scholarly journals Bacteroides clarus sp. nov., Bacteroides fluxus sp. nov. and Bacteroides oleiciplenus sp. nov., isolated from human faeces

2010 ◽  
Vol 60 (8) ◽  
pp. 1864-1869 ◽  
Author(s):  
Yohei Watanabe ◽  
Fumiko Nagai ◽  
Masami Morotomi ◽  
Hiroshi Sakon ◽  
Ryuichiro Tanaka
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Human Faeces ◽  
Type Strains

Three Gram-stain-negative, obligately anaerobic, non-spore-forming, rod-shaped bacteria (strains YIT 12056T, YIT 12057T and YIT 12058T) were isolated from human faeces. These strains were characterized by phylogenetic analyses based on 16S rRNA gene sequence and phenotypic tests. 16S rRNA gene sequence analyses revealed that strains YIT 12056T, YIT 12057T and YIT 12058T were most closely related to the type strains of Bacteroides gallinarum, Bacteroides uniformis and Bacteroides intestinalis with approximate similarity values of 96.6, 95.0 and 96.7 %, respectively. The DNA G+C contents of the novel strains were 45.3 (YIT 12056T), 45.2 (YIT 12057T) and 43.6 mol% (YIT 12058T) and the major respiratory quinones of all three isolates were menaquinones MK-10 and MK-11. These properties were typical for members of the genus Bacteroides. The results of the other phenotypic analyses also supported the affiliation of these strains to the genus Bacteroides. The 16S rRNA gene sequence analysis, analysis of the major cellular fatty acids and other biochemical tests enabled the genotypic and phenotypic differentiation of the three new strains. Based on these data, three novel species, Bacteroides clarus sp. nov., Bacteroides fluxus sp. nov. and Bacteroides oleiciplenus sp. nov. are proposed. The type strains of B. clarus, B. fluxus and B. oleiciplenus are YIT 12056T (=JCM 16067T=DSM 22519T), YIT 12057T (=JCM 16101T=DSM 22534T) and YIT 12058T (=JCM 16102T=DSM 22535T), respectively.

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 Pedobacter ardleyensis sp. nov., isolated from soil in Antarctica

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3841-3846 ◽  
Author(s):  
Xuyang Da ◽  
Fan Jiang ◽  
Xulu Chang ◽  
Lvzhi Ren ◽  
Xia Qiu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
South Shetland Islands ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests

A red-pigmented, non-motile, Gram-stain-negative, rod-shaped bacterium, strain R2-28T, was isolated from a soil sample collected from Ardley Island, South Shetland Islands, Antarctica, and was characterized taxonomically by using a polyphasic approach. The organism grew optimally at 18 °C in TSB. On the basis of phylogenetic analyses of the 16S rRNA gene sequence, strain R2-28T was most closely related to the genus Pedobacter of the family Sphingobacteriaceae. The highest levels of 16S rRNA gene sequence similarity were found with respect to Pedobacter alluvionis NWER-II11T (95.6 %) and Pedobacter terrae DS-57T (95.2 %). The DNA G+C content was 39.9 mol%, and MK-7 was the only respiratory quinone. The major polar lipids were phosphatidylethanolamine and a sphingolipid. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). These chemotaxonomic and phylogenetic data supported the allocation of strain R2-28T to the genus Pedobacter. Additionally, the results of physiological and biochemical tests allowed phenotypic differentiation of strain R2-28T from species of the genus Pedobacter with validly published names. Therefore, strain R2-28T represents a novel species within the genus Pedobacter, for which the name Pedobacter ardleyensis sp. nov. is proposed. The type strain is R2-28T ( = CCTCC AB 2013365T = LMG 28255T).

Alishewanella agri sp. nov., isolated from landfill soil

2010 ◽  
Vol 60 (9) ◽  
pp. 2199-2203 ◽  
Author(s):  
Min-Soo Kim ◽  
Seon Kyung Jo ◽  
Seong Woon Roh ◽  
Jin-Woo Bae
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Type Strains

Strain BL06T was isolated from landfill soil in Pohang, Korea. Strain BL06T is Gram-negative, aerobic, non-motile and rod-shaped. For growth, the NaCl range is 0–6 % (w/v), the temperature range is 10–44 °C and the pH range is 5.5–12.0. Based on the 16S rRNA gene and gyrase B (gyrB) gene sequences, phylogenetic analysis showed that strain BL06T is associated with the genus Alishewanella and related closely to the type strains of Alishewanella species (98.8 % 16S rRNA gene sequence similarity to Alishewanella aestuarii, 98.7 % to Alishewanella fetalis and 98.5 % to Alishewanella jeotgali). Physiological and biochemical tests verified that strain BL06T is genotypically and phenotypically different from previously described species in the genus Alishewanella. DNA–DNA hybridization experiments showed that relatedness between the genomic DNA of strain BL06T and type strains of other Alishewanella species is <41 %. These findings suggest strongly that the strain represents a novel species, despite high 16S rRNA gene sequence similarity between strain BL06T and related strains. Therefore, strain BL06T (=KCTC 22400T=JCM 15597T) is proposed to represent a novel species in the genus Alishewanella, named Alishewanella agri sp. nov.

scholarly journals Variovorax ginsengisoli sp. nov., a denitrifying bacterium isolated from soil of a ginseng field

2010 ◽  
Vol 60 (7) ◽  
pp. 1565-1569 ◽  
Author(s):  
Wan-Taek Im ◽  
Qing-Mei Liu ◽  
Kang-Jin Lee ◽  
Se-Young Kim ◽  
Sung-Taik Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
The Family ◽  
Type Strains

A Gram-negative, aerobic or facultatively anaerobic, non-spore-forming, motile, rod-shaped bacterium (strain Gsoil 3165T) was isolated from soil of a ginseng field in Pocheon, South Korea. Its taxonomic position was determined by using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain Gsoil 3165T was shown to belong to the family Comamonadaceae, class Betaproteobacteria, and was related most closely to the type strains of Variovorax boronicumulans (98.9 % similarity), Variovorax paradoxus (98.3 %), Variovorax soli (98.2 %) and Variovorax dokdonensis (96.6 %). Levels of 16S rRNA gene sequence similarity between strain Gsoil 3165T and the type strains of other species in the family Comamonadaceae were less than 97.0 %. The G+C content of the genomic DNA of strain Gsoil 3165T was 66 mol%. Phenotypic and chemotaxonomic data (Q-8 as the major ubiquinone; C16 : 0 and C17 : 0 cyclo as major fatty acids) supported the affiliation of strain Gsoil 3165T to the genus Variovorax. The results of physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain Gsoil 3165T from recognized Variovorax species. Gsoil 3165T is therefore considered to represent a novel species of the genus Variovorax, for which the name Variovorax ginsengisoli sp. nov. is proposed. The type strain is Gsoil 3165T (=KCTC 12583T =LMG 23392T).

scholarly journals Paenibacillus pocheonensis sp. nov., a facultative anaerobe isolated from soil of a ginseng field

2010 ◽  
Vol 60 (5) ◽  
pp. 1163-1167 ◽  
Author(s):  
Sang-Hoon Baek ◽  
Tae-Hoo Yi ◽  
Sung-Taik Lee ◽  
Wan-Taek Im
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Bacterium Strain ◽  
Type Strains

A Gram-positive, aerobic or facultatively anaerobic, rod-shaped, spore-forming bacterium, strain Gsoil 1138T, was isolated from soil of a ginseng field in Pocheon Province, South Korea, and was characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence analysis, strain Gsoil 1138T was shown to belong to the family Paenibacillaceae and was most closely related to the type strains of Paenibacillus chondroitinus (98.2 % similarity) and Paenibacillus alginolyticus (96.5 %). Levels of 16S rRNA gene sequence similarity between strain Gsoil 1138T and the type strains of other recognized species of the genus Paenibacillus were below 96.5 %. The G+C content of the genomic DNA of strain Gsoil 1138T was 52.1±0.2 mol% (mean±sd of three determinations). Phenotypic and chemotaxonomic data (MK-7 as the major menaquinone and anteiso-C15 : 0 and iso-C16 : 0 as the predominant fatty acids) supported the affiliation of strain Gsoil 1138T to the genus Paenibacillus. The results of DNA–DNA hybridization experiments and physiological and biochemical tests allowed strain Gsoil 1138T to be distinguished genotypically and phenotypically from recognized species of the genus Paenibacillus. Strain Gsoil 1138T is therefore considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus pocheonensis sp. nov. is proposed. The type strain is Gsoil 1138T (=KCTC 13941T=LMG 23404T).

scholarly journals Arcanobacterium pinnipediorum sp. nov., isolated from a harbour seal

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4539-4543 ◽  
Author(s):  
Osama Sammra ◽  
Anna Balbutskaya ◽  
Hivda Ülbegi-Mohyla ◽  
Samy Nagib ◽  
Christoph Lämmler ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Harbour Seal ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Polar Lipid Profile ◽  
Type Strains

A polyphasic taxonomic study was performed on an unidentified Arcanobacterium-like, Gram-stain-positive bacterium, strain 2710T, isolated from a harbour seal. Comparative 16S rRNA gene sequence analysis showed that this bacterial strain belonged to the genus Arcanobacterium and was related most closely to the type strains of Arcanobacterium phocae (98.4 % similarity) and Arcanobacterium phocisimile (97.5 %). 16S rRNA gene sequence similarities to the type strains of other Arcanobacterium species were between 95.3 and 96.9 %. DNA–DNA hybridization values between strain 2710T and A. phocae DSM 10002T and A. phocisimile LMG 27073T were 4.7 % (reciprocal 56 %) and 23 % (reciprocal 7.7 %), respectively. The presence of the major menaquinone MK-9(H4) and a polar lipid profile with the major compounds diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside supported the affiliation of strain 2710T to the genus Arcanobacterium. The major fatty acids were C16:0, C18:1ω9c, C18:0 and C18:2ω6,9c/anteiso-C18:0. The peptidoglycan structure was of cross-linkage type A5α (l-Lys–l-Lys–d-Glu). Physiological and biochemical tests clearly distinguished the isolate from other members of the genus Arcanobacterium. Based on these tests, it is proposed that this unknown bacterium should be classified as a novel species of the genus Arcanobacterium, with the name Arcanobacterium pinnipediorum sp. nov. The type strain is 2710T ( = DSM 28752T = LMG 28298T).

scholarly journals Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., isolated from human faeces

2005 ◽  
Vol 55 (5) ◽  
pp. 2143-2147 ◽  
Author(s):  
Maki Kitahara ◽  
Mitsuo Sakamoto ◽  
Masako Ike ◽  
Shinji Sakata ◽  
Yoshimi Benno
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Divergence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Human Faeces ◽  
Type Strains ◽  
Sequence Similarities

Nine strains of Gram-negative, anaerobic rod were isolated from human faeces. Based on phylogenetic analysis and specific phenotypic characteristics, these strains were included within the Bacteroides cluster and were divided into two clusters. Strains from the two clusters showed 16S rRNA gene sequence similarities of 90·4 and 92·7 % to the nearest recognized species, Bacteroides vulgatus. The strains also formed two clusters exhibiting a 16S rRNA gene sequence divergence of approximately 6 %. DNA–DNA hybridization studies confirmed that the two novel strain clusters were distinct from each other. Based on the phenotypic and phylogenetic findings, two novel species, Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., are proposed, each representing one of the two strain clusters. The DNA G+C content of the type strains were 43·9 mol% for B. plebeius (M12T=JCM 12973T=DSM 17135T) and 42·4 mol% for B. coprocola (M16T=JCM 12979T=DSM 17136T).

scholarly journals Parabacteroides johnsonii sp. nov., isolated from human faeces

2007 ◽  
Vol 57 (2) ◽  
pp. 293-296 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Maki Kitahara ◽  
Yoshimi Benno
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Human Faeces ◽  
Gene Sequence Analysis

A bacterial strain isolated from human faeces, M-165T, was characterized in terms of its phenotypic and biochemical features, cellular fatty acid profile, menaquinone profile and phylogenetic position (based on 16S rRNA gene sequence analysis). A 16S rRNA gene sequence analysis showed that the isolate was a member of the genus Parabacteroides. Strain M-165T was closely related to Parabacteroides merdae strains, showing 98 % sequence similarity. The strain was obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative, rod-shaped and was able to grow on media containing 20 % bile. Although the phenotypic characteristics of the strain M-165T were similar to those of P. merdae, the isolate could be differentiated from P. merdae by means of API 20A tests for l-arabinose and l-rhamnose fermentation. DNA–DNA hybridization experiments revealed the genomic distinctiveness of the novel strain with respect to P. merdae JCM 9497T (⩽60 % DNA–DNA relatedness). The DNA G+C content of the strain is 47.6 mol%. On the basis of these data, strain M-165T represents a novel species of the genus Parabacteroides, for which the name Parabacteroides johnsonii sp. nov. is proposed. The type strain is M-165T (=JCM 13406T=DSM 18315T).

scholarly journals Planococcus salinarum sp. nov., isolated from a marine solar saltern, and emended description of the genus Planococcus

2010 ◽  
Vol 60 (4) ◽  
pp. 754-758 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Soo-Young Lee ◽  
Ki-Hoon Oh ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Solar Saltern ◽  
Rrna Gene Sequence ◽  
Marine Solar Saltern ◽  
Emended Description ◽  
Type Strains

A Gram-positive, non-motile and coccoid-, short rod- or rod-shaped bacterial strain, ISL-16T, was isolated from a marine solar saltern in Korea and its taxonomic position was investigated using a polyphasic taxonomic approach. Strain ISL-16T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-16T joined the cluster comprising species of the genus Planococcus. Its 16S rRNA gene sequence contained the same signature nucleotides as those defined for the genus Planococcus. Strain ISL-16T exhibited 16S rRNA gene sequence similarity values of 96.9–98.2 % to the type strains of species of the genus Planococcus. Strain ISL-16T contained MK-8 and MK-7 as the predominant menaquinones and anteiso-C15 : 0, C16 : 1 ω7c alcohol and anteiso-C17 : 0 as the major fatty acids. The DNA G+C content was 48.3 mol%. DNA–DNA relatedness values between strain ISL-16T and the type strains of species of the genus Planococcus were 15–28 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, enabled strain ISL-16T to be differentiated from recognized species of the genus Planococcus. On the basis of the data presented, strain ISL-16T is considered to represent a novel species of the genus Planococcus, for which the name Planococcus salinarum sp. nov. is proposed. The type strain is ISL-16T (=KCTC 13584T=CCUG 57753T). An emended description of the genus Planococcus is also given.

Sign in / Sign up

Export Citation Format

Share Document