resistance protein NlpE being unique to 17AT. Combined data from phenotypic, phylogenetic and chemotaxonomic studies demonstrated that strain 17AT is a representative of a novel species within the genus Flavobacterium, for which the name Flavobacterium potami sp. nov. is proposed. The type strain is 17AT (= GDMCC 1.2723T = JCM 34833T).
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Affiliation(s)
- Shucheng Li
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Sidi Mao
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Weidong Mu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Bai Guo
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Chen Li
- Shandong International Talent Exchange Service Center, Jinan, 250101, People's Republic of China
| | - Qing Zhu
- Shandong Institute of Innovation and Development, Jinan, 250101, People's Republic of China
| | - Xiaoxiao Hou
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Yanfang Zhao
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Shuzhen Wei
- Center for Wetland Conservation and Research, Hengshui University, Hengshui, 053000, People's Republic of China
- Collaborative Innovation Center for Wetland Conservation and Green Development of Hebei Province, Hengshui, 053000, People's Republic of China
- Hebei Key Laboratory of Wetland Ecology and Conservation, Hengshui, 053000, People's Republic of China
| | - Hongliang Liu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China.
- Collaborative Innovation Center for Wetland Conservation and Green Development of Hebei Province, Hengshui, 053000, People's Republic of China.
| | - Aiju Liu
- Collaborative Innovation Center for Wetland Conservation and Green Development of Hebei Province, Hengshui, 053000, People's Republic of China.
- School of Resources and Environmental Engineering, Shandong University of Technology, Zibo, 255000, People's Republic of China.
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Choi A, Cha IT, Lee KE, Son YK, Yu J, Seol D. The Role of Flavobacterium enshiense R6S-5-6 in the Wetland Ecosystem Revealed by Whole-Genome Analysis. Curr Microbiol 2023; 80:83. [PMID: 36680647 PMCID: PMC9867689 DOI: 10.1007/s00284-022-03157-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 11/25/2022] [Indexed: 01/22/2023]
Abstract
The wetland is an important ecosystem for purifying pollutants and circulating nutrients. Numerous microorganisms contribute to maintaining this function. We obtained Flavobacterium enshiense R6S-5-6 which was isolated from Ungok (Ramsar) Wetland and conducted whole-genome sequencing to investigate what contribution R6S-5-6 could make to the wetland community. The complete genome sequence of R6S-5-6 has a size of 3,251,289 bp with 37.68% of GC content. Gene annotation revealed that R6S-5-6 has several pathways to break down pollutants, including denitrification, assimilatory sulfate reduction (ASR), and polyphosphate-accumulating process. Furthermore, R6S-5-6 has genes that can have a positive effect on plants living in wetlands, such as storing essential nutrients, promoting plant growth, and protecting plants against pathogens.
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Affiliation(s)
- Ahhyeon Choi
- eGnome, Inc, 26 Beobwon-ro 9-Gil, Songpa-gu, Seoul, 05836 Republic of Korea
| | - In-Tae Cha
- grid.419519.10000 0004 0400 5474National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689 Republic of Korea
| | - Ki-Eun Lee
- grid.419519.10000 0004 0400 5474National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689 Republic of Korea
| | - Youn Kyoung Son
- grid.419519.10000 0004 0400 5474National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689 Republic of Korea
| | - Jaewoong Yu
- eGnome, Inc, 26 Beobwon-ro 9-Gil, Songpa-gu, Seoul, 05836 Republic of Korea
| | - Donghyeok Seol
- grid.31501.360000 0004 0470 5905Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 Republic of Korea ,grid.412480.b0000 0004 0647 3378Present Address: Department of Surgery, Seoul National University Bundang Hospital, 172 Dolma-ro, Bundang-gu, Seongnam, 13605 Republic of Korea
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10
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Wang J, Xiong J, Feng Q, Wan Z, Zhou Z, Xiao B, Zhang J, Singdala O. Intimately coupled photocatalysis and functional bacterial system enhance degradation of 1,2,3- and 1,3,5-trichlorobenzene. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 318:115595. [PMID: 35772268 DOI: 10.1016/j.jenvman.2022.115595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 06/07/2022] [Accepted: 06/18/2022] [Indexed: 06/15/2023]
Abstract
Intimate coupling of photocatalysis and biodegradation (ICPB) is considered a promising approach for the degradation of recalcitrant organic compounds. In this work, using Trichoderma with benzene degradation ability coupled with activated sludge as a biological source and sugarcane bagasse cellulose composite as a carrier, the ICPB system showed excellent degradation and mineralization of trichlorobenzene under visible light induction. The biofilm inside the ICPB carrier can degrade and mineralize the photocatalytic products. ICPB increased the degradation efficiency of 1,2,3-TCB and 1,3,5-TCB by 12.43% and 4.67%, respectively, compared to photocatalysis alone. The biofilms inside the ICPB carriers can mineralize photocatalytic products, which increases the mineralization efficiency by 18.74%. According to the analysis of intermediates, the degradation of 1,2,3-TCB in this coupled system involved stepwise dechlorination and ring opening. The biofilm in ICPB carrier evolved to be enriched in Cutaneotrichosporon, Trichoderma, Apiotrichum, Zoogloea, Dechloromonas, Flavihumibacter and Cupriavidus, which are known for biodegradable aromatic hydrocarbon and halogenate. Novel microbial seeds supplemented with Trichoderma-based ICPB seem to provide a new potential strategy for effective degradation and mineralization of TCB.
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Affiliation(s)
- Jue Wang
- School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, PR China.
| | - Jianhua Xiong
- School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, PR China; Guangxi Key Laboratory of Clean Pulp & Papermaking and Pollution Control, Nanning, 530004, China.
| | - Qilin Feng
- School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, PR China.
| | - Zhou Wan
- School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, PR China.
| | - Zhenqi Zhou
- School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, PR China.
| | - Bing Xiao
- School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, PR China.
| | - Jiaming Zhang
- School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, PR China.
| | - Outhay Singdala
- Guangxi Bossco Environmental Protection Technology Co., Ltd., Nanning, 530007, China.
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11
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Flavobacterium soyae sp. nov., isolated from the rhizosphere of soya bean. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, rod-shaped bacterium without flagella, designated SCIV07T, was isolated from soya bean rhizosphere soil collected from Bazhong, Sichuan Province, PR China and characterized by using polyphasic taxonomy. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SCIV07T belonged to the genus
Flavobacterium
and most closely related to the type strains
Flavobacterium chungangense
LMG 26729T (97.91 %),
Flavobacterium reichenbachii
LMG 25512T (97.77 %),
Flavobacterium oncorhynchi
CCUG 59446T (97.7 %),
Flavobacterium chilense
LMG 26360T (97.7 %) and
Flavobacterium plurextorum
CCUG 60112T (97.63 %). The average nucleotide identity and in silico DNA–DNA hybridization values between strain SCIV07T and closely related
Flavobacterium
species were lower than thresholds of 95 and 70 %, respectively, for species delineation. Catalase and oxidase were positive. Strain SCIV07T produced flexirubin-type pigments. Menaquinone-6 was the sole respiratory quinone. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and two unidentified lipids. The predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3OH and summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c). Physiological and biochemical features differentiated strain SCIV07T from the closely related
Flavobacterium
species. Based on the polyphasic taxonomic data, strain SCIV07T represents a novel species of the genus
Flavobacterium
, for which the name Flavobacterium soyae sp. nov. is proposed. The type strain is SCIV07T (=GDMCC 1.2481T=JCM 34673T).
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12
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Flavobacterium litorale sp. nov., isolated from red alga. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative and rod-shaped bacterial strain (WSW3-B6T) was isolated from red alga collected from the West Sea, Republic of Korea. Cells of strain WSW3-B6T were non-motile, aerobic and produced slightly yellow and mucoid colonies on marine agar. The strain grew optimally at 23–30 °C, with 0.5–4 % NaCl (w/v) and at pH 6.5–8.5. A phylogenetic analysis of the 16S rRNA gene revealed that strain WSW3-B6T belongs to the genus
Flavobacterium
within the family
Flavobacteriaceae
, having the highest sequence similarity to
Flavobacterium arcticum
SM1502T (96.7%), followed by
Flavobacterium salilacus
subsp.
altitudinum
LaA7.5T (96.2%) and
Flavobacterium salilacus
subsp.
salilacus
SaA2.12T (96.2%). The complete sequence of a circular chromosome of strain WSW3-B6T determined by combination of Oxford Nanopore and Illumina platforms comprised a total 2 725 095 bp with G+C content of 37.1 mol%. A comparative analysis based on the whole genome also showed the distinctiveness of strain WSW3-B6T. The average nucleotide identity (ANI) values between strain WSW3-B6T and the closest strains
F. arcticum
SM1502T,
F. salilacus
subsp.
altitudinum
LaA7.5T and
F. salilacus
subsp.
salilacus
SaA2.12T were 78.3, 77.8 and 77.7 %, respectively, while the digital DNA–DNA hybridization (dDDH) values between strain WSW3-B6T and the above closely related strains were 21.0, 20.4 and 20.3 %, respectively. Both the ANI and dDDH values supported the creation of a new species in the genus
Flavobacterium
. The major fatty acids (>10 %) were iso-C15 : 0 (19.3 %), C16 : 0 (14.0 %), iso-C17 : 0 3-OH (13.1 %) and C18 : 0 (10.7 %). The polar lipids of strain WSW3-B6T included phosphatidylethanolamine, three unidentified aminolipids and three unidentified lipids. Moreover, MK-6 was the only respiratory quinone. A comparison of the phylogenetic distinctiveness and the unique phenotypic and chemotaxonomic characteristics among strain WSW3-B6T and closely related type strains supported that strain WSW3-B6T (=KCTC 82708T=GDMCC 1.2627T) represents a novel species of the genus
Flavobacterium
, for which the name Flavobacterium litorale sp. nov. is proposed.
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13
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Qi J, Ji M, Wang W, Zhang Z, Liu K, Huang Z, Liu Y. Effect of Indian monsoon on the glacial airborne bacteria over the Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 831:154980. [PMID: 35378188 DOI: 10.1016/j.scitotenv.2022.154980] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/26/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
The glacier of the Tibetan Plateau (TP) is influenced by the Indian monsoon and continental westerlies. Wind flow can carry a variety of bacteria and disperse across the TP. Once these bacteria are colonized to the glacier surface, they could affect the biogeochemical cycle of the glacial ecosystems. However, very few studies have focused on the relationships between these airborne bacteria and atmospheric circulation over glaciers of the TP. Here we studied the diversity, taxonomic composition, and community structure of airborne bacteria on six TP glaciers using 16S rRNA gene sequencing. The results revealed an increase in the airborne bacterial diversity over the glaciers under the effect of the Indian monsoon. Airborne bacteria were dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, while relative abundances of Bacteroidetes and Firmicutes were significantly higher under the influence of the Indian monsoon in the southern and central of the TP, respectively. Moreover, significantly different airborne bacterial community structures were observed over glaciers under the influence of the Indian monsoon, which could be explained by the increased community stochasticity. In addition, the Indian monsoon increases the diversity and relative abundance of potential pathogens, which includes the most notorious bacteria such as Pseudomonas fluorescens, Staphylococcus aureus, and Clostridium butyricum. Our results revealed for the first time that atmospheric circulation influences the composition of airborne bacteria over the glaciers on the TP, this may provide critical insights into the distinct microbial community structure and function in glaciers across the TP.
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Affiliation(s)
- Jing Qi
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China; School of Life Sciences, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Mukan Ji
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Wenqiang Wang
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China; School of Life Sciences, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhihao Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhongwei Huang
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yongqin Liu
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.
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14
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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). J Microbiol 2022; 60:890-898. [DOI: 10.1007/s12275-022-2075-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/13/2022] [Accepted: 05/20/2022] [Indexed: 11/26/2022]
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15
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Flavobacterium taihuense sp. nov., a bacterium isolated from lake sediment. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005432] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterium, designated NAS39T, was isolated from the interfacial sediment of Taihu Lake in PR China and its taxonomic position was investigated by using a polyphasic approach. Cells of the isolate were Gram-stain-negative, aerobic, non-motile, catalase-positive, yellow and rod-shaped. Phylogenetic analyses based on 16S rRNA gene sequences supported that strain NAS39T formed a cluster within the genus
Flavobacterium
, and was most closely related to
Flavobacterium laiguense
LB2P30T (98.4 %), followed by
Flavobacterium tiangeerense
0563T (97.4 %). The average nucleotide identity values between strain NAS39T and
F. laiguense
LB2P30T and
F. tiangeerense
0563T were 82.5 and 75.3 %, respectively. The digital DNA–DNA hybridization values between strain NAS39T and
F. laiguense
LB2P30T and
F. tiangeerense
0563T were 40.9 and 18.6 %, respectively. The genomic DNA G+C content was 34.1 mol%. The major respiratory quinone was menaquinone-6. The dominant cellular fatty acids were iso-C15 : 0 and summed feature 3 comprising C16 : 1 ω7c/C16 : 1 ω6c. The polar lipids comprised phosphatidyl ethanolamine, two amino lipids, three amino phospholipids and two unidentified lipids. Based on the phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, strain NAS39T (=MCCC 1K06094T=KACC 22328T) represents a novel species of the genus
Flavobacterium
, for which the name Flavobacterium taihuense sp. nov. is proposed.
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16
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Flavobacterium hungaricum sp. nov. a novel soil inhabitant, cellulolytic bacterium isolated from plough field. Arch Microbiol 2022; 204:301. [PMID: 35524012 PMCID: PMC9076710 DOI: 10.1007/s00203-022-02905-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 11/15/2022]
Abstract
A Gram-negative bacterial strain, named Kb82, was isolated from agricultural soil and a polyphasic approach was used for characterisation and to determine its taxonomic position. Based on 16S rRNA gene sequence analysis, the highest similarity was found with Flavobacterium artemisiae SYP-B1015 (98.2%). The highest ANI (83.3%) and dDDH (26.5%) values were found with Flavobacterium ginsenosidimutans THG 01 and Flavobacterium fluviale HYN0086T, respectively. The isolate is aerobic with rod-shaped cells, positive for catalase and negative for oxidase tests. The DNA G+C content is 34.7 mol%. The only isoprenoid quinone is menaquinone 6 (MK-6). The major fatty acids are iso-C15:0, summed feature 3 (C16:1ω7c/C16:1ω6c) and iso-C17:0 3OH. The major polar lipid is phosphatidylethanolamine. On the bases of phenotypic characteristics and analysis of 16S rRNA gene sequences, it is concluded that strain Kb82T represents a novel species in the Flavobacterium genus, for which the name Flavobacterium hungaricum sp. nov. is proposed. The type strain of the species is strain Kb82T (= LMG 31576T = NCAIM B.02635T).
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17
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Hou X, Li S, Mao S, Mu W, Guo B, Wei S, Huang M, Zhao Y, Deng H, Sang F, Chen Z, Liu H, Liu A. Flavobacterium selenitireducens sp. nov., isolated from rhizosphere soil of ancient mulberry. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005304] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, aerobic, yellow, convex, rod-shaped mesophilic bacterial strain, designated strain D33T, was isolated from rhizosphere soil of ancient mulberry in Dezhou city, Shandong province, PR China. The strain grew at 8–37 °C (optimum, 30 °C), pH 4–9 (optimum, pH 7) and growth occurred at 0.5–5.5 % (w/v) NaCl (optimally at 1 %). The results of the phylogenetic analyses of 16S rRNA gene and whole genome sequences indicated that D33T was closely related to members of the genus
Flavobacterium
and had the highest 16S rRNA gene sequence similarity with ‘Flavobacterium agri’ KACC 19300 (95.4 %),
Flavobacterium ichthyis
NST-5T (94.6 %),
Flavobacterium ahnfeltiae
KCTC 32467T (93.6 %) and
Flavobacterium longum
JCM 19141T (93.6 %). The genome size of D33T was 3.8 Mb and the DNA G+C content was 48.0 mol%. The average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH) and average amino acid identity (AAI) values among D33T and reference strains were lower than the threshold values for species delineation. The only respiratory quinone of D33T was menaquinone 6 (MK-6). The predominant fatty acids (>5 %) were C15:0, C16 : 0, C18 : 0, iso-C15:0, iso–C17 : 0 3-OH, anteiso-C15 : 0 and summed feature 9 . The polar lipid profile contained phosphatidylethanolamine, two unidentified aminophospholipids, three unidentified aminolipids and two unidentified lipids. Combined data from phenotypic, phylogenetic and chemotaxonomic studies indicated that D33T is a representative of a novel species of the genus Flavobacterium, for which the name Flavobacterium selenitireducens sp. nov. is proposed. The type strain is D33T (=GDMCC 1.1946T=KACC 22131T).
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Affiliation(s)
- Xiaoxiao Hou
- School of Life Sciences, Lanzhou University, Gansu 730000, PR China
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, Shandong Province,, PR China
| | - Shucheng Li
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, Shandong Province,, PR China
| | - Sidi Mao
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, Shandong Province,, PR China
| | - Weidong Mu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, Shandong Province,, PR China
| | - Bai Guo
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, Shandong Province,, PR China
| | - Shuzhen Wei
- Hengshui University, Hengshui 053000, Hebei, PR China
| | - Mei Huang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, Shandong Province,, PR China
| | - Yanfang Zhao
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, Shandong Province,, PR China
| | - Hongkuan Deng
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, Shandong Province,, PR China
| | - Feng Sang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, Shandong Province,, PR China
| | - Zhiwei Chen
- Institute of Food and Nutrition Science, Shandong University of Technology, Zibo 255000, PR China
| | - Hongliang Liu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, Shandong Province,, PR China
| | - Aijv Liu
- School of Resources and Environmental Engineering, Shandong University of Technology, Zibo 255000, PR China
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18
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Seo J, Peng Y, Jiang L, Lee SB, Jeong RD, Park SJ, Kim CY, Choi MS, Lee J. Flavobacterium endoglycinae sp. nov., an endophytic bacterium isolated from soybean ( Glycine max L. cv. Gwangan) stems. Int J Syst Evol Microbiol 2022; 72. [PMID: 35130136 DOI: 10.1099/ijsem.0.005220] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
A Gram-stain-negative, facultatively anaerobic, motile by gliding, rod-shaped, oxidase- and catalase-positive bacterial strain, designated BB8T, was isolated from the stems of a Korean soybean cultivar (Glycine max L. cv. Gwangan). The strain produced a yellow pigment on tryptic soy agar. Growth of strain BB8T occurred at pH 5.0-8.0 (optimum, pH 7.0), at 10-35 °C (optimum, 25-30 °C) and in the presence of 0-1 % (w/v) NaCl (optimum, 0.5%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BB8T formed a lineage within the genus Flavobacterium and was most closely related to Flavobacterium artemisiae SYP-B1015T (96.9 % 16S rRNA gene sequence similarity) and Flavobacterium ustbae T13T (96.8%). The complete genome sequence of strain BB8T was 5 513 159 bp long with a G+C content of 34.1 mol%. The major fatty acids (>10 %) of strain BB8T were iso-C15 : 0 (21 %), summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c, 20.3%) and iso-C16 : 0 3-OH (13.7%). The predominant polar lipids were phosphatidylethanolamine and unidentified aminolipids, and the major respiratory quinone was menaquinone-6. Based on these phenotypic, genotypic and chemotaxonomic characteristics, strain BB8T is considered to represent a novel species of the genus Flavobacterium, for which the name Flavobacterium endoglycinae sp. nov. is proposed. The type strain is BB8T (=KCTC 82167T=CCTCC AB 2020070T).
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Affiliation(s)
- Jiyoon Seo
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
- Department of Applied Biology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Yuxin Peng
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Lingmin Jiang
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Sang-Beom Lee
- Crop Foundation Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Soon Ju Park
- Division of Biological Science, Wonkwang University, Iksan 54538, Republic of Korea
| | - Cha Young Kim
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Man-Soo Choi
- Crop Foundation Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Jiyoung Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
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19
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Sun H, Zheng H, Wang X, Jiang Y, Liao B, Li A, Xiao B. Flavobacterium coralii sp. nov., a marine bacterium isolated from coral culture seawater. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005201] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, strictly aerobic, rod-shaped bacterium, with one polar flagellum and named D11R37T, was isolated from coral culture seawater of Acropora digitifera. Strain D11R37T grew with 0–6 % (w/v) NaCl (optimum, 0.5%), at 10–41 °C (optimum, 28 °C) and at pH 6.0–7.0 (optimum, 7.0). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain D11R37T formed a lineage within the genus
Flavobacterium
, and it was distinct from the most closely related species
Flavobacterium suzhouense
XIN-1T and
Flavobacterium suaedae
G16-7T with 16S rRNA gene sequences similarities of 95.97% and 95.48 %. The major respiratory quinone was menaquinone-6. The polar lipids comprised one phosphatidylethanolamine, two aminolipids and one unknown polar lipid. The predominant fatty acids (more than 10 % of total fatty acids) were iso-C15 : 0 (18.0%), iso-C17 : 0 3-OH (11.9 %) and summed feature 3 (10.9 %). The DNA G+C content was 41.3 mol%. Based on polyphasic taxonomic data, strain D11R37T is considered to represent a novel species within the genus
Flavobacterium
, for which the name Flavobacterium coralii sp. nov. is proposed. The type strain is D11R37T (=KCTC 82968T=MCCC 1K06440T).
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Affiliation(s)
- Hao Sun
- Institute of Hydrobiology, Chinese Academy of Science, Wuhan, 430072, PR China
- Shenzhen Institute of Guangdong Ocean University, Binhai 2 Road, Shenzhen, 518120, PR China
| | - Huina Zheng
- College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, 524088, PR China
- Shenzhen Institute of Guangdong Ocean University, Binhai 2 Road, Shenzhen, 518120, PR China
| | - Xiaolei Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China
| | - Yiwei Jiang
- Shenzhen Institute of Guangdong Ocean University, Binhai 2 Road, Shenzhen, 518120, PR China
| | - Baolin Liao
- Shenzhen Institute of Guangdong Ocean University, Binhai 2 Road, Shenzhen, 518120, PR China
| | - Aihua Li
- Institute of Hydrobiology, Chinese Academy of Science, Wuhan, 430072, PR China
| | - Baohua Xiao
- Shenzhen Institute of Guangdong Ocean University, Binhai 2 Road, Shenzhen, 518120, PR China
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, PR China
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20
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Flavobacterium proteolyticum sp. nov., isolated from aquaculture water. Arch Microbiol 2022; 204:146. [DOI: 10.1007/s00203-021-02744-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/09/2021] [Accepted: 12/27/2021] [Indexed: 11/02/2022]
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21
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Králová S, Busse HJ, Bezdíček M, Sandoval-Powers M, Nykrýnová M, Staňková E, Krsek D, Sedláček I. Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov., Two Multidrug-Resistant Psychrotrophic Species Isolated From Antarctica. Front Microbiol 2021; 12:729977. [PMID: 34745033 PMCID: PMC8570120 DOI: 10.3389/fmicb.2021.729977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
Despite unfavorable Antarctic conditions, such as cold temperatures, freeze-thaw cycles, high ultraviolet radiation, dryness and lack of nutrients, microorganisms were able to adapt and surprisingly thrive in this environment. In this study, eight cold-adapted Flavobacterium strains isolated from a remote Antarctic island, James Ross Island, were studied using a polyphasic taxonomic approach to determine their taxonomic position. Phylogenetic analyses based on the 16S rRNA gene and 92 core genes clearly showed that these strains formed two distinct phylogenetic clusters comprising three and five strains, with average nucleotide identities significantly below 90% between both proposed species as well as between their closest phylogenetic relatives. Phenotyping revealed a unique pattern of biochemical and physiological characteristics enabling differentiation from the closest phylogenetically related Flavobacterium spp. Chemotaxonomic analyses showed that type strains P4023T and P7388T were characterized by the major polyamine sym-homospermidine and a quinone system containing predominantly menaquinone MK-6. In the polar lipid profile phosphatidylethanolamine, an ornithine lipid and two unidentified lipids lacking a functional group were detected as major lipids. These characteristics along with fatty acid profiles confirmed that these species belong to the genus Flavobacterium. Thorough genomic analysis revealed the presence of numerous cold-inducible or cold-adaptation associated genes, such as cold-shock proteins, proteorhodopsin, carotenoid biosynthetic genes or oxidative-stress response genes. Genomes of type strains surprisingly harbored multiple prophages, with many of them predicted to be active. Genome-mining identified biosynthetic gene clusters in type strain genomes with a majority not matching any known clusters which supports further exploratory research possibilities involving these psychrotrophic bacteria. Antibiotic susceptibility testing revealed a pattern of multidrug-resistant phenotypes that were correlated with in silico antibiotic resistance prediction. Interestingly, while typical resistance finder tools failed to detect genes responsible for antibiotic resistance, genomic prediction confirmed a multidrug-resistant profile and suggested even broader resistance than tested. Results of this study confirmed and thoroughly characterized two novel psychrotrophic Flavobacterium species, for which the names Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov. are proposed.
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Affiliation(s)
- Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Vienna, Austria
| | - Matěj Bezdíček
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czechia.,Department of Internal Medicine - Hematology and Oncology, Masaryk University, Brno, Czechia
| | | | - Markéta Nykrýnová
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Eva Staňková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
| | - Daniel Krsek
- NRL for Diagnostic Electron Microscopy of Infectious Agents, National Institute of Public Health, Prague, Czechia
| | - Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
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22
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Chhetri G, Kim I, Kang M, Kim J, So Y, Seo T. Flavobacterium tagetis sp. nov., a novel urea-hydrolysing bacterium isolated from the roots of Tagetes patula. Int J Syst Evol Microbiol 2021; 71. [PMID: 34542390 DOI: 10.1099/ijsem.0.004984] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped, motile by gliding, non-sporulating and strictly aerobic bacterium, designated strain GN10T, was isolated from the roots of Tagetes patula, collected from the garden of Dongguk University, Goyang, Republic of Korea. The cells could grow at 10-42 °C and at pH 5.5-9.0. Strain GN10T was sensitive to NaCl and tolerated up to 4 % NaCl (w/v). Comparative analysis of 16S rRNA gene sequences revealed the highest similarities to Flavobacterium tistrianum GB 56.1T (98.9 %), Flavobacterium sharifuzzamanii A7.6T (98.6 %), Flavobacterium zhairuonense A5.7T (98.3 %) and Flavobacterium anhuiense D3T (98 %). Phylogenetic analysis showed that strain GN10T clustered within the genus Flavobacterium and formed a monophyletic cluster with its close relative members. The average nucleotide identity and digital DNA-DNA hybridization values between strain GN10T and related species belonging to the genus Flavobacterium were well below the standard threshold for prokaryotic species delineation. The DNA G+C content of strain GN10T was 33.6 mol%. The predominant cellular fatty acids (>10 %) were identified as iso-C15 : 0, C16 : 0 and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c). Strain GN10T contained menaquinone 6 as the major respiratory quinone. The major polar lipids were phosphatidylethanolamine, three unidentified aminoglycolipids, two unidentified glycolipids, one unidentified phosphoglycolipid and five unidentified lipids. Urease is a nickel-containing enzyme found in archaea, bacteria, plants and unicellular eukaryotes. It serves as a virulence factor and is responsible for pathogenesis in humans and animals. Here, we describe a novel urease-hydrolysing bacterium, strain GN10T. The urease activity of this strain may serve as an indicator of pathogenic potential and drug resistance, which may facilitate the development of many diseases. The results of physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain GN10T from its closely related members and considered to represent novel species in the genus Flavobacterium, for which the name Flavobacterium tagetis (GN10T=KCTC 82695T=NBRC 114841T) is proposed.
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Affiliation(s)
- Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Minchung Kang
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
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Chen WM, You YX, Young CC, Lin SY, Sheu SY. Flavobacterium difficile sp. nov., isolated from a freshwater waterfall. Arch Microbiol 2021; 203:4449-4459. [PMID: 34136928 DOI: 10.1007/s00203-021-02440-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/25/2021] [Accepted: 06/11/2021] [Indexed: 11/29/2022]
Abstract
A bacterial strain designated KDG-16 T is isolated from a freshwater waterfall in Taiwan and characterized to determine its taxonomic affiliation. Cells of strain KDG-16 T are Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and form light yellow colonies. Optimal growth occurs at 20-25 °C, pH 6-7, and with 0% NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set reveal that strain KDG-16 T is affiliated with species in the genus Flavobacterium. Analysis of 16S rRNA gene sequences shows that strain KDG-16 T shares the highest similarity with Flavobacterium terrigena DSM 17934 T (97.7%). The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain KDG-16 T and the closely related Flavobacterium species are below the cut-off values of 95-96, 90 and 70%, respectively, used for species demarcation. Strain KDG-16 T contains iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH as the predominant fatty acids. The polar lipid profile consists of phosphatidylethanolamine, one uncharacterized aminophospholipid, one uncharacterized phospholipid, two uncharacterized aminolipids and two uncharacterized lipids. The major polyamine is homospermidine. The major isoprenoid quinone is MK-6. Genomic DNA G + C content of strain KDG-16 T is 31.6%. Based on the polyphasic taxonomic data obtained, strain KDG-16 T is considered to represent a novel species in the genus Flavobacterium, for which the name Flavobacterium difficile sp. nov. is proposed. The type strain is KDG-16 T (= BCRC 81194 T = LMG 31332 T).
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Affiliation(s)
- Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City, 811, Taiwan
| | - Ya-Xiu You
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City, 811, Taiwan
| | - Chiu-Chung Young
- College of Agriculture and Natural Resources, Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung, 402, Taiwan
| | - Shih-Yao Lin
- College of Agriculture and Natural Resources, Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung, 402, Taiwan
| | - Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City, 811, Taiwan.
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24
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Saticioglu IB, Ay H, Altun S, Duman M, Sahin N. Flavobacterium turcicum sp. nov. and Flavobacterium kayseriense sp. nov. isolated from farmed rainbow trout in Turkey. Syst Appl Microbiol 2021; 44:126186. [PMID: 33647765 DOI: 10.1016/j.syapm.2021.126186] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 12/14/2022]
Abstract
During a study on culturable microorganisms from fish farms, four yellow-pigmented gram negative, rod shaped isolates, F-47T, F-339T, F-380 and F-400, were recovered from rainbow trout samples exhibiting clinical signs. Based on 16S rRNA gene sequence analysis, the strains were identified as members of the genus Flavobacterium. Strains F-47T and F-380 shared the highest 16S rRNA gene sequence identity level of 97.6% with the type strain of Flavobacterium frigoris DSM 15719T while strains F-339T and F-400 shared the highest identity level of 97.6% with the type strain of F. caseinilyticum AT-3-2T. A polyphasic taxonomic approach including phenotypic and genomic characterization as well as whole-cell MALDI-TOF mass spectrometry analyses was employed to ascertain the taxonomic position of the strains within the genus Flavobacterium. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses between strains F-47T, F-339T and their close neighbours F. frigoris DSM 15719T and F. caseinilyticum AT-3-2T, respectively, confirmed that both strains represent novel species in the genus Flavobacterium. The DNA G+C contents of the strains F-47T and F-339T are 34.3% and 35.3%, respectively. It can be concluded on the basis of polyphasic characterization as well as pairwise genome comparisons that the strains F-47T and F-339T represent two novel species within the genus Flavobacterium, for which Flavobacterium kayseriense sp. nov. F-47T (=JCM 34195T=KCTC 82255T) and Flavobacterium turcicum sp. nov. F-339T (=JCM 34202T=KCTC 82262T) are proposed, respectively.
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Affiliation(s)
- Izzet Burcin Saticioglu
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey.
| | - Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Science and Arts, Ondokuz Mayis University, 55139 Samsun, Turkey
| | - Soner Altun
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey
| | - Muhammed Duman
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey
| | - Nevzat Sahin
- Department of Molecular Biology and Genetics, Faculty of Science and Arts, Ondokuz Mayis University, 55139 Samsun, Turkey
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Wu JH, You YX, Young CC, Kwon SW, Chen WM. Flavobacterium lotistagni sp. nov. and Flavobacterium celericrescens sp. nov., isolated from freshwater habitats. Int J Syst Evol Microbiol 2021; 71. [PMID: 33555245 DOI: 10.1099/ijsem.0.004682] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This study presents taxonomic descriptions of strains CYK-4T and TWA-26T isolated from freshwater habitats in Taiwan. Both strains were Gram-stain-negative, strictly aerobic, motile by gliding and rod-shaped. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that both strains belonged to the genus Flavobacterium. Analysis of 16S rRNA gene sequences showed that strains CYK-4T and TWA-26T shared 92.7 % sequence similarity and were most closely related to Flavobacterium ovatum W201ET (95.6 %) and Flavobacterium aquaticum JC164T (96.7 %), respectively. Both strains shared common chemotaxonomic characteristics comprising MK-6 as the main isoprenoid quinone, iso-C15 : 0 and iso-C15 : 1 G as the predominant fatty acids, phosphatidylethanolamine as the principal polar lipid, and homospermidine as the major polyamine. The DNA G+C contents of strains CYK-4T and TWA-26T were 41.5 and 31.8 mol%, respectively. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between these two novel isolates and their closest relatives were below the cut-off values of 95-96, 90 and 70 %, respectively, used for species demarcation. On the basis of phenotypic and genotypic properties and phylogenetic inference, both strains should be classified as novel species within the genus Flavobacterium, for which the names Flavobacterium lotistagni sp. nov. (type strain CYK-4T=BCRC 81192T=LMG 31330T) and Flavobacterium celericrescens sp. nov. (type strain TWA-26T=BCRC 81200T=LMG 31333T) are proposed.
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Affiliation(s)
- Jia-Hong Wu
- Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing 100084, PR China
| | - Ya-Xiu You
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Chiu-Chung Young
- College of Agriculture and Natural Resources, Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
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26
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Flavobacterium pokkalii sp. nov., a novel plant growth promoting native rhizobacteria isolated from pokkali rice grown in coastal saline affected agricultural regions of southern India, Kerala. Microbiol Res 2020; 240:126533. [DOI: 10.1016/j.micres.2020.126533] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/06/2020] [Indexed: 01/26/2023]
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27
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Chen WM, Xie YR, Kwon SW, Sheu SY. Flavobacterium undicola sp. nov., isolated from a freshwater lake. Arch Microbiol 2020; 203:989-1000. [PMID: 33108487 DOI: 10.1007/s00203-020-02096-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/22/2020] [Accepted: 10/15/2020] [Indexed: 11/25/2022]
Abstract
Bacterial strain BBQ-18T, isolated from a freshwater lake in Taiwan, is characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicate that strain BBQ-18T forms a phylogenetic lineage in the genus Flavobacterium. Strain BBQ-18T is most closely related to Flavobacterium alvei HR-AYT with 98.5% 16S rRNA gene sequence similarity. Strain BBQ-18T shows 70.5-89.5% average nucleotide identity and 13.7-38.2% digital DNA-DNA hybridization identity with the type strains of other closely related Flavobacterium species. The strain is Gram-stain negative, strictly aerobic, motile by gliding, rod shaped and formed yellow colonies. Optimal growth occurs at 25 °C, pH 6, and in the absence of NaCl. Strain BBQ-18T contains iso-C15:0, summed feature 3 (C16:1ω6c and/or C16:1ω7c) and anteiso-C15:0 as the predominant fatty acids. The polar lipid profile consists of phosphatidylethanolamine, four uncharacterized aminophospholipids and two uncharacterized phospholipids. The major polyamine is homospermidine. The major isoprenoid quinone is MK-6. The DNA G+C content of the genomic DNA is 33.8%. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain BBQ-18T should be classified as a novel species of the genus Flavobacterium, for which the name Flavobacterium undicola sp. nov. is proposed. The type strain is BBQ-18T (= BCRC 81050T = LMG 30052T = KCTC 52810T).
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Affiliation(s)
- Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City, 811, Taiwan
| | - Yi-Ru Xie
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City, 811, Taiwan
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City, 811, Taiwan.
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Akter S, Lee SY, Moon B, Huq MA. Flavobacterium agri sp. nov., a novel bacterial species isolated from rhizospheric soil of Coriandrum sativum. Arch Microbiol 2020; 203:701-706. [PMID: 33040181 DOI: 10.1007/s00203-020-02068-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/14/2020] [Accepted: 09/30/2020] [Indexed: 11/26/2022]
Abstract
A Gram-stain-negative, strictly aerobic, cream yellow colored, non-motile, rod-shaped bacterial strain, designated MAH-1T was isolated from rhizospheric soil of Coriandrum sativum. A polyphasic taxonomic study was performed on the isolated strain. Optimal growth occurred at 28-30 °C, pH 6.5 and 0% NaCl. The strain showed activity for both catalase and oxidase tests. Cell growth occurs on R2A agar, nutrient agar and Luria-Bertani agar. Cells were able to hydrolyze starch, aesculin, gelatin, and Tween 20. Alignment of 16S rRNA gene sequences indicated that strain MAH-1T was associated with the genus Flavobacterium and was most closely related to Flavobacterium longum YIT 12745T (94.5% sequence similarity) and Flavobacterium caeni LM5T (93.0%). Strain MAH-1T had a genome size of 3,975,600 bp. Genome contained 67 contigs encoded by 3,522 protein-coding genes with 38 tRNA and 6 rRNA genes. The genomic DNA G + C contents of strain MAH-1T was 47.1 mol %. The genomic ANI and dDDH values between strain MAH-1T and one of the close relatives F. caeni LM5T were 72.2 and 18.8%, respectively. The major fatty acids were C15:0 iso, C16:0 iso and C15:0 anteiso. The predominant respiratory quinone was menaquinone 6 (MK-6). Based on physiological, biochemical and phylogenetic data for this isolate, it was confirmed that strain MAH-1T was affiliated to the genus Flavobacterium and represented a novel species, for which the name Flavobacterium agri sp. nov. is proposed. The type strain is MAH-1T (= KACC 19300T = CGMCC 1.16617T).
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Affiliation(s)
- Shahina Akter
- Department of Food Science and Biotechnology, Gachon University, Seongnam, 461-701, Republic of Korea
| | - Sun-Young Lee
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| | - BoKyung Moon
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, 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.
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Chen WM, Yang CC, Sheu C, Kwon SW, Sheu SY. Flavobacterium ichthyis sp. nov., isolated from a fish pond. Int J Syst Evol Microbiol 2020; 70:5075-5086. [DOI: 10.1099/ijsem.0.004384] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial strain NST-5T, isolated from a fish pond in Taiwan, was characterized using a polyphasic taxonomy approach. Results of phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain NST-5T formed a phylogenetic lineage in the genus
Flavobacterium
. Analysis of 16S rRNA gene sequences showed that strain NST-5T showed the highest similarity to
Flavobacterium enshiense
DK69T (94.9 %),
Flavobacterium ahnfeltiae
10Alg 130T (94.8 %) and
Flavobacterium vireti
THG-SM1T (94.8 %). Strain NST-5T showed 68.9–72.5% average nucleotide identity and 19.1–23.7% digital DNA–DNA hybridization identity with the type strains of other close related
Flavobacterium
species. Cells of the strain were Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and formed yellow colonies. Optimal growth occurred at 30 °C, pH 7 and with 0.5% NaCl. Strain NST-5T contained iso-C15:0, C15:0 and iso-C16:0 as the predominant fatty acids. The major hydroxyl fatty acids were iso-C16:0 3-OH and iso-C17:0 3-OH. The polar lipid profile consisted of phosphatidylethanolamine, three uncharacterized aminophospholipids, two uncharacterized phospholipids and one uncharacterized aminolipid. The major polyamine was homospermidine. The major isoprenoid quinone was MK-6. The DNA G+C content of the genomic DNA was 35.5 mol%. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain NST-5T should be classified as a novel species of the genus
Flavobacterium
, for which the name Flavobacterium ichthyis sp. nov. is proposed. The type strain is NST-5T (=BCRC 81198T=LMG 31341T).
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Affiliation(s)
- Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung City 811, Taiwan, ROC
| | - Che-Chia Yang
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Kaohsiung City 811, Taiwan, ROC
| | - Ceshing Sheu
- Department of Applied Chemistry, Chaoyang University of Technology, Taichung, Taiwan, ROC
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Kaohsiung City 811, Taiwan, ROC
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Wang Q, Cai SD, Liu J, Zhang DC. Flavobacterium profundi sp. nov., isolated from a deep-sea seamount. Int J Syst Evol Microbiol 2020; 70:3633-3638. [PMID: 32421487 DOI: 10.1099/ijsem.0.004205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Gram-stain-negative, rod-shaped, facultative anaerobic, motile bacterial strain, designated TP390T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain TP390T was related to the genus Flavobacterium and had highest 16S rRNA gene sequence identity with the type strain of Flavobacterium jejuense EC11T (97.8 %). Sequence similarities to all other type strains of current species of the genus Flavobacterium were below 97 %. The predominant cellular fatty acids were iso-C15 : 0 and iso-C15 : 1G. The quinone system for strain TP390T comprised predominantly menaquinone MK-6 and the polar lipid profile contained phosphatidylethanolamine, four unknown aminolipids, one glycolipid and six unknown polar lipids. The genomic DNA G+C content of strain TP390T was 31.2 mol%. In addition, the maximum values of in silico DNA-DNA hybridization (isDDH) and average nucleotide identity (ANI) between strain TP390T with F. jejuense KCTC 42149T were 22.60 and 80.01% respectively. Combined data from phenotypic, phylogenetic, isDDH and ANI data demonstrated that the strain TP390T is representative of a novel species of the genus Flavobacterium, for which we propose the name Flavobacterium profundi sp. nov. (type strain TP390T=KACC 18559T=CGMCC 1.15398T).
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Affiliation(s)
- Qian Wang
- University of Chinese Academy of Sciences, 100049, Beijing, PR China
- Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, PR China
| | - Sheng-Dong Cai
- Department of Bioengineering, College of Marine Sciences and Biological Engineering, Qingdao University of Science and Technology, 266042, PR China
| | - Jie Liu
- Department of Bioengineering, College of Marine Sciences and Biological Engineering, Qingdao University of Science and Technology, 266042, PR China
| | - De-Chao Zhang
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, PR China
- University of Chinese Academy of Sciences, 100049, Beijing, PR China
- Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, PR China
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Debnath SC, Chen C, Khan I, Wang WJ, Zheng DQ, Xu JZ, Wang PM. Flavobacterium salilacus sp. nov., isolated from surface water of a hypersaline lake, and descriptions of Flavobacterium salilacus subsp. altitudinum subsp. nov. and Flavobacterium salilacus subsp. salilacus subsp. nov. Int J Syst Evol Microbiol 2020; 70:4250-4260. [PMID: 32568031 DOI: 10.1099/ijsem.0.004281] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two yellow-pigmented, Gram-stain-negative, aerobic, rod-shaped bacteria were isolated from the water of the hypersaline Chaka Salt Lake (strain SaA2.12T) and sediment of Qinghai Lake (strain LaA7.5T), PR China. According to the 16S rRNA phylogeny, the isolates belong to the genus Flavobacterium, showing the highest 16S rRNA sequence similarities to Flavobacterium arcticum SM1502T(97.6-97.7 %) and Flavobacterium suzhouense XIN-1T(96.5-96.6 %). Moreover, strains SaA2.12T and LaA7.5T showed 99.73 % 16S rRNA sequence similarity to each other. Major fatty acids, respiratory quinones and polar lipids detected in these isolates were iso-C15 : 0, menaquinone-6 and phosphatidylethanolamine, respectively. Strains SaA2.12T and LaA7.5T showed significant unique characteristics between them as well as between the closest phylogenetic members. The highest digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between SaA2.12T and its closest neighbours were 25.3 and 82.8 %, respectively; whereas these values (highest) between LaA7.5T and its closest members were 25.2 and 82.8 %, respectively. The dDDH and ANI values between strains SaA2.12T and LaA7.5T were calculated as 75.9 and 97.2 %, respectively. Therefore, based on polyphasic data, we propose that strain SaA2.12T represents a novel species with the name Flavobacterium salilacus sp. nov., with the type strain SaA2.12T (=KCTC 72220T=MCCC 1K03618T) and strain LaA7.5T as a subspecies within novel Flavobacterium salilacus with the name Flavobacterium salilacus subsp. altitudinum subsp. nov., with the type strain LaA7.5T (=KCTC 72806T=MCCC 1K04372T). These propositions automatically create Flavobacterium salilacus subsp. salilacus subsp. nov. with SaA2.12T (=KCTC 72220T=MCCC 1K03618T) as the type strain.
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Affiliation(s)
| | - Can Chen
- Ocean College, Zhejiang University, Zhoushan, PR China
| | - Ishrat Khan
- Ocean College, Zhejiang University, Zhoushan, PR China
| | - Wen-Jie Wang
- Ocean College, Zhejiang University, Zhoushan, PR China
| | | | - Jin-Zhong Xu
- Ocean College, Zhejiang University, Zhoushan, PR China
| | - Pin-Mei Wang
- Ocean College, Zhejiang University, Zhoushan, PR China
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Lin SY, Chen WM, Huang GH, Hameed A, Chang CT, Tsai CF, Young CC. Flavobacterium supellecticarium sp. nov., isolated from an abandoned construction timber. Int J Syst Evol Microbiol 2020; 70:3731-3739. [PMID: 32453684 DOI: 10.1099/ijsem.0.004227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain CC-CTC003T was isolated from a synthetic wooden board. Cells of strain CC-CTC003T were Gram-stain-negative, rod-shaped, motile by gliding and formed yellow colonies. Optimal growth occurred at 25 °C, pH 7 and in the presence of 1 % NaCl. The phylogenetic analyses based on 16S rRNA genes revealed that strain CC-CTC003T belonged to the genus Flavobacterium and was most closely related to Flavobacterium cerinum (95.3 % sequence identity), Flavobacterium maris (94.9 % sequence identity), Flavobacterium qiangtangense (94.8 %) and Flavobacterium subsaxonicum (94.7 %) and had less than 94.7 % sequence similarity to other members of the genus. Average nucleotide identity (ANI) values between strain CC-CTC003T and the type strains of other closely related species were 70.1-74.1 %. The digital DNA-DNA hybridization (dDDH) with F. cerinum was 19.4 %. Strain CC-CTC003T contained C15 : 0, iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1 ω6c / C16 : 1 ω7c) and summed feature 9 (C16 : 0 10-methyl / iso-C17 : 1 ω9c) as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, four uncharacterized aminophospholipids, two aminolipids and one unidentified glycolipid. The major polyamine was sym-homospermidine and contained MK-6 as major isoprenoid quinone. The DNA G+C content of the genomic DNA was 39.2 mol%. On the basis of the phylogenetic inference and phenotypic data, strain CC-CTC003T should be classified as a novel species, for which the name Flavobacterium supellecticarium sp. nov. is proposed. The type strain is CC-CTC003T (=BCRC 81146T=JCM 32838T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan, ROC
| | - Guan-Hua Huang
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Chun-Tse Chang
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Chia-Fang Tsai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Chiu-Chung Young
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan, ROC.,Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
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Chaudhary DK, Khulan A, Kim DU, Kim J. Flavobacterium cellulosilyticum sp. nov., a novel psychrophilic bacterium isolated from Arctic soil. Int J Syst Evol Microbiol 2020; 70:44-50. [PMID: 31513007 DOI: 10.1099/ijsem.0.003707] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel psychrophilic, light-yellow-coloured, aerobic, Gram-stain-negative, rod-shaped, non-motile bacterium, designated strain AR-3-4T was isolated from a sample of Arctic soil. Strain AR-3-4T grew at 0-25 °C, pH 6.0-9.0 and 0-1.0 % (w/v) NaCl concentration. The 16S rRNA gene sequence analysis showed that strain AR-3-4T belonged to the genus Flavobacterium, with nearest phylogenetic neighbour being Flavobacterium fluvii H7T (97.5 % sequence similarity). The strain comprised phosphatidylethanolamine as the main polar lipid, MK-6 as predominant respiratory quinone, and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), anteiso-C15 : 0 and iso-C15 : 0 as the major fatty acids. The average nucleotide identity and in silico DNA-DNA hybridization values between strain AR-3-4T and closest members were below the threshold values of 95 % and 70 %, respectively. The DNA G+C content was 33.0 mol%. Based on the polyphasic taxonomic data, the novel species Flavobacterium cellulosilyticum sp. nov. is proposed with the type strain AR-3-4T (=KEMB 9005-740T=KACC 21171T=NBRC 113787T).
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Affiliation(s)
- Dhiraj Kumar Chaudhary
- Ecology Laboratory, Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
| | - Altankhuu Khulan
- Ecology Laboratory, Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
| | - Dong-Uk Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, Republic of Korea
| | - Jaisoo Kim
- Ecology Laboratory, Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
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Liu Y, Le Han H, Zou Y, Kim SG. Flavobacterium ustbae sp. nov., isolated from rhizosphere soil of Alhagi sparsifolia. Int J Syst Evol Microbiol 2019; 69:3955-3960. [DOI: 10.1099/ijsem.0.003717] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yang Liu
- College of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, PR China
| | - Ho Le Han
- University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeonbuk 56212, Republic of Korea
| | - Yuanyuan Zou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Song-Gun Kim
- University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeonbuk 56212, Republic of Korea
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Kim I, Kim J, Chhetri G, Seo T. Flavobacterium humi sp. nov., a flexirubin-type pigment producing bacterium, isolated from soil. J Microbiol 2019; 57:1079-1085. [DOI: 10.1007/s12275-019-9350-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/10/2019] [Accepted: 10/28/2019] [Indexed: 01/02/2023]
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Yang LL, Liu Q, Liu HC, Zhou YG, Xin YH. Flavobacterium psychrotolerans sp. nov., a psychrotolerant bacterium isolated from Renlongba glacier on the Tibetan Plateau. Int J Syst Evol Microbiol 2019; 70:1031-1036. [PMID: 31702532 DOI: 10.1099/ijsem.0.003868] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
One aerobic, Gram-stain-negative, rod-shaped bacterium, designated strain RB1R5T, was isolated from Renlongba glacier in Tibet Autonomous Region, China. Growth was observed at 4-25 °C and pH 7.0-8.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain RB1R5T belongs to the genus Flavobacterium, and its closest relatives are Flavobacterium luteum IMCC26026T and Flavobacterium psychroterrae CCM 8827T with 97.75 and 97.42% gene sequence similarities, respectively. The average nucleotide identity and DNA-DNA hybridization values between strain RB1R5T and its closest relative Flavobacterium luteum IMCC26026T were 78.02 and 21.8 %, respectively. The major cellular fatty acids were anteiso-C15 : 0 and summed feature 3 (comprising C16:1ω7c/C16:1ω6c). The sole menaquinone was MK-6. The major phospholipid was phosphatidylethanolamine. On the basis of phenotypic, phylogenetic and chemotaxonomic characterizations, strain RB1R5T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium psychrotolerans sp. nov. is proposed. The type strain is RB1R5T (=CGMCC 1.23024T=NBRC 113060T).
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Affiliation(s)
- Lei-Lei Yang
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Qing Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Guang Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.,China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Hua Xin
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Li Y, Tang BL, Ren XB, Dang YR, Sun LL, Zhang XY, Chen XL, Qin QL, Wang P. Complete genome sequence of Flavobacterium arcticum SM1502T, exhibiting adaption to the Arctic marine salty environment. Mar Genomics 2019. [DOI: 10.1016/j.margen.2019.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Flavobacterium zhairuonensis sp. nov., a gliding bacterium isolated from marine sediment of the East China Sea. J Microbiol 2019; 57:1065-1072. [DOI: 10.1007/s12275-019-9194-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/19/2019] [Accepted: 09/03/2019] [Indexed: 10/25/2022]
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García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Göker M. Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Front Microbiol 2019; 10:2083. [PMID: 31608019 PMCID: PMC6767994 DOI: 10.3389/fmicb.2019.02083] [Citation(s) in RCA: 190] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/23/2019] [Indexed: 11/25/2022] Open
Abstract
Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Richard L. Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Chen WM, Guo YP, Kwon SW, Sheu C, Sheu SY. Flavobacterium stagni sp. nov., isolated from a freshwater reservoir. Int J Syst Evol Microbiol 2019; 69:2372-2379. [DOI: 10.1099/ijsem.0.003488] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Wen-Ming Chen
- 1Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Ya-Ping Guo
- 2Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Soon-Wo Kwon
- 3National Agrobiodiversity Center, National Academy of Agricultural Science, Suwon 441-707, Republic of Korea
| | - Ceshing Sheu
- 4Department of Applied Chemistry, Chaoyang University of Technology, No.168, Jifong E. Rd., Wufeng, Taichung, Taiwan, ROC
| | - Shih-Yi Sheu
- 2Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
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Chaudhary DK, Dahal RH, Kim J. Flavobacterium silvisoli sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2019; 69:2762-2766. [PMID: 31237532 DOI: 10.1099/ijsem.0.003551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During a study of the Kyonggi University soil bacterial diversity, an aerobic, non-motile, Gram-stain-negative, non-spore-forming, rod-shaped, yellow pigmented bacterium, designated strain RD-2-33T was isolated. Strain RD-2-33T grew optimally at 28-35 °C and pH 7.0-7.5; hydrolysed gelatin and DNA; and tolerated 1 % of NaCl. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain RD-2-33T clustered with the genus Flavobacterium. The closest member was Flavobacterium dankookense ARSA-19T (97.1 % sequence similarity) and Flavobacterium cheonhonense ARSA-15T (96.7 %). Sole respiratory quinone was MK-6. The major polar lipids were phosphatidylethanolamine and an unidentified polar lipid. The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, and iso-C15 : 1 G. The DNA G+C content was 38.6 mol%. The average nucleotide identity (ANI) and in silico DNA-DNA hybridisation relatedness between strain RD-2-33T and Flavobacterium dankookense DSM 25687T were 75.2 and 19.3 %, respectively. Based on the polyphasic and phylogenetic data, strain RD-2-33T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium silvisoli sp. nov. is proposed. The type strain is RD-2-33T (=KEMB 9005-742T=KACC 21178T=NBRC 113789T).
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Affiliation(s)
- Dhiraj Kumar Chaudhary
- Ecology Laboratory, Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
| | - Ram Hari Dahal
- Ecology Laboratory, Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
| | - Jaisoo Kim
- Ecology Laboratory, Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
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Yang LL, Liu Q, Liu HC, Zhou YG, Xin YH. Flavobacterium laiguense sp. nov., a psychrophilic bacterium isolated from Laigu glacier on the Tibetan Plateau. Int J Syst Evol Microbiol 2019; 69:1821-1825. [DOI: 10.1099/ijsem.0.003400] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Lei-Lei Yang
- 1China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Qing Liu
- 1China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hong-Can Liu
- 1China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Guang Zhou
- 1China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- 2State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Hua Xin
- 1China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Chen WM, Xie YR, Kwon SW, Sheu SY. Flavobacterium sufflavum sp. nov., isolated from a freshwater lake. Int J Syst Evol Microbiol 2019; 69:1705-1713. [DOI: 10.1099/ijsem.0.003382] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Wen-Ming Chen
- 1Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung City 811, PR China
| | - Yi-Ru Xie
- 1Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung City 811, PR China
| | - Soon-Wo Kwon
- 2Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Shih-Yi Sheu
- 3Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Kaohsiung City 811, PR China
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Chen WM, Guo YP, Kwon SW, Sheu SY. Flavobacterium piscinae sp. nov., isolated from a fish pond. Int J Syst Evol Microbiol 2019; 69:1775-1782. [DOI: 10.1099/ijsem.0.003391] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Wen-Ming Chen
- 1Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, PR China
| | - Ya-Ping Guo
- 2Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, PR China
| | - Soon-Wo Kwon
- 3National Agrobiodiversity Center, National Academy of Agricultural Science, Suwon 441-707, Republic of Korea
| | - Shih-Yi Sheu
- 2Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, PR China
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Sheu SY, Guo YP, Chen WM. Flavobacterium amnicola sp. nov., isolated from a sub-tropical stream. Int J Syst Evol Microbiol 2019; 69:2283-2291. [PMID: 31120829 DOI: 10.1099/ijsem.0.003463] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain LLJ-11T, isolated from water sampled from a freshwater stream in Taiwan, was characterized using a polyphasic taxonomy approach. Cells of strain LLJ-11T were Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and formed translucent yellow colonies. Optimal growth occurred at 25 °C, pH 7 and 0 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain LLJ-11T is affiliated with species in the genus Flavobacterium. Strain LLJ-11T was most closely related to Flavobacterium amniphilum KYPY10T with 98.0 % 16S rRNA gene sequence identity. The DNA-DNA relatedness of strain LLJ-11T with respect to Flavobacterium species was less than 35 %. Average nucleotide identity and digital DNA-DNA hybridization values between strain LLJ-11T and the type strains of other closely related Flavobacterium species were 70.0-76.3 % and 21.1-23.9 %, respectively. Strain LLJ-11T contained iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0) as the predominant fatty acids. The major isoprenoid quinone was MK-6. The polar lipid profile consisted of phosphatidylethanolamine, three uncharacterized aminophospholipids and two uncharacterized phospholipids. The major polyamine was homospermidine. The DNA G+C content was 34.8 mol%. On the basis of the phylogenetic inference and phenotypic data, strain LLJ-11T is considered a representative of a novel species within the genus Flavobacterium. The name Flavobacterium amnicola sp. nov. is proposed, with strain LLJ-11T (=BCRC 81124T=LMG 30599T=KCTC 62514T) as the type strain.
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Affiliation(s)
- Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung Marine University, Kaohsiung City, Taiwan, ROC
| | - Ya-Ping Guo
- Department of Marine Biotechnology, National Kaohsiung Marine University, Kaohsiung City, Taiwan, ROC
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, Kaohsiung City, Taiwan, ROC
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Flavobacterium aquariorum sp. nov., isolated from freshwater of the North Han River. J Microbiol 2019; 57:343-349. [DOI: 10.1007/s12275-019-8436-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/02/2018] [Accepted: 11/13/2018] [Indexed: 10/27/2022]
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Debnath SC, Chen C, Liu SX, Di YN, Zheng DQ, Li XY, Xu XW, Xu JZ, Wang PM. Flavobacterium sharifuzzamanii sp. nov., Isolated from the Sediments of the East China Sea. Curr Microbiol 2019; 76:297-303. [PMID: 30603961 DOI: 10.1007/s00284-018-1609-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/30/2018] [Indexed: 10/27/2022]
Abstract
A novel bacterial strain A7.6T was isolated from the sediments collected near the Zhairuo Island located in the East China Sea and characterized using a polyphasic approach. Cells were Gram-stain-negative, rod-shaped, non-spore forming, non-flagellated but motile by gliding. The strain was aerobic, positive for oxidase and catalase activities. The strain can grow at 4-35 °C, pH 5.5-9.0, and 0-3% (w/v) NaCl concentration. The major polar lipid was phosphatidylethanolamine, the predominant fatty acids (> 10%) were iso-C15:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The genomic G+C content was 33.6 mol% and the major respiratory quinone was menaquinone 6. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain A7.6T belonged to the genus Flavobacterium and was closely related to Flavobacterium tistrianum GB 56.1T (98.4% similarity), F. nitrogenifigens NXU-44T (98.4%), F. ginsenosidimutans THG 01T (98.0%) and F. anhuiense D3T (97.7%). Average nucleotide identities and digital DNA-DNA hybridizations values for genomes ranged from 75.9 to 91.4% and 21.4 to 43.9% between strain A7.6T and its closest phylogenetic neighbors. The polyphasic characterization indicated that strain A7.6T represented a novel species of the genus Flavobacterium, for which the name Flavobacterium sharifuzzamanii is proposed. The type strain is A7.6T (= KCTC 62405T = MCCC 1K03485T). The NCBI GenBank accession number for the 16S rRNA gene of A7.6T is MH396692, and for the genome sequence is QJGZ00000000. The digital protologue database (DPD) Taxon Number is TA00643.
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Affiliation(s)
- Sanjit C Debnath
- Ocean College, Zhejiang University, Zhoushan, People's Republic of China
| | - Can Chen
- Ocean College, Zhejiang University, Zhoushan, People's Republic of China
| | - Shu-Xia Liu
- Ocean College, Zhejiang University, Zhoushan, People's Republic of China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China
| | - Ya-Nan Di
- Ocean College, Zhejiang University, Zhoushan, People's Republic of China
| | - Dao-Qiong Zheng
- Ocean College, Zhejiang University, Zhoushan, People's Republic of China
| | - Xin-Yang Li
- Ocean College, Zhejiang University, Zhoushan, People's Republic of China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, People's Republic of China
| | - Jin-Zhong Xu
- Ocean College, Zhejiang University, Zhoushan, People's Republic of China.
| | - Pin-Mei Wang
- Ocean College, Zhejiang University, Zhoushan, People's Republic of China.
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Joung Y, Jang HJ, Song J, Cho JC. Flavobacterium hydrophilum sp. nov. and Flavobacterium cheongpyeongense sp. nov., isolated from freshwater. Int J Syst Evol Microbiol 2018; 69:602-609. [PMID: 30566071 DOI: 10.1099/ijsem.0.003083] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative, non-motile, yellow-pigmented bacterial strains, designated IMCC34758T and IMCC34759T, were isolated from freshwater. Phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains formed a distinct clade within the genus Flavobacterium and they shared 97.9 % sequence similarity. The average nucleotide identity (ANI) and digital DNA-DNA hybridization values (dDDH) between the two strains were 85.5 and 30.2 %, respectively, indicating that they are separate species. The two strains showed ≤98.5 % 16S rRNA gene sequence similarities, 80.6-81.3 % of ANI and 24.7-25.1 % of dDDH values to closely related species of the genus Flavobacterium, indicating that the two strains each represent novel Flavobacteriumspecies. The respiratory quinone detected in both strains was menaquinone-6 (MK-6). The major polar lipids of the two strains were phosphatidylethanolamine, an unidentified aminolipid, an unidentified aminophospholipid and an unidentified polar lipid. The DNA G+C contents of strains IMCC34758T and IMCC34759T were 34.0 and 34.1 mol%, respectively. The major fatty acids of the two strains were very similar to each other, comprising iso-C15 : 0, iso-C15 : 1 G, anteiso-C15 : 0 and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c). Phenotypic characteristics including enzyme activities and carbon source utilization differentiated the two strains from other Flavobacteriumspecies. Based on these results, strains IMCC34758T and IMCC34759T were considered to represent novel species in the genus Flavobacterium, for which the names Flavobacterium hydrophilum (IMCC34758T=KACC 19591T=NBRC 113423T) and Flavobacterium cheongpyeongense (IMCC34759T=KACC 19592T=NBRC 113424T) are proposed, respectively.
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Affiliation(s)
- Yochan Joung
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Hye-Jin Jang
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Jaeho Song
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
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Chen WM, Chen WT, Young CC, Sheu SY. Flavobacterium niveum sp. nov., isolated from a freshwater creek. Int J Syst Evol Microbiol 2018; 69:271-277. [PMID: 30499767 DOI: 10.1099/ijsem.0.003150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain TAPW14T was isolated from a freshwater creek in Taiwan. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TAPW14T belonged to the genus Flavobacterium and was most closely related to Flavobacterium akiainvivens IK-1T (96.6 % sequence identity) and Flavobacterium hauense BX12T (96.0 %) and less than 96 % sequence similarity to other members of the genus. Cells of strain TAPW14T were Gram-negative, strictly aerobic, motile by gliding, rod-shaped and formed white colonies. Optimal growth occurred at 20 °C, pH 7 and in the presence of 0.5 % NaCl. Strain TAPW14T contained summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), iso-C15 : 0 and C16 : 0 as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, three uncharacterized aminophospholipids, one uncharacterized phospholipid and one uncharacterized lipid. The major polyamine was homospermidine. The major isoprenoid quinone was MK-6. The DNA G+C content of the genomic DNA was 46.0 mol%. On the basis of the phylogenetic inference and phenotypic data, strain TAPW14T should be classified as a novel species, for which the name Flavobacteriumniveum sp. nov. is proposed. The type strain is TAPW14T (=BCRC 81055T=LMG 30057T=KCTC 52808T).
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Affiliation(s)
- Wen-Ming Chen
- 1Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Wei-Ting Chen
- 1Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Chiu-Chung Young
- 2College of Agriculture and Natural Resources, Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Shih-Yi Sheu
- 3Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
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Phurbu D, Lu H, Xue X, Tian Y, Pema Y, Ma C, Xing P. Flavobacterium tibetense sp. nov., isolated from a wetland. Int J Syst Evol Microbiol 2018; 69:165-170. [PMID: 30457510 DOI: 10.1099/ijsem.0.003124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, Gram-stain-negative, non-motile and rod-shaped bacterium, designated YH5T, was isolated from the YonghuCo wetland on the Tibetan Plateau. The strain was able to grow optimally with 1 % (w/v) NaCl and tolerated up to 3 % NaCl. Growth occurred at pH 6-9 (optimum pH 7) and 10-37 °C (optimum 30 °C). Vitamins were not required for growth. The major polar lipid of strain YH5T was phosphatidylethanolamine. The predominant respiratory quinone was menaquinone 6 (MK-6). The major fatty acids were iso-C15 : 0, C16 : 0 10-methyl and/or iso-C17 : 1ω9c, iso-C17 : 0 3-OH, iso-C15 : 1 G and iso-C15 : 0 3-OH. Genome sequencing revealed a genome size of 2.74 Mbp and a G+C content of 33.3 mol%. Analysis of 16S rRNA gene sequences showed that strain YH5T belonged to the genus Flavobacterium, with the closest neighbours Flavobacterium luticocti xz20T (96.7 % similarity), Flavobacterium jejuense EC11T (96.4 %), Flavobacterium jumunjinense HME7102T (95.9 %) and Flavobacterium dongtanense LW30T (95.6 %). DNA-DNA relatedness between strain YH5T and the closest phylogenetically related strain F. luticocti xz20T was 27.0 %. Strain YH5T was clearly distinguished from the reference type strains based on phylogenetic analysis, DNA-DNA hybridization, fatty acid composition and a range of physiological and biochemical characteristics. Based on its phenotypic and chemotaxonomic characteristics, strain YH5T is classified as a representative of a novel species of the genus Flavobacterium, for which the name Flavobacterium tibetense sp. nov. is proposed. The type strain is YH5T (=CICC 24247T=KCTC 62174T).
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Affiliation(s)
- Dorji Phurbu
- 1Tibet Plateau Institute of Biology, Lhasa 850000, PR China
| | - Hubin Lu
- 2State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
- 3University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xiaofeng Xue
- 2State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
- 4College of Life Sciences, Nanjing Normal University, Nanjing 210046, PR China
| | - Yanling Tian
- 2State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
- 3University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yangzom Pema
- 1Tibet Plateau Institute of Biology, Lhasa 850000, PR China
| | - Chao Ma
- 1Tibet Plateau Institute of Biology, Lhasa 850000, PR China
| | - Peng Xing
- 2State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
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