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Zhang L, Geng C, Chen X, Chen L, Deng T, Xu M. Niabella digestorum sp. nov., a High Cell-Surface Hydrophobic Bacterium Isolated from Waste Digestion System. Curr Microbiol 2024; 81:348. [PMID: 39251411 DOI: 10.1007/s00284-024-03873-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 08/24/2024] [Indexed: 09/11/2024]
Abstract
A high cell-surface hydrophobic bacterium, strain A18T, was isolated from a waste digestion system in Chaozhou, China. Cells of strain A18T were Gram-stain-positive, aerobic, non-spore-forming, non-motile, and rod-shaped. Phylogenetic analyses based on the 16S rRNA gene showed that strain A18T shared less than 94.2% sequence similarity to all validated species in the family Chitinophagaceae, and formed a distinct lineage close to genera Niabella and Terrimonas in the neighbor-joining tree, indicating that strain A18T is a novel species. Genome-based phylogenetic analyses revealed that strain A18T is affiliated to the genus Niabella. The cellular components, including iso-C15:0 and iso-C15:1 G as the major fatty acids, menaquinone-7 as the respiratory quinone and a DNA G + C content of 40.54% supported strain A18T as a member of the genus Niabella. However, the physiological and biochemical properties, such as enzyme activities, carbon source utilization and C18:0 3-OH as another major fatty acids, distinguished strain A18T from its close related species. Therefore, the name Niabella digestorum sp. nov. is proposed for this novel species. The type strain is A18T (= GDMCC 1.3242 T = KCTC 92386 T).
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Affiliation(s)
- Ling Zhang
- College of Life Sciences, South Agriculral University, Guangzhou, 510642, Guangdong, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, 510070, Guangdong, China
| | - Chuansheng Geng
- College of Life Sciences, South Agriculral University, Guangzhou, 510642, Guangdong, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, 510070, Guangdong, China
| | - Xingjuan Chen
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, 510070, Guangdong, China
| | - Letian Chen
- College of Life Sciences, South Agriculral University, Guangzhou, 510642, Guangdong, China
| | - Tongchu Deng
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, 510070, Guangdong, China.
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, 510070, Guangdong, China.
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2
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Jiang T, Jia W, Deng W, Mai Z, Dong M, Huang Y, Wu H, Xu M. Patulibacter defluvii sp. nov., Isolated from a Wastewater Treatment Plant in Guangzhou City, China. Curr Microbiol 2024; 81:291. [PMID: 39088066 DOI: 10.1007/s00284-024-03816-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024]
Abstract
A novel Gram-stain-positive, aerobic, catalase-positive, oxidase-negative, non-motile, and rod-shaped bacterium with ibuprofen-degrading capacity, designated DM4T, was isolated from the sewage of a wastewater treatment plant (WWTP) in Guangzhou city, China. Strain DM4T grew optimally at 0% (w/v) NaCl, pH 5.0-7.0, and 30 °C, forming white colonies on trypticase soy agar. C18:1ω9c, C18:2ω9.12c and C15:1ω10c were the predominant fatty acids. Results of 16S rRNA gene alignment and phylogenetic analysis indicated that strain DM4T belonged to the genus Patulibacter, was closely related to Patulibacter medicamentivorans DSM 25692T (98.5%) and P. brassicae KCTC 39817T (98.1%). Strain DM4T had a genome size of 5.33Mbp, and the DNA G + C content was 75.0%. The average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridisation (dDDH) values between strain DM4T and P. medicamentivorans were 85.2%, 83.9%, and 29.0% respectively, while those between strain DM4T and P. brassicae were 78.5%, 71.3%, and 22.2%, respectively. Strain DM4T could significantly degrade ibuprofen by almost 80% after 84 h of incubation, and the degradation kinetics was well fitted with the first-order kinetics. Evidence from phenotypic, phylogenetic and chemotaxonomic analyses support that strain DM4T (= GDMCC 1.4574T = KCTC 59145T) represents a new species of the genus Patulibacter, for which the name Patulibacter defluvii sp. nov. is proposed.
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Affiliation(s)
- Tianhui Jiang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
- School of Biology and Blialogical Engineering, South China University of Technology, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, 510070, Guangdong, China
| | - Weibin Jia
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, 510070, Guangdong, China
| | - Wenfang Deng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, 510070, Guangdong, China
| | - Zhiyuan Mai
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, 510070, Guangdong, China
| | - Meijun Dong
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, 510070, Guangdong, China
| | - Youda Huang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, 510070, Guangdong, China.
| | - Haizhen Wu
- School of Biology and Blialogical Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, 510070, Guangdong, China
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3
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Jung YH, Kwon YM, Chung D, Yu WJ, Choi G, Kim TW, Bae SS. Lutimonas zeaxanthinifaciens sp. nov. , a zeaxanthin-producing marine bacterium isolated from coastal sediment. Int J Syst Evol Microbiol 2024; 74. [PMID: 38743481 DOI: 10.1099/ijsem.0.006386] [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: 05/16/2024] Open
Abstract
A Gram-stain-negative, yellow-pigmented, strictly aerobic, non-flagellated, motile by gliding, rod-shaped bacterium, designated strain YSD2104T, was isolated from a coastal sediment sample collected from the southeastern part of the Yellow Sea. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain YSD2104T was closely related to three type strains, Lutimonas vermicola IMCC1616T (97.4 %), Lutimonas saemankumensis SMK-142T (96.9 %), and Lutimonas halocynthiae RSS3-C1T (96.8 %). Strain YSD2104T has a single circular chromosome of 3.54 Mbp with a DNA G+C content of 38.3 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain YSD2104T and the three type strains (L. vermicola IMCC1616 T, L. saemankumensis SMK-142T, and L. halocynthiae RSS3-C1T) were 74.0, 86.2 and 73.6 %, and 17.9, 30.3 and 17.8 %, respectively. Growth was observed at 20-30 °C (optimum, 30 °C), at pH 6.5-8.5 (optimum, pH 7.0), and with NaCl concentrations of 1.5-3.5 % (optimum, 2.5 %). The major carotenoid was zeaxanthin, and flexirubin-type pigment was not produced. The major respiratory quinone was menaquinone-6. The major fatty acids (>10 %) were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), and summed feature 9 (iso-C17 : 1 ω9c and/or 10-methyl C16 : 0). The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, two unidentified aminolipids, and eight unidentified lipids. Conclusively, based on this polyphasic approach, we classified strain YSD2104T (=KCTC 102008T=JCM 36287T) as representing a novel species of the genus Lutimonas and proposed the name Lutimonas zeaxanthinifaciens sp. nov.
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Affiliation(s)
- Yoon-Hee Jung
- National Marine Biodiversity Institute of Korea, 101-75, Jangsan-ro, Janghang-eup, Seocheon-gun Chungcheongnam-do 33662, Republic of Korea
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Yong Min Kwon
- National Marine Biodiversity Institute of Korea, 101-75, Jangsan-ro, Janghang-eup, Seocheon-gun Chungcheongnam-do 33662, Republic of Korea
| | - Dawoon Chung
- National Marine Biodiversity Institute of Korea, 101-75, Jangsan-ro, Janghang-eup, Seocheon-gun Chungcheongnam-do 33662, Republic of Korea
| | - Woon-Jong Yu
- National Marine Biodiversity Institute of Korea, 101-75, Jangsan-ro, Janghang-eup, Seocheon-gun Chungcheongnam-do 33662, Republic of Korea
| | - Grace Choi
- National Marine Biodiversity Institute of Korea, 101-75, Jangsan-ro, Janghang-eup, Seocheon-gun Chungcheongnam-do 33662, Republic of Korea
| | - Tae Wan Kim
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Seung Seob Bae
- National Marine Biodiversity Institute of Korea, 101-75, Jangsan-ro, Janghang-eup, Seocheon-gun Chungcheongnam-do 33662, Republic of Korea
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Chen Y, Zhuang Z, Liu J, Wang Z, Guo Y, Chen A, Chen B, Zhao W, Niu J. Effects of Hermetia illucens larvae meal on the Pacific white shrimp (Litopenaeus vannamei) revealed by innate immunity and 16S rRNA gene sequencing analysis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 46:101080. [PMID: 37141643 DOI: 10.1016/j.cbd.2023.101080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/30/2023] [Accepted: 04/20/2023] [Indexed: 05/06/2023]
Abstract
The larvae of the black soldier fly, Hermetia illucens, are now attracting attention and becoming promising sources for aquafeed ingredient due to the nutritious substance. However, the introduction of a novel ingredient into the recipe may have unpredictable effects on the innate immune function and gut bacteria composition of crustaceans. Therefore, the present study aimed to evaluate how dietary black soldier fly larvae meal (BSFLM) affected the antioxidant ability, innate immunity and gut microbiome of shrimp (Litopenaeus vannamei) fed with a practical diet, including the gene expression of Toll and immunodeficiency (IMD) pathways. Six experimental diets were formulated by replacing gradient levels of fish meal (0 %, 10 %, 20 %, 30 %, 40 % and 50 %) based on a commercial shrimp diet. Four replicates of shrimp were fed different diets three times daily for 60 days. Growth performance linearly decreased with increasing BSFLM inclusion. Results of antioxidative enzyme activities and gene expression suggested that low dietary BSFLM levels activated the antioxidant capacity of shrimp, while dietary BSFLM levels up to 100 g/kg may induce oxidative stress and inhibit glutathione peroxidase activity. Although traf6, toll1, dorsal and relish were significantly upregulated in different BSFLM groups, the expression of tak1 was significantly downregulated in groups containing BSFLM, implying the immune susceptibility may be weakened. Gut flora analysis indicated dietary BSFLM altered both beneficial and opportunistic pathogenic bacterial abundance, with low levels of dietary BSFLM increased the abundance of bacteria that may contribute to carbohydrate utilization, while high levels of dietary BSFLM may cause intestinal disease and low intestinal immune response. To conclude, 60-80 g/kg of dietary BSFLM showed no adverse effects on the growth, antioxidant capacity and gut flora of shrimp, which was the adequate level in shrimp diet. While 100 g/kg dietary BSFLM may induce oxidative stress and potentially weaken the innate immunity of shrimp.
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Affiliation(s)
- Yongkang Chen
- State key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong Province, PR China
| | - Zhenxiao Zhuang
- State key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong Province, PR China
| | - Jieping Liu
- State key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong Province, PR China
| | - Ziqiao Wang
- State key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong Province, PR China
| | - Yucai Guo
- State key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong Province, PR China
| | - Anqi Chen
- State key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong Province, PR China
| | - Baoyang Chen
- State key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong Province, PR China
| | - Wei Zhao
- State key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong Province, PR China.
| | - Jin Niu
- State key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong Province, PR China.
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5
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Xu J, Deng T, Huang Y, Dong M, Yang S, Xu M. Tabrizicola rongguiensis sp. nov., isolated from the sediment of a river in Ronggui, Foshan city, China. Int J Syst Evol Microbiol 2022; 72. [PMID: 36260499 DOI: 10.1099/ijsem.0.005539] [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: 06/16/2023] Open
Abstract
A novel Gram-negative, aerobic, non-spore-forming, non-motile and rod-shaped bacterium, designated J26T, was isolated from the sediment of a river in Ronggui, Foshan city, China. Strain J26T grew optimally at 0 % (w/v) NaCl, pH 6.5-7.5, and 30 °C, and it formed milky white irregular colonies on Reasoner's 2A agar medium. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain J26T had the highest similarity to Tabrizicola aquatica RCRI19T (97.1 %) and formed a distinct clade in the genus Tabrizicola. Cellular components of J26T supported this strain as a member of the genus Tabrizicola. The predominant fatty acids were C18 : 1 ω7c, C18 : 1 ω7c-11 methyl and C16 : 0. Polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphorylethanolamine. Ubiquinone Q-10 was the major respiratory quinone, and the DNA G+C content was 64.2 mol%. However, low 16S rRNA gene sequence similarity and average nucleotide identity (73.56 % for ANIb between strain J26T with RCRI19T) demonstrated that strain J26T should be assigned to a novel species. Moreover, the differences between J26T and RCRI19T in terms of physiological and biochemical properties, such as carbon, nitrogen and sulphur metabolism, further supported that J26T represents a novel species, for which the name Tabrizicola rongguiensis sp. nov. is proposed. The type strain is J26T (=GDMCC 1.2843T=KCTC 92112T).
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Affiliation(s)
- Jiarou Xu
- College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, PR China
- State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, PR China
| | - Tongchu Deng
- State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, PR China
| | - Youda Huang
- State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, PR China
| | - Meijun Dong
- State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, PR China
| | - Shan Yang
- State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, PR China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, PR China
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Escalas A, Avouac A, Belmaker J, Bouvier T, Clédassou V, Ferraton F, Rieuvilleneuve F, Rilov G, Rovirosa Mulet A, Shapiro Goldberg D, Villéger S. An invasive herbivorous fish (Siganus rivulatus) influences both benthic and planktonic microbes through defecation and nutrient excretion. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156207. [PMID: 35636548 DOI: 10.1016/j.scitotenv.2022.156207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 03/23/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Direct and indirect impacts by invasive animals on plants and other animals through predation and competition have been evidenced in many ecosystems. For instance, the rabbitfish Siganus rivulatus, originating from the Red Sea, is now the most abundant species in costal habitats of South-Eastern Mediterranean Sea where it overgrazes algae. However, little is known about its impacts on microbes through release of metabolic wastes and feces. We used a mesocosm experiment to test the effect of S. rivulatus on planktonic and benthic microbial communities. Excretion of dissolved nutrients by fish resulted in higher concentrations of dissolved inorganic nitrogen (NH4, NO2/NO3). This increase in availability of N was associated with higher N content in macroalgae, higher biomass of phytoplankton, higher abundance of bacterioplankton and shift in the structure of planktonic bacterial communities. The feces released mostly under the shelters where the fish rest at night, led to significant increases in diversity of sediment bacterial communities and shifts in their structure. The impact of S. rivulatus on planktonic microbes was related to the indirect bottom-up effect induced by excreted dissolved nutrients while its effect on benthic microbes was due to the direct release of both organic matter and microbes present in feces. Overall, this first evidence of the impacts of invasive species on planktonic and benthic microbes highlights that ongoing changes in fish biodiversity could have ecosystem-wide consequences.
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Affiliation(s)
- Arthur Escalas
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Montpellier, France.
| | - Amandine Avouac
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Montpellier, France
| | - Jonathan Belmaker
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv-Yafo, Israel; The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Thierry Bouvier
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Montpellier, France
| | - Valentin Clédassou
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Montpellier, France
| | - Franck Ferraton
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Montpellier, France
| | | | - Gil Rilov
- National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa, Israel
| | | | - Daphna Shapiro Goldberg
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Sébastien Villéger
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Montpellier, France.
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Han JE, Kang W, Lee JY, Sung H, Hyun DW, Kim HS, Kim PS, Tak EJ, Jeong YS, Lee JY, Lee SY, Yun JH, Jung MJ, Shin NR, Whon TW, Kang MS, Lee KE, Lee BH, Bae JW. Tabrizicola piscis sp. nov., isolated from the intestinal tract of a Korean indigenous freshwater fish, Acheilognathus koreensis. Int J Syst Evol Microbiol 2020; 70:2305-2311. [DOI: 10.1099/ijsem.0.004034] [Citation(s) in RCA: 10] [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 Gram-negative, obligately aerobic, rod-shaped and non-motile bacterium, designated strain K13M18T, was isolated from the intestinal tract of a Korean indigenous fish, oily bitterling (Acheilognathus koreensis). Strain K13M18T formed creamy-pink colonies on a marine agar plate. Results of phylogenetic analysis based on the 16S rRNA gene sequence similarity indicated that strain K13M18T was most closely related to
Tabrizicola sediminis
DRYC-M-16T, sharing 97.62 % similarity with that strain. Strain K13M18T belonged to the genus
Tabrizicola
, which formed a cluster with
Tabrizicola aquatica
RCRI19T,
Tabrizicola fusiformis
SY72T,
Tabrizicola sediminis
DRYC-M-16T and
Tabrizicola alkalilacus
DJCT in a phylogenetic tree based on the 16S rRNA gene sequences. Strain K13M18T grown optimally in 0 % (w/v) NaCl, at pH 7 and 30 °C, in a marine broth medium. The predominant cellular fatty acids were C18 : 1
ω7c and C18 : 1
ω6c. The major respiratory isoprenoid quinone was ubiquinone Q-10. Polar lipids of strain K13M18T contained phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, diphosphatidylglycerol, six unidentified aminophospholipids, one unidentified aminolipid and an unidentified lipid. Based on genome sequencing, the DNA G+C content of strain K13M18T was 64.08 mol %, with an average nucleotide identity value, calculated by a comparative genomic analysis of strains K13M18T and
T. sediminis
DRYC-M-16T, of 74.82 %. Based on the phylogenetic, genotypic, and phenotypic information, strain K13M18T is proposed to be a novel species of the genus
Tabrizicola
. The type strain is K13M18T (=KCTC 62659T=JCM 33230T).
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Affiliation(s)
- Jeong Eun Han
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Woorim Kang
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - June-Young Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Hojun Sung
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Hyun Sik Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Pil Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Euon Jung Tak
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Yun-Seok Jeong
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Jae-Yun Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - So-Yeon Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Ji-Hyun Yun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Mi-Ja Jung
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Na-Ri Shin
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Tae Woong Whon
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Myung-Suk Kang
- Biological Resources Utilization Department, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Ki-Eun Lee
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Byoung-Hee Lee
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
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8
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Chen X, Li GD, Wei YF, Li YL, Yu H, Zhang K, Jiang CL, Jiang Y. Faecalibacter macacae gen. nov., sp. nov., isolated from the faeces of Macaca assamensis. Int J Syst Evol Microbiol 2020; 70:751-758. [DOI: 10.1099/ijsem.0.003815] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Xiu Chen
- School of Medicine, Kunming University, Kunming 650214, PR China
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, PR China
| | - Gui-Ding Li
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, PR China
| | - Yun-Fang Wei
- School of Medicine, Kunming University, Kunming 650214, PR China
| | - You-Long Li
- Yunnan Wild Animal Park, Kunming, Yunnan 650224, PR China
| | - Hua Yu
- School of Medicine, Kunming University, Kunming 650214, PR China
| | - Kun Zhang
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, PR China
| | - Cheng-Lin Jiang
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, PR China
| | - Yi Jiang
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, PR China
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9
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Li J, Wang T, Yu S, Bai J, Qin S. Community characteristics and ecological roles of bacterial biofilms associated with various algal settlements on coastal reefs. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 250:109459. [PMID: 31479939 DOI: 10.1016/j.jenvman.2019.109459] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/20/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
Bacterial biofilms, which are a group of bacteria attaching to and ultimately forming communities on reefs, perform essential ecological functions in coastal ecosystems. Particularly, they may attract or repulse the settling down of opportunistic algae. However, this phenomenon and the interaction mechanism are not fully understood. This study investigated reefs from the Changdao coastal zone to determine the structures and functions of bacterial biofilms symbiosing with various algae using high-throughput sequencing analysis. The Shannon diversity index of microbiota with algal symbiosis reached 5.34, which was higher than that of microbiota wherein algae were absent (4.80). The beta diversity results for 11 samples revealed that there existed a separation between bacterial communities on reefs with and without attached algae, while communities with similar algae clustered together. The taxa mostly associated with algae-symbiotic microbiota are the Actinobacteria phylum, and the Flavobacteriia and Gammaproteobacteria classes. The Cyanobacteria phylum was not associated with algae-symbiotic microbiota. As revealed by functional analysis, the bacteria mostly involved in the metabolism of sulfur were represented by brown and red algae in the biofilm symbiosis. Bacteria related to the metabolism of certain trace elements were observed only in specific groups. Moreover, phototrophy-related bacteria were less abundant in samples coexisting with algae. This study established the link between bacterial biofilms and algal settlements on costal reefs, and revealed the possible holobiont relationship between them. This may provide new technical directions toward realizing algal cultivation and management during the construction of artificial reef ecosystems.
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Affiliation(s)
- Jialin Li
- Key Lab of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264000, Shandong, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Ting Wang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China; Key Lab of Marine Environmental Science and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Shuxian Yu
- Key Lab of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264000, Shandong, China
| | - Jie Bai
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China; Key Lab of Marine Environmental Science and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China.
| | - Song Qin
- Key Lab of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264000, Shandong, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
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10
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Jeong YS, Kang W, Sung H, Lee JY, Yun JH, Shin NR, Kim HS, Lee SY, Han JE, Lee JY, Tak EJ, Kim PS, Hyun DW, Jung MJ, Whon TW, Kang MS, Lee KE, Lee BH, Bae JW. Flammeovirga pectinis sp. nov., isolated from the gut of the Korean scallop, Patinopecten yessoensis. Int J Syst Evol Microbiol 2019; 70:499-504. [PMID: 31613737 DOI: 10.1099/ijsem.0.003783] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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, aerobic, rod-shaped, reddish-orange-coloured, gliding bacterial strain, designated L12M1T, was isolated from the gut of the Korean scallop, Patinopecten yessoensis. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain L12M1T formed a monophyletic clade with the strains in the genus Flammeovirga and showed highest 16S rRNA gene sequence similarity to Flammeovirga kamogawensis YS10T (98.66 %). The major cellular fatty acids of strain L12M1T were iso-C15 : 0 and C20 : 4ω6,9,12,15c. The predominant isoprenoid quinone was MK-7. The major polyamines were spermidine, cadaverine and the minor polyamine was putrescine. The DNA G+C content was 32.1 mol%. The phylogenetic, phenotypic, biochemical, chemotaxonomic and genotypic results indicated that strain L12M1T represents a novel species of the genus Flammeovirga, for which the name Flammeovirga pectinis sp. nov. is proposed. The type strain is L12M1T (=KCTC 62750T=JCM 33169T).
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Affiliation(s)
- Yun-Seok Jeong
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Woorim Kang
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Hojun Sung
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - June-Young Lee
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Ji-Hyun Yun
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Na-Ri Shin
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Hyun Sik Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - So-Yeon Lee
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Jeong Eun Han
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Jae-Yun Lee
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Euon Jung Tak
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Pil Soo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Dong-Wook Hyun
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Mi-Ja Jung
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Tae Woong Whon
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Myung-Suk Kang
- Biological Resources Utilization Department, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Ki-Eun Lee
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Byoung-Hee Lee
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Jin-Woo Bae
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
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11
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Paracoccus tegillarcae sp. nov., isolated from the gastrointestinal tract of a blood cockle (Tegillarca granosa). Int J Syst Evol Microbiol 2019; 69:2815-2822. [DOI: 10.1099/ijsem.0.003561] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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12
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Hochstein R, Zhang Q, Sadowsky MJ, Forbes VE. The deposit feeder Capitella teleta has a unique and relatively complex microbiome likely supporting its ability to degrade pollutants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 670:547-554. [PMID: 30909032 DOI: 10.1016/j.scitotenv.2019.03.255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/12/2019] [Accepted: 03/17/2019] [Indexed: 06/09/2023]
Abstract
Capitella teleta is a sediment-dwelling marine polychaete that is often found in high densities in association with organic matter and pollutants. While C. teleta has been reported to transform a variety of aromatic hydrocarbons, the mechanisms by which degradation occurs are unknown. Moreover, there is continuing debate on the role of host and microbiota in degradation activity. The aims of this study were to characterize the gut microbiome of C. teleta and to identify microbiota that could potentially play a role in degradation of organic matter and aromatic hydrocarbons. Sequencing analysis of the 16S rRNA genes from the intestinal tracts of adult worms revealed a unique microbiome that was distinct from that of the worm's sediment food source and fecal pellets. About 66% of the 775 identified OTUs from the C. teleta gut microbiome were found to be unique to the worm and displayed high inter-individual variability. The gut microbiome was dominated by members of the genera Arcobacter, Pseudoalteromonas, Methylobacterium, and Propionibacterium. Functional analyses of microbiota revealed that hydrocarbon treatment led to a proliferation of gene classes involved in chemoheterotrophy and aromatic compound degradation. Of the 18 most abundant taxa identified, 50% were members of genera containing hydrocarbon (PAH)-degrading members, including Acinetobacter, Thalassotalea, and Achromobacter. Data obtained in this study will be useful to understand the biology of this marine polychaete and to elucidate the role that gut bacteria play in worm catabolism and the transformation of sediment organic pollutants.
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Affiliation(s)
- Rebecca Hochstein
- Department of Ecology, Evolution, and Behavior, University of Minnesota, United States of America; BioTechnology Institute, University of Minnesota, United States of America
| | - Qian Zhang
- BioTechnology Institute, University of Minnesota, United States of America
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota, United States of America; Department of Soil, Water and Climate, University of Minnesota, United States of America; Department of Plant and Microbial Biology, University of Minnesota, United States of America.
| | - Valery E Forbes
- Department of Ecology, Evolution, and Behavior, University of Minnesota, United States of America.
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13
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Park S, Choi J, Park JM, Yoon JH. Aestuariimonas insulae gen. nov., sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2018; 68:1365-1371. [DOI: 10.1099/ijsem.0.002684] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Jeehyun Choi
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Ji-Min Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
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14
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Ascidiaceibacter salegens gen. nov., sp. nov., isolated from an ascidian. Antonie van Leeuwenhoek 2018; 111:1687-1695. [DOI: 10.1007/s10482-018-1058-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/24/2018] [Indexed: 10/17/2022]
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15
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Tak EJ, Kim HS, Lee JY, Kang W, Hyun DW, Kim PS, Shin NR, Bae JW. Vagococcus martis sp. nov., isolated from the small intestine of a marten, Martes flavigula. Int J Syst Evol Microbiol 2017; 67:3398-3402. [PMID: 28857031 DOI: 10.1099/ijsem.0.002131] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A novel coccus-shaped, Gram-stain-positive, non-motile and facultative aerobic bacterium, designated strain D7T301T, was isolated from the small intestine of a marten, Martes flavigula, which was killed on the road in Pocheon-si, Gyeonggi-do, Republic of Korea. Grown on a tryptic soy yeast agar plate, colonies had a creamy colour and irregular form. The new isolate formed a monophyletic clade with Vagococcus penaei CD276T on a phylogenetic consensus tree based on the 16S rRNA gene sequence. The isolate grew optimally at 37 °C and pH 7 in the presence of 0.5 % (w/v) NaCl. The isolate was catalase- and oxidase-negative. The cell-wall peptidoglycan was type A4α l-Lys-d-Asp. The major cellular fatty acids were C16 : 0, C14 : 0, and C16 : 1ω9c. The predominant respiratory quinone was menaquinone MK-7 (85.1 %). The DNA G+C content based on genome sequencing was 33.8 mol%. The average nucleotide identity value obtained from comparative genomic analysis between strain D7T301T and V. penaei CIP 109914T was 72.6 %. On the basis of the phenotypic, phylogenetic, biochemical, chemotaxonomic, and genotypic analyses, Vagococcusmartis is proposed as a novel species of the genus Vagococcus. The type strain is D7T301T (=KCTC 21069T=JCM 31178T).
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Affiliation(s)
- Euon Jung Tak
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Hyun Sik Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - June-Young Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Woorim Kang
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Pil Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Na-Ri Shin
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
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16
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Lee JY, Kim PS, Hyun DW, Kim HS, Shin NR, Jung MJ, Yun JH, Kim MS, Whon TW, Bae JW. Microbulbifer echini sp. nov., isolated from the gastrointestinal tract of a purple sea urchin, Heliocidaris crassispina. Int J Syst Evol Microbiol 2017; 67:998-1004. [PMID: 27959777 DOI: 10.1099/ijsem.0.001731] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterium, designated as strain AM134T, was isolated from the gut of a purple sea urchin (Heliocidaris crassispina) gathered from the coastal waters of Dokdo, Korea. Strain AM134T was Gram-stain-negative, both catalase- and oxidase-positive, strictly aerobic and showed a rod-coccus cell cycle. Optimum growth occurred at 30 °C, in the presence of 2 % (w/v) NaCl and at pH 7. The 16S rRNA gene sequence analysis showed that strain AM134T belonged to the genus Microbulbifer in the family Alteromonadaceae and had high 16S rRNA gene sequence similarity (>97 %) with Microbulbifer epialgicus F-104T (98.9 % similarity) and Microbulbifer variabilis Ni-2088T (98.6 % similarity). The polar lipid profile of strain AM134T was composed of phosphatidylethanolamine, phosphatidylserine, three unidentified aminophospholipids, two unidentified phospholipids, an unidentified amino lipid and six unidentified lipids. The major respiratory quinone was identified as ubiquinone-8 (Q-8). The major cellular fatty acids were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C16 : 0. The DNA-DNA hybridization analysis showed that the strain shared less than 28 % genomic relatedness with Microbulbifer epialgicus DSM 18651T (27±3 %) and Microbulbifer variabilis ATCC 700307T (15±1 %). The G+C content of the genomic DNA was 56.1 mol%. The results of the phylogenetic, phenotypic and genotypic analyses suggest that strain AM134T represents a novel species in the genus Microbulbifer, for which the name Microbulbifer echini is proposed. The type strain is AM134T (=KACC 18258T=JCM 30400T).
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Affiliation(s)
- June-Young Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Pil Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Hyun Sik Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Na-Ri Shin
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Mi-Ja Jung
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Ji-Hyun Yun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Min-Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Tae Woong Whon
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
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17
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Kang W, Hyun DW, Kim PS, Shin NR, Kim HS, Lee JY, Tak EJ, Roh JR, Park SD, Shim HE, Bae JW. Flexivirga lutea sp. nov., isolated from the faeces of a crested ibis, Nipponia nippon, and emended description of the genus Flexivirga. Int J Syst Evol Microbiol 2016; 66:3594-3599. [PMID: 27295948 DOI: 10.1099/ijsem.0.001238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-staining-positive, aerobic, non-motile and coccus-shaped bacterium, designated strain TBS-100T, was isolated from the faeces of a crested ibis, Nipponia nippon. The phylogenetic analysis based on the 16S rRNA gene sequences showed that the closest relative of TBS-100T was Flexivirga alba DSM 24460T with 97.11 % sequence similarity, and that strain TBS-100T belonged to the genus Flexivirga. The optimum growth conditions for strain TBS-100T were 30 °C, at a pH of 7 and in the presence of 0 % (w/v) NaCl. The primary cellular fatty acids of strain TBS-100T were anteiso-C17 : 0 and iso-C17 : 0. The predominant isoprenoid quinones were MK-8 (H4) (70.2 %) and MK-8 (H6) (29.7 %). The polar lipids were diphosphatidylglycerol, phosphatidylinositol, seven unidentified lipids and an unidentified phospholipid. The whole-cell sugars of strain TBS-100T were ribose, glucose, galactose, rhamnose and mannose. The peptidoglycan contained alanine, lysine, glutamic acid, glycine and aspartic acid. The DNA G+C content was 64.8 mol%. The phenotypic, phylogenetic and genotypic analyses indicated that strain TBS-100T represents a novel species of the genus Flexivirga for which the name Flexivirga lutea sp. nov. is proposed. The type strain is TBS-100T (=KCTC 39625T=JCM 31200T). In addition, an emended description of the genus Flexivirga is proposed.
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Affiliation(s)
- Woorim Kang
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Pil Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Na-Ri Shin
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Hyun Sik Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - June-Young Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Euon Jung Tak
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Jeong Rae Roh
- Seoul Grand Park, 102, Daegongwongwangjang-ro, Gwacheon-si, Gyeonggi-do, Republic of Korea
| | - Sun Duk Park
- Seoul Grand Park, 102, Daegongwongwangjang-ro, Gwacheon-si, Gyeonggi-do, Republic of Korea
| | - Hyung Eun Shim
- Seoul Grand Park, 102, Daegongwongwangjang-ro, Gwacheon-si, Gyeonggi-do, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
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18
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Lee JY, Hyun DW, Soo Kim P, Sik Kim H, Shin NR, Yun JH, Jung MJ, Kim MS, Woong Whon T, Bae JW. Arthrobacter echini sp. nov., isolated from the gut of a purple sea urchin, Heliocidaris crassispina. Int J Syst Evol Microbiol 2016; 66:1887-1893. [DOI: 10.1099/ijsem.0.000965] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- June-Young Lee
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Korea
| | - Dong-Wook Hyun
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Korea
| | - Pil Soo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Korea
| | - Hyun Sik Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Korea
| | - Na-Ri Shin
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Korea
| | - Ji-Hyun Yun
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Korea
| | - Mi-Ja Jung
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Korea
| | - Min-Soo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Korea
| | - Tae Woong Whon
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Korea
| | - Jin-Woo Bae
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Korea
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19
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Hyun DW, Jung MJ, Kim MS, Shin NR, Kim PS, Whon TW, Bae JW. Proteus cibarius sp. nov., a swarming bacterium from Jeotgal, a traditional Korean fermented seafood, and emended description of the genus Proteus. Int J Syst Evol Microbiol 2016; 66:2158-2164. [PMID: 26944634 DOI: 10.1099/ijsem.0.001002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Proteus-like, Gram-stain-negative, facultatively anaerobic, rod-shaped bacterium, designated strain JS9T, was isolated from Korean fermented seafood, Jeotgal. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain JS9T belonged to the genus Proteus in the family Enterobacteriaceae. The highest 16S rRNA gene sequence similarity of strain JS9T was to Proteus vulgaris KCTC 2579T (98.98 %) and the genomic DNA G+C content is 39.0 mol%. DNA-DNA hybridization values were measured and strain JS9T showed <20.8 % genomic relatedness with closely-related members of the genus Proteus. The isolate showed bacterial motility and swarming activity similar to those of pathogenic Proteus mirabilis but distinct from those of other species of the genus Proteus. The isolate grows optimally at 30 °C, at pH 7, and in the presence of 2 % (w/v) NaCl. The main respiratory quinones are ubiquinone Q-8 and Q-10, and the major cellular fatty acids are C16 : 0, summed feature 3 and summed feature 8. The polar lipids comprise phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unidentified amino lipid, two unidentified amino-phospholipids, and three unidentified lipids. Based on phylogenetic, phenotypic, chemotaxonomic and genotypic analyses, strain JS9T represents a novel species of the genus Proteus, for which the name Proteus cibarius sp. nov. is proposed. The type strain is JS9T (=KACC 18404T=JCM 30699T). An emended description of the genus Proteus is also provided.
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Affiliation(s)
- Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Republic of Korea
| | - Mi-Ja Jung
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Republic of Korea
| | - Min-Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Republic of Korea
| | - Na-Ri Shin
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Republic of Korea
| | - Pil Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Republic of Korea
| | - Tae Woong Whon
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Republic of Korea
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Kim HS, Kim PS, Hyun DW, Lee JY, Kang W, Shin NR, Whon TW, Bae JW. Pseudahrensia todarodis sp. nov., isolated from the gut of a Japanese flying squid, Todarodes pacificus. Int J Syst Evol Microbiol 2016; 66:1389-1393. [DOI: 10.1099/ijsem.0.000888] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Hyun Sik Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Korea
| | - Pil Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Korea
| | - Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Korea
| | - June-Young Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Korea
| | - Woorim Kang
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Korea
| | - Na-Ri Shin
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Korea
| | - Tae Woong Whon
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Korea
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Hyun DW, Oh SJ, Kim MS, Whon TW, Jung MJ, Shin NR, Kim PS, Kim HS, Lee JY, Kang W, Bae JW. Simplicispira piscis sp. nov., isolated from the gut of a Korean rockfish, Sebastes schlegelii. Int J Syst Evol Microbiol 2015; 65:4689-4694. [DOI: 10.1099/ijsem.0.000635] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, aerobic, motile and rod-shaped bacterium, designated strain RSG39T, was isolated from the gut of a Korean rockfish, Sebastes schlegelii. The 16S rRNA gene sequence analysis revealed that strain RSG39T belonged to the genus Simplicispira in the class Betaproteobacteria and its highest sequence similarity was shared with S. psychrophila (98.4 %). The isolate grew optimally at 20 °C, at pH 7 and with 0 % (w/v) NaCl. The main respiratory quinone of the isolate was ubiquinone Q-8. The major cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The polar lipids of the isolate were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and six unidentified lipids. The DNA–DNA hybridization values showed < 7.4 % genomic relatedness with closely related strains. The genomic DNA G+C content was 65.2 mol %. Based on phylogenetic, phenotypic, chemotaxonomic and genotypic analyses, strain RSG39T represents a novel species of the genus Simplicispira, for which the name Simplocospira piscis sp. nov. is proposed. The type strain is RSG39T ( = KACC 17539T = JCM 19291T).
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Affiliation(s)
- Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Sei Joon Oh
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Min-Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Tae Woong Whon
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Mi-Ja Jung
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Na-Ri Shin
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Pil Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Hyun Sik Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - June-Young Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Woorim Kang
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
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Kim HS, Hyun DW, Kim PS, Lee JY, Shin NR, Yun JH, Whon TW, Kim MS, Jung MJ, Bae JW. Bizionia fulviae sp. nov., isolated from the gut of an egg cockle, Fulvia mutica. Int J Syst Evol Microbiol 2015; 65:3066-3072. [DOI: 10.1099/ijs.0.000380] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-staining-negative, non-spore-forming, non-flagellated, non-motile, aerobic, saffron-coloured, rod-shaped bacterium that did not produce flexirubin-type pigments was designated strain EM7T and was distinct from other members of the genus Bizionia by produce carotenoid-type pigments and being able to grow independently of NaCl. Strain EM7T was isolated from the intestinal tract of an egg cockle, Fulvia mutica, which had been collected from the West Sea in Korea. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain EM7T belonged to the genus Bizionia, and showed sequence similarity to Bizionia paragorgiae KMM 6029T (97.9 %) and Bizionia saleffrena HFDT (97.73 %). Growth occurred on marine agar 2216 at 0–25 °C (optimum, 20 °C) and at pH 6–9 (optimum, pH 7). Growth occurred in the presence of 0–10 % (w/v) NaCl (optimum, 2 %, w/v, NaCl). The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C15 : 1 G, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH and iso-C16 : 0 3-OH. The major respiratory quinone was menaquinone MK-6. The polar lipids of strain EM7T comprised phosphatidylethanolamine, three unidentified aminolipids, an unidentified aminophospholipid and two unidentified lipids. The genomic DNA G+C content was 34.8 mol%. Bizionia paragorgiae KMM 6029T and Bizionia saleffrena HFDT to Bizionia paragorgiae KCTC 12304T and Bizionia saleffrena CIP 108534T, respectively. Thus, it is proposed that the isolate represents a novel species, Bizionia fulviae sp. nov., with strain EM7T ( = KACC 18255T = JCM 30417T) as the type strain.
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Affiliation(s)
- Hyun Sik Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Pil Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - June-Young Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Na-Ri Shin
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Ji-Hyun Yun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Tae Woong Whon
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Min-Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Mi-Ja Jung
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
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