Actinomyces haliotis sp. nov., a bacterium isolated from the gut of an abalone, Haliotis discus hannai

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 456-461 ◽  
Author(s):  
Dong-Wook Hyun ◽  
Na-Ri Shin ◽  
Min-Soo Kim ◽  
Pil Soo Kim ◽  
Joon Yong Kim ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Northern Coast ◽  
Haliotis Discus Hannai ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Haliotis Discus

A novel, Gram-staining-positive, facultatively anaerobic, non-motile and coccus-shaped bacterium, strain WL80T, was isolated from the gut of an abalone, Haliotis discus hannai, collected from the northern coast of Jeju in Korea. Optimal growth occurred at 30 °C, pH 7–8 and with 1 % (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that strain WL80T fell within the cluster of the genus Actinomyces , with highest sequence similarity to the type strains of Actinomyces radicidentis (98.8 % similarity) and Actinomyces urogenitalis (97.0 % similarity). The major cellular fatty acids were C18 : 1ω9c and C16 : 0. Menaquinone-10 (H4) was the major respiratory quinone. The genomic DNA G+C content of the isolate was 70.4 mol%. DNA–DNA hybridization values with closely related strains indicated less than 7.6 % genomic relatedness. The results of physiological, biochemical, chemotaxonomic and genotypic analyses indicated that strain WL80T represents a novel species of the genus Actinomyces , for which the name Actinomyces haliotis sp. nov. is proposed. The type strain is WL80T ( = KACC 17211T = JCM 18848T).

Shimia haliotis sp. nov., a bacterium isolated from the gut of an abalone, Haliotis discus hannai

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4248-4253 ◽  
Author(s):  
Dong-Wook Hyun ◽  
Min-Soo Kim ◽  
Na-Ri Shin ◽  
Joon Yong Kim ◽  
Pil Soo Kim ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Northern Coast ◽  
Haliotis Discus Hannai ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Haliotis Discus ◽  
Abalone Haliotis Discus

A novel Gram-stain-negative, motile, rod-shaped bacterium, designated strain WM35T, was isolated from the intestinal tract of an abalone, Haliotis discus hannai, which was collected from the northern coast of Jeju in Korea. The cells of the isolate grew optimally at 30 °C, pH 7, and with 3 % (w/v) NaCl. Based on 16S rRNA gene sequence similarity comparisons, strain WM35T was grouped in the genus Shimia and was closely related to the type strains of Shimia isoporae (98.7 % similarity) and Shimia marina (97.8 % similarity). The major cellular fatty acids were summed feature 8 and C16 : 0 2-OH. Ubiquinone Q-10 was the predominant respiratory quinone. The polar lipids of strain WM35T comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminolipid and an unidentified lipid. The DNA G+C content of the isolate was 53.8 mol%. DNA–DNA hybridization values indicated <16 % genomic relatedness with members of the genus Shimia . The physiological, chemical and genotypic analyses indicated that strain WM35T represents a novel species of the genus Shimia , for which the name Shimia haliotis sp. nov. is proposed. The type strain is WM35T ( = KACC 17212T = JCM 18870T).

Pseudoruegeria haliotis sp. nov., isolated from the gut of the abalone Haliotis discus hannai

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4626-4632 ◽  
Author(s):  
Dong-Wook Hyun ◽  
Na-Ri Shin ◽  
Min-Soo Kim ◽  
Pil Soo Kim ◽  
Joon Yong Kim ◽  
...  
Keyword(s):  
Type Strain ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Northern Coast ◽  
Haliotis Discus Hannai ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Haliotis Discus

A novel Gram-negative, aerobic, non-motile and rod-shaped bacterium, designated strain WM67T, was isolated from the gut of an abalone (Haliotis discus hannai) collected from the northern coast of Jeju Island in Korea. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that strain WM67T clustered in the genus Pseudoruegeria , and the highest sequence similarity was shared with Pseudoruegeria lutimaris (98.0 % similarity to the type strain). Optimal growth of the isolate occurred at 30 °C, pH 7–8 and with 1 % (w/v) NaCl. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. Ubiquinone Q-10 was the major respiratory quinone. The polar lipids of strain WM67T comprised phosphatidylserine, phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, an unidentified glycolipid and three unidentified lipids. The genomic DNA G+C content was 66.5 mol%. DNA–DNA hybridization indicated <17 % genomic relatedness to other members of the genus Pseudoruegeria . The physiological, biochemical, chemotaxonomic and genotypic analyses indicated that strain WM67T represents a novel species of Pseudoruegeria , for which the name Pseudoruegeria haliotis sp. nov. is proposed. The type strain is WM67T ( = KACC 17214T = JCM 18872T).

Cloacibacterium haliotis sp. nov., isolated from the gut of an abalone, Haliotis discus hannai

2014 ◽  
Vol 64 (Pt_1) ◽  
pp. 72-77 ◽  
Author(s):  
Dong-Wook Hyun ◽  
Na-Ri Shin ◽  
Min-Soo Kim ◽  
Joon Yong Kim ◽  
Pil Soo Kim ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Northern Coast ◽  
Haliotis Discus Hannai ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Haliotis Discus ◽  
Major Respiratory Quinone

A novel Gram-stain-negative, aerobic, non-motile, yellow-pigmented and rod-shaped bacterium, designated strain WB5T, was isolated from the intestinal tract of an abalone, Haliotis discus hannai, collected from the northern coast of Jeju in Korea. The isolate grew optimally at 30 °C, at pH 7 and in the presence of 0.5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain WB5T was clustered in the genus Cloacibacterium and shared the highest sequence similarity with C. normanense (98.2 % similarity). The predominant fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. Menaquinone-6 was the major respiratory quinone. The genomic DNA G+C content was 29.6 mol%. The DNA–DNA hybridization values indicated <22 % genomic relatedness with other members of the genus Cloacibacterium . The results of physiological, biochemical, chemotaxonomic and genotypic analyses showed that strain WB5T represents a novel species of the genus Cloacibacterium , for which the name Cloacibacterium haliotis sp. nov. is proposed. The type strain is WB5T ( = KACC 17210T = JCM 18869T).

scholarly journals Actibacter haliotis sp. nov., isolated from the gut of an abalone, Haliotis discus hannai, and emended description of the genus Actibacter

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 49-55 ◽  
Author(s):  
Dong-Wook Hyun ◽  
Joon Yong Kim ◽  
Min-Soo Kim ◽  
Na-Ri Shin ◽  
Hyun Sik Kim ◽  
...  
Keyword(s):  
Type Strain ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Northern Coast ◽  
Haliotis Discus Hannai ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Haliotis Discus

A novel strain, designated strain W113T, was isolated from the gut of an abalone, Haliotis discus hannai, which was collected from the northern coast of Jeju in Korea. The isolate was a Gram-staining-negative, facultatively anaerobic, non-motile, rod-shaped bacterium producing yellow-to-orange carotenoid-type pigments. 16S rRNA gene sequence analysis showed that the isolate belonged to the genus Actibacter in the family Flavobacteriaceae and it shared the highest sequence similarity with the type strain of Actibacter sediminis (98.8 % similarity). Optimal growth occurred at 25 °C, at pH 7 and with 2 % (w/v) NaCl. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C15 : 1 G. Menaquinone-6 was the main respiratory quinone. The polar lipids of the isolate were phosphatidylethanolamine, three unidentified amino lipids, and three unidentified lipids. The genomic DNA G+C content was 42.6 mol% and DNA–DNA hybridization values indicated that the strain shared <18 % genomic relatedness with the most closely related species. The results of the phylogenetic, phenotypic and genotypic analyses indicated that strain W113T represents a novel species in the genus Actibacter , for which the name Actibacter haliotis sp. nov. is proposed. The type strain is W113T ( = KACC 17209T = JCM 18868T).

scholarly journals Rufibacter latericius sp. nov., isolated from Baiyang Lake

2020 ◽  
Vol 70 (11) ◽  
pp. 5943-5949 ◽  
Author(s):  
Yun-zhen Yang ◽  
Ji-feng Chen ◽  
Wan-ru Huang ◽  
Ran-ran Zhang ◽  
Shuangjiang Liu ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Pr China

A novel Gram-stain-negative, strictly aerobic, rod-shaped, brick red-pigmented bacterium, designated R-22-1 c-1T, was isolated from water from Baiyang Lake, Hebei Province, PR China. The strain was able to grow at 20–30 °C (optimum, 30 °C) and pH 6–7 (optimum, pH 6) in Reasoner’s 2A medium. 16S rRNA gene sequence and phylogenetic analyses of R-22-1 c-1T revealed closest relationships to Rufibacter immobilis MCC P1T (97.8 %), Rufibacter sediminis H-1T (97.9 %) and Rufibacter glacialis MDT1-10-3T (97.0 %), with other species of the genus Rufibacter showing less than 97.0 % sequence similarity. The predominant polar lipids were phosphatidylethanolamine, two unidentified aminophospholipids and three unidentified lipids. The major cellular fatty acids were iso-C15 : 0, C15 : 1  ω6c, C17 : 1  ω6c, anteiso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 4 (iso-C17 : 1I and/or anteiso-C17 : 1B). The respiratory quinone was MK-7. The draft genome of R-22-1 c-1T was 5.6 Mbp in size, with a G+C content of 50.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization relatedness values between strain R-22-1 c-1T and related type strains were R. immobilis MCC P1T (77.2 and 21.8 %), R. sediminis H-1T (81.6 and 21.4 %) and R. tibetensis 1351T (78.5 and 22.9 %). Based on these phylogenetic, chemotaxonomic and genotypic results, strain R-22-1 c-1T represents a novel species in the genus Rufibacter , for which the name Rufibacter latericius sp. nov. is proposed. The type strain is R-22-1 c-1T (=CGMCC 1.13570T=KCTC 62781T).

Croceimicrobium hydrocarbonivorans gen. nov., sp. nov., a novel marine bacterium isolated from a bacterial consortium that degrades polyethylene terephthalate

2021 ◽  
Vol 71 (4) ◽  
Author(s):  
Renju Liu ◽  
Qiliang Lai ◽  
Li Gu ◽  
Peisheng Yan ◽  
Zongze Shao
Keyword(s):  
Polyethylene Terephthalate ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family

A novel Gram-stain-negative, aerobic, gliding, rod-shaped and carotenoid-pigmented bacterium, designated A20-9T, was isolated from a microbial consortium of polyethylene terephthalate enriched from a deep-sea sediment sample from the Western Pacific. Growth was observed at salinities of 1–8 %, at pH 6.5–8 and at temperatures of 10–40 °C. The results of phylogenetic analyses based on the genome indicated that A20-9T formed a monophyletic branch affiliated to the family Schleiferiaceae , and the 16S rRNA gene sequences exhibited the maximum sequence similarity of 93.8 % with Owenweeksia hongkongensis DSM 17368T, followed by similarities of 90.4, 90.1 and 88.8 % with Phaeocystidibacter luteus MCCC 1F01079T, Vicingus serpentipes DSM 103558T and Salibacter halophilus MCCC 1K02288T, respectively. Its complete genome size was 4 035 598 bp, the genomic DNA G+C content was 43.2 mol%. Whole genome comparisons indicated that A20-9T and O. hongkongensis DSM 17368T shared 67.8 % average nucleotide identity, 62.7 % average amino acid identity value, 46.6% of conserved proteins and 17.8 % digital DNA–DNA hybridization identity. A20-9T contained MK-7 as the major respiratory quinone. Its major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phospatidylcholine; and the major fatty acids were iso-C15 : 0 (37.5 %), iso-C16 : 0 3-OH (12.4 %), and summed feature 3 (C16 : 1ω7c /C16 : 1ω6c, 11.6 %). Combining the genotypic and phenotypic data, A20-9T could be distinguished from the members of other genera within the family Schleiferiaceae and represents a novel genus, for which the name Croceimicrobium hydrocarbonivorans gen. nov., sp. nov. is proposed. The type strain is A20-9T (=MCCC 1A17358T =KCTC 72878T).

Luteimonas deserti sp. nov., a novel strain isolated from desert soil

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Xiao-Xian Huang ◽  
Jia Shang ◽  
Lian Xu ◽  
Rui Yang ◽  
Ji-Quan Sun
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Desert Soil ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, named SJ-16T, was isolated from desert soil collected in Inner Mongolia, northern PR China. Strain SJ-16T grew at pH 6.0–11.0 (optimum, pH 8.0–9.0), 4–40 °C (optimum, 30–35 °C) and in the presence of 0–8 % (w/v) NaCl (optimum, 0–2 %). The strain was negative for catalase and positive for oxidase. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SJ-16T clustered with Luteimonas chenhongjianii 100111T and Luteimonas terrae THG-MD21T, and had 98.8, 98.6, 98.3 and <97.9 % of 16S rRNA gene sequence similarity to strains L. chenhongjianii 100111T, L. terrae THG-MD21T, L. aestuarii B9T and all other type strains of the genus Luteimonas , respectively. The major cellular fatty acids were iso-C15 : 0, iso-C16 : 0, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1  ω9c). Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids, and ubiquinone-8 was the only respiratory quinone. The genomic DNA G+C content was 69.3 mol%. The digital DNA–DNA hybridization and average nucleotide identity values of strain SJ-16T to L. chenhongjianii 100111T, L. terrae THG-MD21T, L. rhizosphaerae 4-12T and L. aestuarii B9T were 36.9, 37.5, 24.0 and 21.1 %, and 80.9, 80.6, 80.7 and 76.3 %, respectively. Based on phenotypic, physiological and phylogenetic results, strain SJ-16T represents a novel species of the genus Luteimonas , for which the name Luteimonas deserti is proposed. The type strain is SJ-16T (=CGMCC 1.17694T=KCTC 82207T).

Dokdonella immobilis sp. nov., isolated from a batch reactor for the treatment of triphenylmethane dye effluent

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1557-1561 ◽  
Author(s):  
Ying Liu ◽  
Jing-Hua Jin ◽  
Hong-Can Liu ◽  
Zhi-Pei Liu
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Batch Reactor ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Triphenylmethane Dye ◽  
Content Type ◽  
Link Type ◽  
Gram Staining

A Gram-staining-negative, non-endospore-forming, non-flagellated, non-motile and rod-shaped bacterium, designated strain LM2-5T, was isolated from activated sludge in a sequencing batch reactor used for the treatment of triphenylmethane dye effluent. The taxonomy of strain LM2-5T was studied by phenotypic, chemotaxonomic and phylogenetic methods. Strain LM2-5T was aerobic, heterotrophic and positive for oxidase but negative for catalase activity. It grew at 16–37 °C (optimum 25 °C) and at pH 5.0–8.5 (optimum between pH 6.5 and pH 7.0). NaCl was not obligatory for growth but was tolerated at concentrations up to 2.0 % (w/v) NaCl. The novel strain formed yellow colonies on trypticase soy agar. Cells of strain LM2-5T were rods that measured 0.3–0.5 µm in width and 3.0–5.0 µm in length. The predominant respiratory quinone was Q-8. The major fatty acids were iso-C15 : 0 and iso-C17 : 1ω9c. The genomic DNA G+C content was 66.7 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, strain LM2-5T clustered with members of the genus Dokdonella and appeared most closely related to Dokdonella koreensis DS-123T (96.4 % sequence similarity), Dokdonella fugitiva A3T (96.1 %), Dokdonella soli KIS28-6T (95.7 %) and Dokdonella ginsengisoli Gsoil 191T (95.7 %). On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain LM2-5T was considered to represent a novel species of the genus Dokdonella , for which the name Dokdonella immobilis is proposed. The type strain is LM2-5T ( = CGMCC 1.7659T  = JCM 15763T).

Pseudooceanicola endophyticus sp. nov., a novel endophytic bacterium isolated from bark Aegiceras corniculatum

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Zhou-Qing Zheng ◽  
Ming-Sheng Chen ◽  
Xiao-Rui Yan ◽  
Li Tuo
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Aegiceras Corniculatum ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, aerobic, short-rod-shaped bacterium, designated strain CBS1P-1T, was isolated from a surface-sterilized bark of Aegiceras corniculatum. Growth of strain CBS1P-1T was observed with between 0 and 12.0 % (w/v) NaCl (optimally with 5.0 %) and at between pH 6.0–9.0. It grew at temperatures between 25–37 °C (optimum, 30 °C). Chemotaxonomic analysis showed that ubiquinone-10 was the respiratory quinone. The lipids comprised diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid, an unidentified phospholipid and an unidentified aminolipid. The major fatty acids of strain CBS1P-1T were C18 : 1  ω7c, C16 : 0 and C19 : 0 cyclo ω8c. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CBS1P-1T was most related to Pseudooceanicola antarcticus CGMCC 1.12662T with a sequence similarity of 96.5 %. The average nucleotide identity and digital DNA–DNA hybridization values between strain CBS1P-1T and P. antarcticus 1.12662T were 77.5 and 21.1 %, respectively. The G+C content of the genomic DNA was 67.3 mol%. Based on phylogenetic, chemotaxonomic and phenotypic data, strain CBS1P-1T is considered to represent a novel species of the genus Pseudooceanicola , for which the name Pseudooceanicola endophyticus is proposed. The type strain is CBS1P-1T (=KCTC 62836T=CGMCC 1.13743T).

Roseivivax isoporae sp. nov., isolated from a reef-building coral, and emended description of the genus Roseivivax

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1259-1264 ◽  
Author(s):  
Ming-Hui Chen ◽  
Shih-Yi Sheu ◽  
Chaolun Allen Chen ◽  
Jih-Terng Wang ◽  
Wen-Ming Chen
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

A bacterial strain, isolated from a sample of reef-building coral (Isopora palifera) collected off the coast of southern Taiwan, was characterized using a polyphasic taxonomic approach. The strain, designated sw-2T, was Gram-staining-negative, aerobic, rod-shaped and motile, with subpolar flagella, and formed greyish pink colonies. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain sw-2T was most closely related to Roseivivax halodurans Och 239T (97.4 % sequence similarity) and Roseivivax halotolerans Och 210T (96.4 %). The novel strain did not require NaCl for growth and exhibited optimal growth at 35–40 °C, at pH 7.5–8.0 and with 3–7 % (w/v) NaCl. It produced bacteriochlorophyll a under aerobic conditions. Summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 63.7 %) predominated in the cellular fatty acid profile. The novel strain’s major respiratory quinone was ubiquinone Q-10 and its genomic DNA G+C content was 68.8 mol%. The polar lipid profile consisted of a mixture of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, sulfo-quinovosyl diacylglycerol and three uncharacterized phospholipids. The level of DNA–DNA relatedness between strain sw-2T and Roseivivax halodurans Och 239T was only 15.0 %. The results of physiological and biochemical tests allowed the clear phenotypic differentiation of the novel strain from all established species of the genus Roseivivax . Based on the genotypic, phenotypic and chemotaxonomic data, strain sw-2T represents a novel species in the genus Roseivivax , for which the name Roseivivax isoporae sp. nov. is proposed. The type strain is sw-2T ( = LMG 25204T = BCRC 17966T).

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