scholarly journals Paenibacillus massiliensis sp. nov., Paenibacillus sanguinis sp. nov. and Paenibacillus timonensis sp. nov., isolated from blood cultures

2004 ◽  
Vol 54 (4) ◽  
pp. 1049-1054 ◽  
Author(s):  
Véronique Roux ◽  
Didier Raoult
Keyword(s):  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
Blood Cultures ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Phenotypic Data ◽  
Type Strains

Gram-positive, spore-forming rods were isolated from blood cultures of three different patients. Based on phylogenetic analyses, these strains were placed within the Paenibacillus cluster and specific phenotypic characteristics for each strain were described. Levels of 16S rRNA gene sequence similarity between existing Paenibacillus species and the three novel strains 2301065T, 2301032T and 2301083T were 87·6–94·4, 88·5–95·4 and 87·5–96·0 %, respectively, and anteiso-branched C15 : 0 was the major fatty acid. On the basis of phenotypic data and phylogenetic inference, it is proposed that these strains should be designated Paenibacillus massiliensis sp. nov., Paenibacillus sanguinis sp. nov. and Paenibacillus timonensis sp. nov. The type strains are respectively strain 2301065T (=CIP 107939T=CCUG 48215T), strain 2301083T (=CIP 107938T=CCUG 48214T) and strain 2301032T (=CIP 108005T=CCUG 48216T).

scholarly journals Flavobacterium terrigena sp. nov., isolated from soil

2007 ◽  
Vol 57 (5) ◽  
pp. 947-950 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Jung-Sook Lee ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Type Strains

A Gram-negative, rod-shaped, Flavobacterium-like bacterial strain, DS-20T, was isolated from soil from the island of Dokdo, Korea, and subjected to a polyphasic taxonomic study. Strain DS-20T grew optimally at pH 6.5–7.0 and 25 °C. It contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1 ω9c as the major fatty acids. The DNA G+C content was 38.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-20T belonged to the genus Flavobacterium. Levels of 16S rRNA gene sequence similarity between strain DS-20T and the type strains of recognized Flavobacterium species were below 94.9 %. Strain DS-20T differed from phylogenetically related Flavobacterium species in several phenotypic characteristics. On the basis of its phenotypic and phylogenetic distinctiveness, strain DS-20T was classified in the genus Flavobacterium as representing a novel species, for which the name Flavobacterium terrigena sp. nov. is proposed. The type strain is DS-20T (=KCTC 12761T=DSM 17934T).

scholarly journals Paracoccus fistulariae sp. nov., a lipolytic bacterium isolated from bluespotted cornetfish, Fistularia commersonii

2010 ◽  
Vol 60 (12) ◽  
pp. 2908-2912 ◽  
Author(s):  
Young-Ok Kim ◽  
Hee Jeong Kong ◽  
Sooyeon Park ◽  
So-Jung Kang ◽  
Kyung-Kil Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Type Strains

A Gram-stain-negative, non-motile, non-spore-forming and short rod- or rod-shaped bacterial strain, designated 22-5T, was isolated from a bluespotted cornetfish, Fistularia commersonii, and subjected to taxonomic study. Strain 22-5T grew optimally at 30 °C and in the presence of 2–5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 22-5T belonged to the genus Paracoccus and joined the cluster comprising Paracoccus homiensis DD-R11T and Paracoccus zeaxanthinifaciens ATCC 21588T, with which strain 22-5T exhibited 97.4 and 96.9 % 16S rRNA gene sequence similarity, respectively. Strain 22-5T exhibited 94.0–96.6 % 16S rRNA gene sequence similarity with the other type strains of species of the genus Paracoccus. Strain 22-5T contained Q-10 as the predominant menaquinone and C18 : 1 ω7c as the predominant fatty acid. In this study, P. zeaxanthinifaciens KCTC 22688T also contained Q-10 as the predominant isoprenoid quinone. The DNA G+C content of strain 22-5T was 63.6 mol%. Strain 22-5T exhibited 44 and 32 % DNA–DNA relatedness to P. homiensis KACC 11518T and P. zeaxanthinifaciens KCTC 22688T, respectively. On the basis of phenotypic, phylogenetic and genetic data, strain 22-5T is considered to represent a novel species of the genus Paracoccus, for which the name Paracoccus fistulariae sp. nov. is proposed. The type strain is 22-5T (=KCTC 22803T =CCUG 58401T).

scholarly journals Pedobacter lentus sp. nov. and Pedobacter terricola sp. nov., isolated from soil

2007 ◽  
Vol 57 (9) ◽  
pp. 2089-2095 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Sooyeon Park ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Type Strains

Two Gram-negative, non-motile, pleomorphic bacterial strains, DS-40T and DS-45T, were isolated from a soil sample collected from Dokdo, Korea, and their exact taxonomic positions were investigated by using a polyphasic approach. Strains DS-40T and DS-45T grew optimally at 25 °C and pH 6.5–7.5 in the presence of 0–1.0 % (w/v) NaCl. They contained MK-7 as the predominant menaquinone and possessed iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids. The DNA G+C contents of strains DS-40T and DS-45T were 36.0 and 36.8 mol%, respectively. Strains DS-40T and DS-45T shared a 16S rRNA gene sequence similarity of 96.7 % and demonstrated a mean DNA–DNA relatedness level of 12 %. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains DS-40T and DS-45T were most closely phylogenetically affiliated with the genus Pedobacter of the family Sphingobacteriaceae. Strains DS-40T and DS-45T exhibited 16S rRNA gene sequence similarity values of 91.4–93.7 and 89.9–91.6 % with respect to the type strains of Pedobacter and Sphingobacterium species, respectively. Phenotypic and chemotaxonomic properties, together with the phylogenetic data, support the assignment of strains DS-40T and DS-45T as two distinct species within the genus Pedobacter. On the basis of phenotypic, phylogenetic and genetic data, strains DS-40T and DS-45T represent two novel species of the genus Pedobacter, for which the names Pedobacter lentus sp. nov. and Pedobacter terricola sp. nov. are proposed, respectively. The respective type strains are DS-40T (=KCTC 12875T=JCM 14593T) and DS-45T (=KCTC 12876T=JCM 14594T).

scholarly journals Dyadobacter hamtensis sp. nov., from Hamta glacier, located in the Himalayas, India

2005 ◽  
Vol 55 (5) ◽  
pp. 2113-2117 ◽  
Author(s):  
P. Chaturvedi ◽  
G. S. N. Reddy ◽  
S. Shivaji
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Mountain Ranges ◽  
Himalayan Mountain

Strain HHS 11T was isolated from a water sample collected from the snout of Hamta glacier located in the Himalayan mountain ranges of India. Phenotypic, chemotaxonomic and phylogenetic analyses established the affiliation of the isolate to the genus Dyadobacter. HHS 11T possessed 96 and 95 % 16S rRNA gene sequence similarity with respect to Dyadobacter crusticola and Dyadobacter fermentans, respectively. Furthermore, strain HHS 11T differs from D. crusticola and D. fermentans in a number of phenotypic characteristics. These data suggest that strain HHS 11T represents a novel species of the genus Dyadobacter, for which the name Dyadobacter hamtensis sp. nov. is proposed. The type strain is HHS 11T (=JCM 12919T=MTCC 7023T).

scholarly journals Brevundimonas lenta sp. nov., isolated from soil

2007 ◽  
Vol 57 (10) ◽  
pp. 2236-2240 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Jung-Sook Lee ◽  
Hyun Woo Oh ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Type Strains

A Gram-negative, rod-shaped, Brevundimonas-like bacterial strain, DS-18T, was isolated from soil in Dokdo, Korea, and its exact taxonomic position was investigated by using a polyphasic approach. Strain DS-18T grew optimally at pH 6.5–7.0 and 25 °C without NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-18T belonged to the genus Brevundimonas. Strain DS-18T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c and C16 : 0 as the major fatty acids. The DNA G+C content was 68.7 mol%. Strain DS-18T exhibited levels of 16S rRNA gene sequence similarity of 96.3–98.7 % to the type strains of Brevundimonas species and Mycoplana bullata. Mean DNA–DNA relatedness values between strain DS-18T and the type strains of phylogenetically related Brevundimonas species and M. bullata were in the range 15–32 %. Strain DS-18T differed from Brevundimonas species and M. bullata in several phenotypic characteristics. On the basis of phenotypic, phylogenetic and genetic data, strain DS-18T represents a novel species of the genus Brevundimonas, for which the name Brevundimonas lenta sp. nov. is proposed. The type strain is DS-18T (=KCTC 12871T =JCM 14602T).

scholarly journals Kineococcus gypseus sp. nov., isolated from saline sediment

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3703-3708 ◽  
Author(s):  
Qinyuan Li ◽  
Guiding Li ◽  
Xiu Chen ◽  
Fangji Xu ◽  
Yong Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data

A novel Gram-stain-positive, aerobic, motile, non-spore-forming coccus-shaped actinomycete, designated strain YIM 121300T, was isolated from alkaline sediment in Yuanjiang, Yunnan province, south-west China. Phylogenetic analyses based on the 16S rRNA gene sequence showed that strain YIM 121300T was affiliated to the genus Kineococcus, and was closely related to Kineococcus aurantiacus IFO 15268T (97.3 % similarity). 16S rRNA gene sequence similarity to other species of the genus Kineococcus was < 97 %. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid. The whole-cell sugars contained arabinose, galactose, glucose, mannose and ribose. The predominant menaquinone was MK-9(H2). Mycolic acids were not detected. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and an unknown phospholipid. The predominant fatty acids were anteiso-C15 : 0 and anteiso-C15 : 1 A. The G+C content of the genomic DNA was 75.1 mol%. DNA–DNA relatedness (55 ± 4 % to K. aurantiacus IFO 15268T) and differential phenotypic data demonstrated that strain YIM 121300T was distinguished from all related species of the genus Kineococcus. On the basis of data from the present polyphasic study, the organism should be assigned to a novel species of the genus Kineococcus, for which the name Kineococcus gypseus sp. nov. is proposed. The type strain is YIM 121300T ( = CCTCC AA 2013232T = DSM 27627T).

scholarly journals Nocardioides terrigena sp. nov., isolated from soil

2007 ◽  
Vol 57 (11) ◽  
pp. 2472-2475 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Soo-Young Lee ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Type Strains

A Gram-positive, rod- or coccoid-shaped bacterial strain, DS-17T, was isolated from a soil in Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain DS-17T grew optimally at around pH 8.0 and 30 °C in the presence of 0.5–1.0 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-17T belonged to the genus Nocardioides. The chemotaxonomic properties of strain DS-17T were consistent with those of the genus Nocardioides: the cell-wall peptidoglycan type was based on ll-2,6-diaminopimelic acid, MK-8(H4) was the predominant menaquinone and iso-C16 : 0, C17 : 1 ω8c and C17 : 0 were the major fatty acids. The DNA G+C content was 71.5 mol%. Strain DS-17T exhibited 16S rRNA gene sequence similarity values of 94.5–96.9 % to the type strains of recognized Nocardioides species. Strain DS-17T could be distinguished from recognized Nocardioides species by differences in phenotypic characteristics. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain DS-17T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides terrigena sp. nov. is proposed. The type strain is DS-17T (=KCTC 19217T=JCM 14582T).

scholarly journals Flavobacterium soli sp. nov., isolated from soil

2006 ◽  
Vol 56 (5) ◽  
pp. 997-1000 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Type Strains

A Gram-negative, rod-shaped Flavobacterium-like bacterial strain, DS-6T, was isolated from soil from the island of Dokdo, Korea, and subjected to a polyphasic taxonomic study. Strain DS-6T grew optimally at pH 7.0 and 25 °C in the presence of 0–0.5 % (w/v) NaCl. It contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 36.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain DS-6T belonged to the genus Flavobacterium. Levels of 16S rRNA gene sequence similarity between strain DS-6T and the type strains of Flavobacterium species were below 95.4 %. Strain DS-6T differed from some phylogenetically related Flavobacterium species in several phenotypic characteristics. On the basis of phenotypic and phylogenetic distinctiveness, DS-6T (=KCTC 12542T=CIP 108840T) was classified in the genus Flavobacterium as the type strain of a novel species, for which the name Flavobacterium soli sp. nov. is proposed.

Rhizobium soli sp. nov., isolated from soil

2010 ◽  
Vol 60 (6) ◽  
pp. 1387-1393 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Hwe-Su Yi ◽  
Tae-Kwang Oh ◽  
Choong-Min Ryu
Keyword(s):  
16S Rrna ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Type Strains

A Gram-negative, non-motile, pale-yellow, rod-shaped bacterial strain, DS-42T, was isolated from a soil in Korea and its taxonomic position was investigated by a polyphasic study. Strain DS-42T grew optimally at 25 °C and pH 7.0–8.0. Strain DS-42T did not form nodules on three different legumes, and the nodD and nifH genes were also not detected by PCR. Strain DS-42T contained Q-10 as the predominant ubiquinone. The major cellular fatty acid was C18 : 1 ω7c. The DNA G+C content was 60.8 mol%. Phylogenetic analyses based on 16S rRNA, atpD and recA gene sequences showed that strain DS-42T belonged to the genus Rhizobium. Strain DS-42T showed 16S rRNA gene sequence similarity of 94.1–97.7 % to the type strains of recognized Rhizobium species. DNA–DNA relatedness between strain DS-42T and the type strains of Rhizobium huautlense, R. galegae, R. loessense and R. cellulosilyticum was 13–19 %, indicating that strain DS-42T was distinct from them genetically. Strain DS-42T can also be differentiated from these four phylogenetically related Rhizobium species by various phenotypic properties. On the basis of phenotypic properties, phylogenetic distinctiveness and genetic data, strain DS-42T is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium soli sp. nov. is proposed. The type strain is DS-42T (=KCTC 12873T =JCM 14591T).

scholarly journals Reclassification of Flexibacter tractuosus (Lewin 1969) Leadbetter 1974 and ‘Microscilla sericea’ Lewin 1969 in the genus Marivirga gen. nov. as Marivirga tractuosa comb. nov. and Marivirga sericea nom. rev., comb. nov.

2010 ◽  
Vol 60 (8) ◽  
pp. 1858-1863 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Marc Vancanneyt ◽  
Seung Bum Kim ◽  
Kyung Sook Bae
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Distinct Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data ◽  
Dna Relatedness ◽  
The Family ◽  
Type Strains

The taxonomic position of the misclassified strains [Flexibacter] tractuosus KCTC 2958T and ‘[Microscilla] sericea’ LMG 13021 was studied using a polyphasic approach. The two strains shared 99.1 % 16S rRNA gene sequence similarity and 28 % DNA–DNA relatedness. On the basis of the phylogenetic evidence supported by genotypic and phenotypic data [Flexibacter] tractuosus KCTC 2958T and ‘[Microscilla] sericea’ LMG 13021 are classified as two distinct species in a novel genus, Marivirga, in the family ‘Flammeovirgaceae’, as Marivirga tractuosa comb. nov. and Marivirga sericea nom. rev., comb. nov., with strains KCTC 2958T (=ATCC 23168T =CIP 106410T =DSM 4126T =NBRC 15989T =NCIMB 1408T =VKM B-1430T) and LMG 13021T (=ATCC 23182T =NBRC 15983T =NCIMB 1403T), respectively, as the type strains. The type species is Marivirga tractuosa.

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