scholarly journals Idiomarina aquimaris sp. nov., isolated from the reef-building coral Isopora palifera

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1536-1542 ◽  
Author(s):  
Ming-Hui Chen ◽  
Shih-Yi Sheu ◽  
Chaolun Allen Chen ◽  
Jih-Terng Wang ◽  
Wen-Ming Chen
Keyword(s):  
Type Species ◽  
Ph Value ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type ◽  
Isopora Palifera

A bacterial strain designated SW15T was isolated from a sample of the reef-building coral Isopora palifera, collected in southern Taiwan. The novel strain was characterized using a polyphasic taxonomic approach. Cells of strain SW15T were Gram-negative, aerobic, light yellow, rod-shaped and motile by means of a single polar flagellum. In phylogenetic analyses based on 16S rRNA gene sequences, strain SW15T appeared to belong to the genus Idiomarina in the class Gammaproteobacteria and to be most closely related to Idiomarina homiensis PO-M2T (97.6 % sequence similarity). Strain SW15T exhibited optimal growth between 20 and 30 °C, with NaCl between 3 % and 4 % (w/v) and at a pH value between 7 and 8. Predominant cellular fatty acids were iso-C15 : 0 (31.1 %), iso-C17 : 0 (15.4 %), iso-C17 : 1ω9c (10.0 %) and C16 : 0 (8.8 %). The major respiratory quinone was ubiquinone Q-8. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylserine, an uncharacterized aminolipid and several uncharacterized phospholipids. The DNA G+C content was 51.1 mol%. The level of DNA–DNA relatedness between strain SW15T and Idiomarina homiensis PO-M2T was 42.6–56.5 %. The results of physiological and biochemical tests allowed the clear phenotypic differentiation of the novel strain from established species of the genus Idiomarina . Based on the genotypic, phenotypic and chemotaxonomic data, strain SW15T represents a novel species in the genus Idiomarina , for which the name Idiomarina aquimaris sp. nov. is proposed, with SW15T ( = LMG 25374T = BCRC 80083T) as the type strain.

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).

Pedobacter ginsenosidimutans sp. nov., with ginsenoside-converting activity

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4396-4401 ◽  
Author(s):  
Jung-Eun Yang ◽  
Heung-Min Son ◽  
Jung Min Lee ◽  
Heon-Sub Shin ◽  
Sang-Yong Park ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Biochemical Tests ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
The Republic

A Gram-reaction-negative, strictly aerobic, non-motile, non-spore-forming and rod-shaped bacterial strain, designated THG-45T, was isolated from soil of a ginseng field of Pocheon province in the Republic of Korea and its taxonomic position was investigated by a polyphasic approach. Growth occurred at 4–30 °C, at pH 5.5–9.0 and with 0–2 % (w/v) NaCl on nutrient agar. On the basis of 16S rRNA gene sequence similarity, strain THG-45T was shown to belong to the genus Pedobacter and was related to Pedobacter borealis G-1T (98.8 %), P. alluvionis NWER-II11T (97.9 %), P. agri PB92T (97.9 %), P. terrae DS-57T (97.5 %), P. suwonensis 15-52T (97.4 %), P. sandarakinus DS-27T (97.0 %) and P. soli 15-51T (97.0 %), but DNA relatedness between strain THG-45T and these strains was below 36 %. The G+C content of the genomic DNA was 39 mol%. The only isoprenoid quinone detected in strain THG-45T was menaquinone-7 (MK-7). The predominant fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c) and iso-C17 : 0 3-OH, and the major polar lipids were phosphatidylethanolamine and an unidentified aminophosphoglycolipid. Phenotypic data and phylogenetic inference supported the affiliation of strain THG-45T to the genus Pedobacter , and a number of biochemical tests differentiated strain THG-45T from the recognized species of the genus Pedobacter . Therefore, the novel isolate represents a novel species, for which the name Pedobacter ginsenosidimutans sp. nov. is proposed, with THG-45T as the type strain ( = KACC 14530T = JCM 16721T).

Amycolatopsis dongchuanensis sp. nov., an actinobacterium isolated from soil

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2650-2656 ◽  
Author(s):  
Guo-Xing Nie ◽  
Hong Ming ◽  
Shuai Li ◽  
En-Min Zhou ◽  
Juan Cheng ◽  
...  
Keyword(s):  
Cell Wall ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Western China ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type

A novel actinomycete strain, designated YIM 75904T, was isolated from a soil sample that had been collected from a dry and hot river valley in Dongchuan county, Yunnan province, south-western China. The taxonomic position of the novel strain was investigated by a polyphasic approach. In phylogenetic analyses based on 16S rRNA gene sequences, strain YIM 75904T formed a distinct clade within the genus Amycolatopsis and appeared to be closely related to Amycolatopsis sacchari K24T (99.3 % sequence similarity). Strain YIM 75904T had a type-IV cell wall, with no detectable mycolic acids, and had MK-9(H4) as its predominant menaquonine. Its cell wall contained meso-diaminopimelic acid, galactose, glucose and arabinose, and its major cellular fatty acids were iso-C16 : 0, iso-C15 : 0, anteiso-C17 : 0 and anteiso-C15 : 0. The genomic DNA G+C content of the novel strain was 68.5 mol%. Based on the results of physiological and biochemical tests and DNA–DNA hybridizations, strain YIM 75904T represents a novel species of the genus Amycolatopsis for which the name Amycolatopsis dongchuanensis sp. nov. is proposed. The type strain is YIM 75904T ( = CCTCC AA 2011016T  = JCM 18054T).

Parabacteroides chinchillae sp. nov., isolated from chinchilla (Chincilla lanigera) faeces

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3470-3474 ◽  
Author(s):  
Maki Kitahara ◽  
Mitsuo Sakamoto ◽  
Sayaka Tsuchida ◽  
Koh Kawasumi ◽  
Hiromi Amao ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Distinct Line

Strains of Gram-stain-negative, anaerobic, rod-shaped bacteria were isolated from chinchilla (Chinchilla lanigera) faeces, and strain ST166T was investigated taxonomically. Phylogenetic analyses of 16S rRNA gene sequences revealed that strain ST166T belonged to the genus Parabacteroides . Strain ST166T formed a distinct line of descent, and the highest sequence similarity to ST166T was found with Parabacteroides merdae JCM 9497T (95.6 %) and Parabacteroides johnsonii JCM 13406T (95.0 %). Analysis of hsp60 gene sequences also supported these relationships. Based on the phenotypic and phylogenetic characteristics, the novel species Parabacteroides chinchillae sp. nov. is proposed. The type strain of P. chinchillae sp. nov. is ST166T ( = JCM 17104T = CCUG 62154T).

Deinococcus humi sp. nov., isolated from soil

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2844-2850 ◽  
Author(s):  
Sathiyaraj Srinivasan ◽  
Jae-Jin Lee ◽  
Sangyong Lim ◽  
Minho Joe ◽  
Myung Kyum Kim
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
Gram Staining

A Gram-staining-positive, strictly aerobic, spherical, non-motile, red-pigmented bacterium, designated strain MK03T, was isolated from a soil sample collected in South Korea. The taxonomic position of the novel strain was investigated using a polyphasic approach. In phylogenetic analyses based on 16S rRNA gene sequences, strain MK03T was placed in a clade formed by members of the genus Deinococcus in the family Deinococcaceae and appeared to be most closely related to Deinococcus aerolatus 5516T-9T (97.4 % sequence similarity), Deinococcus marmoris AA-63T (97.2 %), Deinococcus radiopugnans ATCC 19172T (97.2 %) and Deinococcus saxicola AA-1444T (96.9 %). The genomic DNA G+C content of the novel strain was 64.5 mol%. The chemotaxonomic characteristics of strain MK03T were typical of members of the genus Deinococcus : MK-8 was identified as the predominant respiratory quinine, the major fatty acids were C16 : 1ω7c, C15 : 1ω6c, C16 : 0 and C15 : 0, ornithine was found to be the diamino acid in the cell-wall peptidoglycan and the novel strain showed resistance to gamma radiation, with a D10 value (i.e. the dose required to reduce the bacterial population by 10-fold) in excess of 9 kGy. In hybridization experiments, only low DNA–DNA relatedness values (11.6–34.5 %) were recorded between the novel strain and its closest relatives in the genus Deinococcus . Based on the phylogenetic, chemotaxonomic, phenotypic and DNA–DNA relatedness data, strain MK03T represents a novel species of the genus Deinococcus , for which the name Deinococcus humi sp. nov. is proposed. The type strain is MK03T ( = KCTC 13619T  = JCM 17915T).

Erythrobacter jejuensis sp. nov., isolated from seawater

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1421-1426 ◽  
Author(s):  
Byoung-Jun Yoon ◽  
Dong-Heon Lee ◽  
Duck-Chul Oh
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gram Staining

A Gram-staining-negative, yellow-pigmented, non-motile, strictly aerobic, rod-shaped bacterium, designated strain CNU001T, was isolated from seawater collected on the coast of Jeju Island, South Korea, and subjected to a polyphasic taxonomic study. The temperature, pH and NaCl ranges for growth were 10–30 °C, pH 6.0–10.0 and 2.0–5.0 %, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CNU001T belonged to the genus Erythrobacter in the family Erythrobacteraceae , with Erythrobacter longus DSM 6997T (96.6 % sequence similarity), Erythrobacter gaetbuli SW-161T (96.3 %), Erythrobacter vulgaris 022 2-10T (96.2 %), Erythrobacter nanhaisediminis T30T (96.1 %) and other members of the genus Erythrobacter (<96.0 %) identified as the novel strain’s closest relatives. The major cellular fatty acids were C18 : 1ω7c and C17 : 1ω6c. The polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, one sphingoglycolipid, one unidentified aminolipid and six other unidentified lipids. The major respiratory quinone was ubiquinone-10 (UQ-10) and the genomic DNA G+C content of the novel strain was 58.9 mol%. On the basis of phenotypic, phylogenetic and genotypic data, strain CNU001T represents a novel species within the genus Erythrobacter , for which the name Erythrobacter jejuensis sp. nov. is proposed. The type strain is CNU001T ( = KCTC 23090T  = JCM 16677T).

scholarly journals Streptococcus cuniculi sp. nov., isolated from the respiratory tract of wild rabbits

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2486-2490 ◽  
Author(s):  
A. I. Vela ◽  
V. Sánchez del Rey ◽  
L. Zamora ◽  
A. Casamayor ◽  
L. Domínguez ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type

Biochemical and molecular genetic studies were performed on four unknown Gram-stain-positive, catalase-negative, coccus-shaped organisms isolated from tonsils (n = 3) and nasal samples (n = 1) of four wild rabbits. The micro-organism was identified as a streptococcal species based on its cellular morphological and biochemical tests. Comparative 16S rRNA gene sequencing confirmed its identification as a member of the genus Streptococcus , but the organism did not correspond to any recognized species of this genus. The closest phylogenetic relative of the unknown cocci from wild rabbits was Streptococcus acidominimus NCIMB 702025T (97.9 % 16S rRNA gene sequence similarity). rpoB and sodA sequence analysis of the novel isolate showed interspecies divergence of 16.2 % and 20.3 %, respectively, from the type strain of its closest 16S rRNA gene phylogenetic relative, S. acidominimus . The novel bacterial isolate could be distinguished from the type strain of S. acidominimus by several biochemical characteristics, such as the production of esterase C4, acid phosphatase and naphthol-AS-BI-phosphohydrolase and acidification of different sugars. Based on both phenotypic and phylogenetic findings, it is proposed that the unknown bacterium be classified as a novel species of the genus Streptococcus , Streptococcus cuniculi sp. nov. The type strain is NED12-00049-6BT ( = CECT 8498T = CCUG 65085T).

Gemmobacter tilapiae sp. nov., a poly-β-hydroxybutyrate-accumulating bacterium isolated from a freshwater pond

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1550-1556 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Der-Shyan Sheu ◽  
Fu-Sian Sheu ◽  
Wen-Ming Chen
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Cichlid Fish ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Freshwater Pond

A novel bacterium, designated strain Ruye-53T, was isolated from a freshwater pond used to rear tilapiine cichlid fish in Taiwan. The taxonomic position of the novel strain was determined using a polyphasic approach. Strain Ruye-53T was Gram-reaction-negative, aerobic, cream–white coloured, rod-shaped, non-motile and poly-β-hydroxybutyrate-accumulating. Growth occurred at 10–37 °C (optimum between 20 and 25 °C), at pH 6.0–9.0 (optimum between pH 8.0 and pH 9.0) and with 0–1 % (w/v) NaCl (optimum 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Ruye-53T belonged to the genus Gemmobacter and that its most closely related neighbour was Gemmobacter aquatilis DSM 3857T (97.6 % sequence similarity). The novel strain’s predominant fatty acid was C18 : 1ω7c, its major respiratory quinone was Q-10 and its genomic DNA G+C content was 61.2 mol%. The polar lipid profile consisted of a mixture of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one uncharacterized aminolipid and four uncharacterized phospholipids. The DNA–DNA relatedness value between strain Ruye-53T and Gemmobacter aquatilis DSM 3857T was about 45.5 % (48.2±0.4 % in the reciprocal experiment). On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Ruye-53T represents a novel species in the genus Gemmobacter , for which the name Gemmobacter tilapiae sp. nov. is proposed. The type strain is Ruye-53T ( = BCRC 80261T  = KCTC 23310T).

scholarly journals Tropicibacter multivorans sp. nov., an aerobic alphaproteobacterium isolated from surface seawater

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 844-848 ◽  
Author(s):  
Teresa Lucena ◽  
María J. Pujalte ◽  
María A. Ruvira ◽  
Esperanza Garay ◽  
M. Carmen Macián ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Carbon Sources ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
The Family

Strain MD5T, an aerobic marine alphaproteobacterium, was isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. The strain was characterized in a polyphasic study and was placed phylogenetically within the Roseobacter clade in the family Rhodobacteraceae . Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MD5T is related to Tropicibacter naphthalenivorans C02T, Phaeobacter inhibens T5T, P. gallaeciensis BS107T and P. daeponensis TF-218T, with 96.9, 96.2, 96.1 and 96.1 % sequence similarity, respectively. Phylogenetic analyses also showed that strain MD5T forms a stable clade only with T. naphthalenivorans C02T. Strain MD5T requires Na+ plus a divalent cation (either Mg2+ or Ca2+) to grow, does not reduce nitrate to nitrite and uses a large number of carbohydrates as sole carbon sources. It is positive for β-galactosidase and urease activities and aesculin hydrolysis. Enzyme activities displayed in the API ZYM strip were alkaline phosphatase, leucine arylamidase, acid phosphatase and α-glucosidase. Major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 70.9 %) and C16 : 0 (8.2 %). The results of physiological and biochemical tests allowed clear phenotypic differentiation of this isolate from the only described species of the genus Tropicibacter . It is evident from the genotypic and phenotypic data obtained that the strain should be classified in a novel species in the genus Tropicibacter . The name Tropicibacter multivorans sp. nov. is proposed, with the type strain MD5T ( = CECT 7557T  = KCTC 23350T).

Bacteroides reticulotermitis sp. nov., isolated from the gut of a subterranean termite (Reticulitermes speratus)

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 691-695 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Moriya Ohkuma
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Subterranean Termite ◽  
Rrna Gene ◽  
The Novel ◽  
Reticulitermes Speratus ◽  
Content Type ◽  
Link Type ◽  
Gram Staining

An obligately anaerobic, non-pigmented, non-spore-forming, Gram-staining-negative, rod-shaped bacterium, designated strain Rs-03T, was isolated from the gut of the subterranean termite Reticulitermes speratus. The taxonomic position of the novel strain was determined by following a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Rs-03T was a member of the genus Bacteroides and was most closely related to Bacteroides thetaiotaomicron JCM 5827T (95.0 % sequence similarity), Bacteroides faecis JCM 16478T (94.8 %) and Bacteroides xylanisolvens JCM 15633T (94.3 %). The results of hsp60 gene sequence analysis indicated that the novel strain was different from established members of the genus Bacteroides . Strain Rs-03T was saccharolytic and produced succinic and acetic acids, with small amounts of propionic acid, as metabolic end products. The major cellular fatty acids of strain Rs-03T were anteiso-C15 : 0, C18 : 1ω9c and iso-C17 : 0 3-OH. The major menaquinones were MK-10 and MK-9 and the genomic DNA G+C content was 44.9 mol%. Based on these data, strain Rs-03T represents a novel species in the genus Bacteroides , for which the name Bacteroides reticulotermitis sp. nov. is proposed. The type strain is Rs-03T ( = JCM 10512T = CCUG 62153T).

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