scholarly journals Slackia piriformis sp. nov. and Collinsella tanakaei sp. nov., new members of the family Coriobacteriaceae, isolated from human faeces

2010 ◽  
Vol 60 (11) ◽  
pp. 2639-2646 ◽  
Author(s):  
Fumiko Nagai ◽  
Yohei Watanabe ◽  
Masami Morotomi
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Indole Production ◽  
Type Strains

Three Gram-positive, strictly anaerobic, non-spore-forming, rod-shaped organisms (strains YIT 12062T, YIT 12063T and YIT 12064) were isolated from human faeces. Strain YIT 12062T was asaccharolytic and possessed a DNA G+C content of 58.3 mol%. Cells of strain YIT 12062T were negative for catalase, oxidase, urease, hydrolysis of aesculin and gelatin, nitrate reduction and indole production. Based on 16S rRNA gene sequence analysis, strain YIT 12062T was assigned to the genus Slackia (91.7–96.0 % sequence similarities to type strains of Slackia species). Biochemical data showed that the isolate was phenotypically distinct from all recognized species of the genus Slackia. Strain YIT 12062T therefore represents a novel species in the genus Slackia, for which the name Slackia piriformis sp. nov. is proposed. The type strain is YIT 12062T (=DSM 22477T=JCM 16070T). Following 16S rRNA gene sequence analysis, strains YIT 12063T and YIT 12064, which were isolated from different subjects, were shown to be most closely related to species of the genus Collinsella (93.8–95.1 % similarities to type strains). Although their phenotypic characteristics were very similar and they shared >99 % 16S rRNA gene sequence similarity and >97±1.8 % DNA–DNA relatedness, the two isolates could be discriminated by RAPD fingerprints. The DNA G+C contents of strains YIT 12063T and YIT 12064 were 60.8 and 61.0 mol%, respectively. They were saccharolytic in API test systems, positive for aesculin hydrolysis and negative for catalase, oxidase, urease, indole production, nitrate reduction and gelatin hydrolysis. The major end products of glucose fermentation of these strains were lactate, acetate and formate. Biochemical data supported the affiliation of strains YIT 12063T and YIT 12064 to the genus Collinsella and showed that they were phenotypically distinct from all recognized species of the genus Collinsella. Strains YIT 12063T and YIT 12064 therefore represent a novel species of the genus Collinsella, for which the name Collinsella tanakaei sp. nov. is proposed. The type strain is YIT 12063T (=DSM 22478T=JCM 16071T).

Paracoccus caeni sp. nov., isolated from sludge

2011 ◽  
Vol 61 (8) ◽  
pp. 1968-1972 ◽  
Author(s):  
Myungjin Lee ◽  
Song-Geun Woo ◽  
Giho Park ◽  
Myung Kyum Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Type Strains ◽  
Sequence Similarities

A Gram-negative, non-motile bacterium, designated MJ17T, was isolated from sludge at the Daejeon sewage disposal plant in South Korea. Comparative 16S rRNA gene sequence analysis showed that strain MJ17T belonged to the genus Paracoccus in the family Rhodobacteraceae of the class Alphaproteobacteria. 16S rRNA gene sequence similarities between strain MJ17T and type strains of species of the genus Paracoccus were 94.1–97.4 %. The highest similarities were between strain MJ17T and Paracoccus homiensis DD-R11T, Paracoccus zeaxanthinifaciens ATCC 21588T and Paracoccus alcaliphilus JCM 7364T (97.4, 97.2 and 96.3 %, respectively). Strain MJ17T exhibited <22 % DNA–DNA relatedness with P. homiensis KACC 11518T and P. zeaxanthinifaciens JCM 21774T. The G+C content of the genomic DNA was 58.7 mol%. Strain MJ17T contained ubiquinone Q-10. The major fatty acids were C18 : 0 (11.3 %), C16 : 0 (10.2 %) and summed feature 7 (containing one or more of C18 : 1ω7c, C18 : 1ω9c and C18 : 1ω12t; 54.3 %). Poly-β-hydroxybutyrate granules are formed. On the basis of phenotypic and genotypic properties and phylogenetic distinctiveness, strain MJ17T should be classified in a novel species of the genus Paracoccus, for which the name Paracoccus caeni sp. nov. is proposed. The type strain is MJ17T ( = KCTC 22480T  = JCM 16385T  = KEMB 9004-001T).

scholarly journals Planococcus stackebrandtii sp. nov., isolated from a cold desert of the Himalayas, India

2005 ◽  
Vol 55 (1) ◽  
pp. 91-94 ◽  
Author(s):  
S. Mayilraj ◽  
G. S. Prasad ◽  
K. Suresh ◽  
H. S. Saini ◽  
S. Shivaji ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Cold Desert ◽  
Gene Sequence Analysis

The taxonomic position of a bacterium isolated from a cold desert of the Himalayas, India, was analysed by using a polyphasic approach. The isolated strain, designated K22-03T, had phenotypic characteristics that matched those of the genus Planococcus and it represents a novel species. The almost-complete 16S rRNA gene sequence (1464 bases) of the novel strain was compared with those of previously studied Planococcus type strains and confirmed that the strain belongs to the genus Planococcus. 16S rRNA gene sequence analysis indicated that strain K22-03T differs from all other species of Planococcus by at least 2·5 %. DNA–DNA hybridization showed that it had low genomic relatedness with Planomicrobium mcmeekinii (MTCC 3704T, 23 %), Planococcus psychrophilus (MTCC 3812T, 61 %), Planococcus antarcticus (MTCC 3854T, 45 %) and Planomicrobium okeanokoites (MTCC 3703T, 51 %), the four species with which it was most closely related based on 16S rRNA gene sequence analysis (97–97·5 % similarity). Therefore, strain K22-03T should be recognized as a novel species, for which the name Planococcus stackebrandtii sp. nov. is proposed. The type strain is K22-03T (=MTCC 6226T=DSM 16419T=JCM 12481T).

scholarly journals Treponema berlinense sp. nov. and Treponema porcinum sp. nov., novel spirochaetes isolated from porcine faeces

2005 ◽  
Vol 55 (4) ◽  
pp. 1675-1680 ◽  
Author(s):  
Marcel Nordhoff ◽  
David Taras ◽  
Moritz Macha ◽  
Karsten Tedin ◽  
Hans-Jürgen Busse ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Gene Sequence Analysis ◽  
Sequence Similarities

Limit-dilution procedures were used to isolate seven, helically coiled bacterial strains from faeces of swine that constituted two unidentified taxa. Comparative 16S rRNA gene sequence analysis showed highest similarity values with species of the genus Treponema indicating that the isolates are members of this genus. Strain 7CPL208T, as well as five further isolates, and 14V28T displayed the highest 16S rRNA gene sequence similarities with Treponema pectinovorum ATCC 33768T (92·3 %) and Treponema parvum OMZ 833T (89·9 %), respectively. Polar lipid profiles distinguished 7CPL208T and 14V28T from each other as well as from related species. Based on their phenotypic and genotypic distinctiveness, strains 7CPL208T and 14V28T are suggested to represent two novel species of the genus Treponema, for which the names Treponema berlinense sp. nov. and Treponema porcinum sp. nov. are proposed. The type strain for Treponema berlinense is 7CPL208T (=ATCC BAA-909T=CIP 108244T=JCM 12341T) and for Treponema porcinum 14V28T (=ATCC BAA-908T=CIP 108245T=JCM 12342T).

Kaistia geumhonensis sp. nov. and Kaistia dalseonensis sp. nov., two members of the class Alphaproteobacteria

2011 ◽  
Vol 61 (11) ◽  
pp. 2577-2581 ◽  
Author(s):  
Long Jin ◽  
Kwang Kyu Kim ◽  
Sang-Hoon Baek ◽  
Sung-Taik Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Sequence Similarities

Two strains, designated B1-1T and B6-8T, were isolated from the Geumho River and the Dalseo Stream in Korea. Comparative 16S rRNA gene sequence analysis showed a clear affiliation of these two bacteria with the class Alphaproteobacteria, their closest relatives being Kaistia adipata KCTC 12095T, Kaistia granuli KCTC 12575T, Kaistia soli KACC 12605T and Kaistia terrae KACC 12910T with 16S rRNA gene sequence similarities of 95.3 –97.7 % to the two novel strains. Strains B1-1T and B6-8T shared a 16S rRNA gene sequence similarity value of 96.1 %. Cells of the two strains were Gram-reaction-negative, aerobic, non-motile, short rods or cocci. The predominant ubiquinone was Q-10. The major fatty acids were C16 : 0, C18 : 1ω7c, C18 : 0 and C19 : 0ω8c cyclo for strain B1-1T and C16 : 0, C18 : 1ω7c, C18 : 0, C18 : 1 2-OH, and C19 : 0ω8c cyclo for strain B6-8T. The G+C contents of the genomic DNA of the strains B1-1T and B6-8T were 61.6 and 66.5 mol%, respectively. Based on the results of this polyphasic study, strains B1-1T ( = KCTC 12849T  = DSM 18799T) and B6-8T ( = KCTC 12850T  = DSM 18800T) represent two novel species of the genus Kaistia, for which the names Kaistia geumhonensis sp. nov. and Kaistia dalseonensis sp. nov. are proposed, respectively.

Duganella sacchari sp. nov. and Duganella radicis sp. nov., two novel species isolated from rhizosphere of field-grown sugar cane

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1126-1131 ◽  
Author(s):  
M. Madhaiyan ◽  
S. Poonguzhali ◽  
V. S. Saravanan ◽  
K. Hari ◽  
K.-C. Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

Two strains, designated Sac-22T and Sac-41T, were isolated from rhizosphere soil and rhizoplane of field-grown sugar cane clone Co86032. Comparative 16S rRNA gene sequence analysis showed a clear affiliation of these two bacteria with the class Betaproteobacteria , their closest relatives being Pseudoduganella violaceinigra and Duganella zoogloeoides with 16S rRNA gene sequence pairwise similarities of 96.4–97.2 % to the two novel strains. Strains Sac-22T and Sac-41T shared a 16S rRNA gene sequence similarity value of 97.6 %. Cells of the two strains were Gram-reaction-negative, aerobic, motile and rod-shaped. Ubiquinone (Q-8) was the respiratory quinone and the predominant polar lipids consisted of phosphatidylglycerol and phosphatidylethanolamine. The main cellular fatty acids were C16 : 0, C16 : 1ω7c/iso-C15 : 0 2-OH, C17 : 0 cyclo, C10 : 0 3-OH and C12 : 0. The DNA G+C content of the genomic DNA was 56.4 mol% for strain Sac-22T and 54.9 mol% for strain Sac-41T. Based on the results of 16S rRNA gene sequence analysis and physiological and biochemical characterization, that differentiated strains Sac-22T and Sac-41T from all recognized species of the genus Duganella , it was concluded that strains represent two novel species in the genus Duganella for which the names Duganella sacchari sp. nov. (type strain Sac-22T = KCTC 22381T = NCIMB 14475T) and Duganella radicis sp. nov. (type strain Sac-41T = KCTC 22382T = NCIMB 14476T) are proposed.

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 Pedobacter bauzanensis sp. nov., isolated from soil

2010 ◽  
Vol 60 (11) ◽  
pp. 2592-2595 ◽  
Author(s):  
De-Chao Zhang ◽  
Franz Schinner ◽  
Rosa Margesin
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Type Strains ◽  
Sequence Similarities

A Gram-negative, aerobic, rod-shaped, non-motile bacterium, designated BZ42T, was isolated from the soil of an industrial site. Strain BZ42T was able to grow at 5–25 °C. The major fatty acids were iso-C15 : 0 (46.2 %), C16 : 1 ω7c and/or iso-C15 : 0 2-OH (23.2 %) and iso-C17 : 0 3-OH (9.1 %). The predominant menaquinone was MK-7. The genomic DNA G+C content was 36.5 mol% (HPLC). 16S rRNA gene sequence phylogenetic analysis revealed that strain BZ42T was a member of the genus Pedobacter, family Sphingobacteriaceae, and 16S rRNA gene sequence similarities between strain BZ42T and the type strains of species of the genus Pedobacter with validly published names were 90.4–93.2 %. On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain BZ42T was considered to represent a novel species of the genus Pedobacter, for which the name Pedobacter bauzanensis sp. nov. is proposed. The type strain is BZ42T (=DSM 22554T =CGMCC 1.10187T =CIP 110134T).

scholarly journals Pedobacter caeni sp. nov., a novel species isolated from a nitrifying inoculum

2005 ◽  
Vol 55 (3) ◽  
pp. 1315-1318 ◽  
Author(s):  
Bram Vanparys ◽  
Kim Heylen ◽  
Liesbeth Lebbe ◽  
Paul De Vos
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Gene Sequence Analysis

A Gram-negative, rod-shaped, non-spore-forming bacterium was isolated from a nitrifying inoculum. On the basis of 16S rRNA gene sequence similarity, LMG 22862T was shown to belong to the family Sphingobacteriaceae, related to Pedobacter africanus (98·0 %) and Pedobacter heparinus (97·6 %). The results of 16S rRNA gene sequence analysis, DNA–DNA hybridization, SDS-PAGE, analysis of the fatty acid composition and physiological and biochemical tests allowed genotypic and phenotypic differentiation of LMG 22862T from Pedobacter species with validly published names. LMG 22862T therefore represents a novel species within this genus, for which the name Pedobacter caeni sp. nov. is proposed, with the type strain LMG 22862T (=DSM 16990T).

scholarly journals Kaistia terrae sp. nov., isolated from a wetland in Korea

2010 ◽  
Vol 60 (4) ◽  
pp. 949-952 ◽  
Author(s):  
Soo-Jin Kim ◽  
Hang-Yeon Weon ◽  
Yi-Seul Kim ◽  
Rangasamy Anandham ◽  
Seung-Hee Yoo ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

An ivory-coloured bacterium, designated strain 5YN7-3T, was isolated from a wetland, Yongneup, Korea. Cells of the strain were aerobic, Gram-stain-negative, non-motile and short rods. 16S rRNA gene sequence analysis demonstrated that strain 5YN7-3T belongs to the order Rhizobiales of the class Alphaproteobacteria and is closely related to Kaistia soli 5YN9-8T (97.8 %), Kaistia granuli Ko04T (97.6 %) and Kaistia adipata Chj404T (97.4 %). Strain 5YN7-3T showed DNA–DNA hybridization values of 28, 22 and 35 % with K. granuli Ko04T, K. soli 5YN9-8T and K. adipata Chj404T, respectively. The major fatty acids were C18 : 1 ω7c (51.2 %), C19 : 0 cyclo ω8c (25.0 %), C18 : 0 (12.9 %) and C16 : 0 (10.8 %) (>10 % of total fatty acids). Ubiquinone-10 was the major isoprenoid quinone and the DNA G+C content was 66.5 mol%. The phenotypic characteristics in combination with 16S rRNA gene sequence analysis and DNA–DNA hybridization data clearly define strain 5YN7-3T as a novel species of the genus Kaistia, for which the name Kaistia terrae sp. nov. is proposed. The type strain is 5YN7-3T (=KACC 12910T =DSM 21341T).

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