scholarly journals Thermomonas koreensis sp. nov., a mesophilic bacterium isolated from a ginseng field

2006 ◽  
Vol 56 (7) ◽  
pp. 1615-1619 ◽  
Author(s):  
Myung Kyum Kim ◽  
Wan-Taek Im ◽  
Jun-Gyo In ◽  
Sung-Hoon Kim ◽  
Deok-Chun Yang
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Distinct Species ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Gene Sequence Analysis ◽  
Mesophilic Bacterium ◽  
Bacterium Strain ◽  
Physiological And Biochemical

A Gram-negative, non-spore-forming, rod-shaped, motile bacterium, strain Ko06T, was isolated from soil from a ginseng field in South Korea and was characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain Ko06T belongs to the Gammaproteobacteria, and the highest levels of sequence similarity were with Thermomonas brevis LMG 21746T (98.4 %), Thermomonas fusca LMG 21737T (97.7 %), Thermomonas haemolytica A50-7-3T (96.5 %) and Thermomonas hydrothermalis SGM-6T (95.8 %). Chemotaxonomic data revealed that strain Ko06T possesses ubiquinone Q-8 and that the predominant fatty acids are C15 : 0 iso, C11 : 0 iso and C11 : 0 iso 3-OH, all of which corroborated assignment of the strain to the genus Thermomonas. The results of DNA–DNA hybridization and physiological and biochemical tests clearly demonstrated that strain Ko06T represents a distinct species. On the basis of these data, strain Ko06T (=KCTC 12540T=NBRC 101155T) should be classified as the type strain of a novel Thermomonas species, for which the name Thermomonas koreensis sp. nov. is proposed.

scholarly journals Sphingomonas soli sp. nov., a β-glucosidase-producing bacterium in the family Sphingomonadaceae in the α-4 subgroup of the Proteobacteria

2006 ◽  
Vol 56 (4) ◽  
pp. 703-707 ◽  
Author(s):  
Deok-Chun Yang ◽  
Wan-Taek Im ◽  
Myung Kyum Kim ◽  
Hiroyuki Ohta ◽  
Sung-Taik Lee
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Distinct Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Physiological And Biochemical

Strain T5-04T, a Gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from soil of a ginseng field in South Korea and characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain T5-04T belongs to the α-4 subgroup of the Proteobacteria, and the highest degrees of sequence similarity determined were to Sphingomonas asaccharolytica IFO 10564T (97·5 %), Sphingomonas koreensis JSS26T (97·1 %), Sphingomonas mali IFO 15500T (96·7 %) and Sphingomonas pruni IFO 15498T (96·6 %). Chemotaxonomic data revealed that strain T5-04T possesses ubiquinone Q-10 predominantly, C18 : 1 as the predominant fatty acid and sphingoglycolipids, all of which corroborate its assignment to the genus Sphingomonas. The results of DNA–DNA hybridization and physiological and biochemical tests clearly demonstrated that strain T5-04T represents a distinct species. Based on polyphasic evidence, T5-04T (=KCTC 12210T=NBRC 100801T=IAM 15213T) should be classified as the type strain of a novel Sphingomonas species, for which the name Sphingomonas soli sp. nov. is proposed.

scholarly journals Parapedobacter koreensis gen. nov., sp. nov.

2007 ◽  
Vol 57 (6) ◽  
pp. 1336-1341 ◽  
Author(s):  
Myung Kyum Kim ◽  
Ju-Ryun Na ◽  
Dong Ha Cho ◽  
Nak-Kyun Soung ◽  
Deok-Chun Yang
Keyword(s):  
Gene Sequence ◽  
Sequence Similarity ◽  
Distinct Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Novel Genus And Species ◽  
Physiological And Biochemical

Strain Jip14T, a Gram-negative, non-spore-forming, rod-shaped, non-motile bacterium, was isolated from dried rice straw and characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain Jip14T belongs to the family Sphingobacteriaceae, and the highest degree of sequence similarity was determined to be to Pedobacter saltans DSM 12145T (88.5 %), Pedobacter africanus DSM 12126T (87.6 %), Pedobacter heparinus DSM 2366T (87.1 %) and Pedobacter caeni LMG 22862T (86.9 %). Chemotaxonomic data revealed that strain Jip14T possesses menaquinone MK-7 and the predominant fatty acids C15 : 0 iso, C16 : 0, C16 : 0 10-methyl, C17 : 0 iso 3-OH and summed feature 3 (C15 : 0 iso 2-OH/C16 : 1 ω7c). The results of physiological and biochemical tests clearly demonstrated that strain Jip14T represents a distinct species. Based on these data, Jip14T should be classified within a novel genus and species, for which the name Parapedobacter koreensis gen. nov., sp. nov. is proposed. The type strain of Parapedobacter koreensis is Jip14T (=KCTC 12643T=LMG 23493T).

scholarly journals Herminiimonas saxobsidens sp. nov., isolated from a lichen-colonized rock

2007 ◽  
Vol 57 (11) ◽  
pp. 2618-2622 ◽  
Author(s):  
Elke Lang ◽  
Jolantha Swiderski ◽  
Erko Stackebrandt ◽  
P. Schumann ◽  
Cathrin Spröer ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rock Surface ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
Bacterium Strain ◽  
Physiological And Biochemical

A Gram-negative, rod-shaped, non-spore-forming bacterium (strain NS11T) was isolated from a lichen-colonized rock surface. On the basis of 16S rRNA gene sequence similarity, strain NS11T was shown to belong to the Betaproteobacteria, and was most closely related to Herminiimonas arsenicoxydans ULPAs1T (98.8 %), Herminiimonas aquatilis CCUG 36956T (98.0 %) and Herminiimonas fonticola S-94T (98.0 %). Major whole-cell fatty acids were C16 : 0, C17 : 0 cyclo and C16 : 1 ω7c. Strain NS11T also contained high proportions of C10 : 0 3-OH and C18 : 1 ω7c. This pattern is typical for members of the genus Herminiimonas. The results of DNA–DNA hybridization experiments and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain NS11T from the three recognized Herminiimonas species. It is therefore concluded that strain NS11T represents a novel species of the genus Herminiimonas, for which the name Herminiimonas saxobsidens sp. nov. is proposed. The type strain is NS11T (=DSM 18748T=CCM 7436T).

scholarly journals Devosia soli sp. nov., isolated from greenhouse soil in Korea

2006 ◽  
Vol 56 (11) ◽  
pp. 2689-2692 ◽  
Author(s):  
Seung-Hee Yoo ◽  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Seung-Beom Hong ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Greenhouse Soil ◽  
Gene Sequence Analysis ◽  
Physiological And Biochemical ◽  
Sequence Similarities

A Gram-negative, obligately aerobic, rod-shaped bacterium was isolated from greenhouse soil used to cultivate lettuce. The strain, GH2-10T, was characterized on the basis of phenotypic and genotypic data. 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Devosia, with highest sequence similarity (98.5 %) to Devosia riboflavina IFO 13584T. Sequence similarities with other strains tested were below 97.0 %. Strain GH2-10T had Q-10 as the predominant ubiquinone and C18 : 1 ω7c and C16 : 0 as the major fatty acids. The G+C content of the genomic DNA was 59.5 mol%. The results of DNA–DNA hybridization experiments (47 % relatedness between D. riboflavina DSM 7230T and strain GH2-10T) and physiological and biochemical tests suggested that strain GH2-10T represents a novel species of the genus Devosia, for which the name Devosia soli sp. nov. is proposed. The type strain is GH2-10T (=KACC 11509T=DSM 17780T).

Blastochloris gulmargensis sp. nov., isolated from an epilithic phototrophic biofilm

2011 ◽  
Vol 61 (8) ◽  
pp. 1811-1816 ◽  
Author(s):  
V. Venkata Ramana ◽  
Shivali Kapoor ◽  
E. Shobha ◽  
E. V. V. Ramprasad ◽  
Ch. Sasikala ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phototrophic Biofilm ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Blastochloris Viridis

A novel Gram-negative, motile, bacteriochlorophyll b-containing purple non-sulfur bacterium, strain JA248T, was isolated from phototrophic enrichments of a yellow–green epilithic biofilm sample collected from Gulmarg, India. The genomic DNA G+C content of strain JA248T was 63.8 mol%. A phylogenetic tree based on 16S rRNA gene sequence analysis showed that strain JA248T had highest similarity to members of the genus Blastochloris and was closely related to Blastochloris sulfoviridis DSM 729T (98.5 % sequence similarity) and Blastochloris viridis DSM 133T (98.4 %) of the class Alphaproteobacteria. Strain JA248T was characterized based on polyphasic taxonomy, and distinct phenotypic and molecular differences based on DNA–DNA hybridization (relatedness of <46.5 % with the two species of the genus Blastochloris), multilocus sequence analysis, and phenotypic and chemotaxonomic evidence separated strain JA248T from other species of the genus Blastochloris. Strain JA248T therefore represents a novel species in the genus Blastochloris, for which the name Blastochloris gulmargensis sp. nov. is proposed. The type strain is JA248T ( = JCM 14795T  = DSM 19786T).

scholarly journals Halorubrum tibetense sp. nov., a novel haloalkaliphilic archaeon from Lake Zabuye in Tibet, China

2004 ◽  
Vol 54 (4) ◽  
pp. 1213-1216 ◽  
Author(s):  
Huapeng Fan ◽  
Yanfen Xue ◽  
Yanhe Ma ◽  
Antonio Ventosa ◽  
William D. Grant
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Tibetan Plateau ◽  
Phylogenetic Distance ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
Gene Sequence Analysis ◽  
Derivatives Of ◽  
Physiological And Biochemical

A novel haloalkaliphilic archaeon, strain 8W8T, was isolated from Lake Zabuye, on the Tibetan Plateau, China. On the basis of 16S rRNA gene sequence analysis, strain 8W8T was shown to belong to the genus Halorubrum and was related to Halorubrum vacuolatum (96·7 % sequence similarity), Halorubrum saccharovorum (96·0 %), Halorubrum lacusprofundi (95·4 %) and Halorubrum sodomense (95·3 %). The phylogenetic distance from any species within the other genera of Halobacteriales was lower than 90 %. The major polar lipids of strain 8W8T were C20C20 and C20C25 derivatives of phosphatidylglycerol phosphate and phosphatidylglycerol phosphate methyl ester. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 8W8T from the eight Halorubrum species with validly published names. Therefore, strain 8W8T represents a novel species, for which the name Halorubrum tibetense sp. nov. is proposed, with the type strain 8W8T (=AS 1.3239T=JCM 11889T).

scholarly journals Sphingopyxis panaciterrulae sp. nov., isolated from soil of a ginseng field

2010 ◽  
Vol 60 (10) ◽  
pp. 2358-2363 ◽  
Author(s):  
Sathiyaraj Srinivasan ◽  
Myung Kyum Kim ◽  
Gayathri Sathiyaraj ◽  
Vaidyanathan Veena ◽  
Muthusamy Mahalakshmi ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Separate Species ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Physiological And Biochemical

A Gram-negative, rod-shaped, motile bacterium was isolated from the soil of a ginseng field in Daejeon, South Korea, and characterized in order to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequence analysis revealed that strain DCY34T belonged to the family Sphingomonadaceae, and the highest degree of sequence similarity was found with Sphingopyxis witflariensis W-50T (97.1 %), Sphingopyxis ginsengisoli Gsoil 250T (97.0 %), Sphingopyxis chilensis S37T (96.9 %), Sphingopyxis macrogoltabida IFO 15033T (96.8 %), Sphingopyxis alaskensis RB2256T (96.7 %) and Sphingopyxis taejonensis JSS54T (96.7 %). Chemotaxonomic data revealed that strain DCY34T possessed ubiquinone Q-10 as the predominant respiratory lipoquinone, which is common to members of the genus Sphingopyxis. The predominant fatty acids were C18 : 1 ω7c (27.5 %), summed feature 4 (C16 : 1 ω7c and/or C15 : 0 iso 2-OH; 18.6 %), C16 : 0 (15.6 %) and summed feature 8 (C19 : 1 ω6c and/or unknown 18.864; 15.4 %). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid and an unknown polar lipid. The results of physiological and biochemical tests clearly demonstrated that strain DCY34T represented a separate species and supported its affiliation to the genus Sphingopyxis. Based on these data, the new isolate represents a novel species, for which the name Sphingopyxis panaciterrulae sp. nov. is proposed. The type strain is DCY34T (=KCTC 22112T=JCM 14844T).

scholarly journals Devosia limi sp. nov., isolated from a nitrifying inoculum

2005 ◽  
Vol 55 (5) ◽  
pp. 1997-2000 ◽  
Author(s):  
Bram Vanparys ◽  
Kim Heylen ◽  
Liesbeth Lebbe ◽  
Paul De Vos
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
Sds Page ◽  
Spore Forming Bacteria ◽  
Physiological And Biochemical

A Gram-negative, rod-shaped, non-spore-forming bacteria was isolated from a nitrifying inoculum. On the basis of 16S rRNA gene sequence similarity, this strain, designated LMG 22951T, was shown to belong to the ‘Alphaproteobacteria’ and to be related to Devosia neptuniae (97·4 %) and Devosia riboflavina (97·0 %). The results of DNA–DNA hybridization, analysis of fatty acid composition, SDS-PAGE, physiological and biochemical tests allowed genotypic and phenotypic differentiation of LMG 22951T from the two recognized Devosia species. LMG 22951T therefore represents a novel species within this genus, for which the name Devosia limi is proposed. The type strain is LMG 22951T (=DSM 17137T).

scholarly journals Stenotrophomonas ginsengisoli sp. nov., isolated from a ginseng field

2010 ◽  
Vol 60 (7) ◽  
pp. 1522-1526 ◽  
Author(s):  
Ho-Bin Kim ◽  
Sathiyaraj Srinivasan ◽  
Gayathri Sathiyaraj ◽  
Lin-Hu Quan ◽  
Se-Hwa Kim ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Gene Sequence Analysis ◽  
Stenotrophomonas Nitritireducens ◽  
Physiological And Biochemical

A Gram-negative, non-spore-forming, rod-shaped bacterium, designated strain DCY01T, was isolated from soil from a ginseng field in South Korea and was characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain DCY01T belonged to the Gammaproteobacteria and was most closely related to Stenotrophomonas koreensis KCTC 12211T (98.4 % similarity), Stenotrophomonas humi R-32729T (97.2 %), Stenotrophomonas terrae R-32768 (97.1 %), Stenotrophomonas maltophilia DSM 50170T (96.9 %) and Stenotrophomonas nitritireducens DSM 12575T (96.8 %). Chemotaxonomic analyses revealed that strain DCY01T possessed a quinone system with Q-8 as the predominant compound, and iso-C15 : 0 (28.2 %), C16 : 0 10-methyl (13.2 %), iso-C15 : 1 F (10.8 %) and C15 : 0 (7.5 %) as major fatty acids, corroborating assignment of strain DCY01T to the genus Stenotrophomonas. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The results of DNA–DNA hybridization and physiological and biochemical tests clearly demonstrated that strain DCY01T represents a species distinct from recognized Stenotrophomonas species. Based on these data, DCY01T (=KCTC 12539T=NBRC 101154T) should be classified as the type strain of a novel species of the genus Stenotrophomonas, for which the name Stenotrophomonas ginsengisoli sp. nov. is proposed.

scholarly journals Brevundimonas vancanneytii sp. nov., isolated from blood of a patient with endocarditis

2010 ◽  
Vol 60 (9) ◽  
pp. 2129-2134 ◽  
Author(s):  
Andréia B. Estrela ◽  
Wolf-Rainer Abraham
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
Sulfoquinovosyl Diacylglycerol ◽  
Type Strains ◽  
Physiological And Biochemical

A Gram-negative, rod-shaped, non-spore-forming bacterial strain, designated LMG 2337T, was isolated from the blood of a patient with endocarditis and characterized. The strain was affiliated with the alphaproteobacterial genus Brevundimonas, with Brevundimonas diminuta LMG 2089T (98.3 % 16S rRNA gene sequence similarity) and Brevundimonas terrae KSL-145T (97.5 %) as its closest relatives. This affiliation was supported by chemotaxonomic data: the G+C content was 66.3 mol %, the major polar lipids were phosphatidyl diacylglycerol, sulfoquinovosyl diacylglycerol and phosphatidyl glucopyranosyl diacylglycerol and the major fatty acids were summed feature 7 (one or more of C18 : 1 ω7c, C18 : 1 ω9t and C18 : 1 ω12t) and C16 : 0. Strain LMG 2337T displayed an unusually broad substrate spectrum. The results from DNA–DNA hybridization and physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain LMG 2337T from all of the type strains of hitherto-described Brevundimonas species. The strain therefore represents a novel species, for which the name Brevundimonas vancanneytii sp. nov. is proposed, with type strain LMG 2337T (=CCUG 1797T =ATCC 14736T).

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