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 Dyella koreensis sp. nov., a β-glucosidase-producing bacterium

2005 ◽  
Vol 55 (4) ◽  
pp. 1625-1628 ◽  
Author(s):  
Dong-Shan An ◽  
Wan-Taek Im ◽  
Hee-Chan Yang ◽  
Deok-Chun Yang ◽  
Sung-Taik Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Sequence Similarities ◽  
Straight Rod

A bacterial strain (designated BB4T), which has β-glucosidase activity, was isolated from soil around the roots of bamboo plants. Cells were Gram-negative, aerobic, non-motile and straight-rod-shaped. Phylogenetic analysis of 16S rRNA gene sequences revealed a clear affiliation with members of the family ‘Xanthomonadaceae’. The 16S rRNA gene sequence of strain BB4T showed the following sequence similarities: 97·7 % to Dyella japonica XD53T, 97·1 % to Frateuria aurantia LMG 1558T, 96·2 % to Fulvimonas soli LMG 19981T, 94·3 % to Rhodanobacter lindaniclasticus RP5575T and <90 % to other members of the ‘Gammaproteobacteria’. The G+C content of the genomic DNA was 63·8 mol%. The major fatty acids were branched forms, especially large proportions of iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1 ω9c, similar to the profile of the genus Dyella. The results of DNA–DNA hybridization with D. japonica XD53T and Frateuria aurantia LMG 1558T, in combination with phenotypic characteristics and 16S rRNA gene sequence analysis, demonstrated that strain BB4T should be classified as a novel Dyella species. The name Dyella koreensis sp. nov. is proposed, with strain BB4T (=KCTC 12359T=NBRC 100831T) as the type strain.

scholarly journals Pseudosphingobacterium domesticum gen. nov., sp. nov., isolated from home-made compost

2007 ◽  
Vol 57 (7) ◽  
pp. 1535-1538 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
M. Fernanda Nobre ◽  
Olga C. Nunes ◽  
Célia M. Manaia
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family

A bacterial strain, DC-186T, isolated from home-made compost, was characterized for its phenotypic and phylogenetic properties. The isolate was a Gram-negative rod that was able to grow at 15–36 °C and pH 5.5–8.0. Strain DC-186T was positive in tests for catalase, oxidase and β-galactosidase activities and aesculin hydrolysis. The predominant fatty acids were the summed feature C16 : 1/iso-C15 : 0 2-OH (42 %) and iso-C15 : 0 (26 %), the major respiratory quinone was menaquinone-7 and the genomic DNA G+C content was 42 mol%. 16S rRNA gene sequence analysis and phenetic characterization indicated that this organism belongs to the phylum Bacteroidetes and revealed its affiliation to the family Sphingobacteriaceae. Of recognized taxa, strain DC-186T was most closely related to Sphingobacterium daejeonense (90 % sequence similarity) based on 16S rRNA gene sequence analysis. The low 16S rRNA gene sequence similarity with other recognized taxa and the identification of distinctive phenetic features for this isolate support the definition of a new genus within the family Sphingobacteriaceae. The name Pseudosphingobacterium domesticum gen. nov., sp. nov. is proposed, with strain DC-186T (=CCUG 54353T=LMG 23837T) as the type strain.

Oribacterium sinus gen. nov., sp. nov., within the family ‘Lachnospiraceae’ (phylum Firmicutes)

2004 ◽  
Vol 54 (5) ◽  
pp. 1611-1615 ◽  
Author(s):  
Jean-Philippe Carlier ◽  
Guylène K'ouas ◽  
Isabelle Bonne ◽  
Alain Lozniewski ◽  
Francine Mory
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
The Public ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Uncultivated Bacteria

A hitherto unknown anaerobic bacillus isolated from sinus pus in a young child (strain AIP 354.02T) was characterized by using phenotypic and genotypic methods. 16S rRNA gene sequence analysis indicated that this strain was phylogenetically affiliated with several sequences of cloned 16S rRNA gene inserts previously deposited in the public databases. According to their 16S rRNA gene sequence similarities, these uncultivated bacteria, together with strain AIP 354.02T, formed a separate subgroup belonging to the family ‘Lachnospiraceae’ within the phylum Firmicutes. Oribacterium gen. nov. is proposed for this group of organisms and Oribacterium sinus gen. nov. sp. nov. for strain AIP 354.02T (=CIP 107991T=CCUG 48084T).

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).

scholarly journals Solirubrobacter ginsenosidimutans sp. nov., isolated from soil of a ginseng field

2011 ◽  
Vol 61 (11) ◽  
pp. 2606-2609 ◽  
Author(s):  
Dong-Shan An ◽  
Liang Wang ◽  
Minseok S. Kim ◽  
Heon-Meen Bae ◽  
Sung-Taik Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Active Components ◽  
Gene Sequence Analysis ◽  
Sequence Similarities

A Gram-reaction-positive, non-motile, non-spore-forming, aerobic rod, designated BXN5-15T, was isolated from the soil of a ginseng field on Baekdu Mountain in China. Strain BXN5-15T grew optimally at 30 °C and pH 6.0–7.0 in the absence of NaCl on R2A agar. Strain BXN5-15T displayed β-glucosidase activity, which allowed it to transform ginsenoside Rb1 (one of the dominant active components of ginseng) via Rd to minor ginsenoside F2. On the basis of 16S rRNA gene sequence analysis, strain BXN5-15T was shown to belong to the genus Solirubrobacter. The closest phylogenetic relatives were Solirubrobacter soli Gsoil 355T (98.4 % 16S rRNA gene sequence similarity) and Solirubrobacter pauli B33D1T (96.4 %). Lower sequence similarities (<96.0 %) were found with all of the other recognized members of the order Solirubrobacterales. The predominant quinone was MK-7(H4). The major fatty acids (>10 %) were C18 : 1ω9c, iso-C16 : 0 and C18 : 3ω6,9,12c. The G+C content of the genomic DNA was 70.6 mol%. DNA−DNA relatedness between strain BXN5-15T and S. soli KCTC 12628T was 23.3 %. On the basis of genotypic, phenotypic and chemotaxonomic data, strain BXN5-15T represents a novel species within the genus Solirubrobacter, for which the name Solirubrobacter ginsenosidimutans sp. nov. is proposed. The type strain is BXN5-15T ( = KACC 20671T  = LMG 24459T).

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.

Pusillimonas soli sp. nov., isolated from farm soil

2010 ◽  
Vol 60 (10) ◽  
pp. 2326-2330 ◽  
Author(s):  
Myungjin Lee ◽  
Sung-Geun Woo ◽  
Myoungsoo Chae ◽  
Leonid N. Ten
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Low Levels

A Gram-negative, motile, non-spore-forming bacterial strain, designated MJ07T, was isolated from a farm soil and was characterized to determine its taxonomic position by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ07T belongs to the family Alcaligenaceae, class Betaproteobacteria, and is related most closely to Pusillimonas ginsengisoli KCTC 22046T (98.6 % sequence similarity) and Pusillimonas noertemannii BN9T (96.9 %). The levels of 16S rRNA gene sequence similarity between strain MJ07T and members of all other recognized species of the family Alcaligenaceae were below 95.2 %. The G+C content of the genomic DNA of strain MJ07T was 59.4 mol%. The detection of a quinone system with ubiquinone Q-8 as the major respiratory lipoquinone, putrescine as the predominant polyamine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unknown aminolipids as major polar lipids and a fatty acid profile with C16 : 0 (32.0 %), C17 : 0 cyclo (24.7 %) and C19 : 0 cyclo ω8c (11.5 %) as the major components supported the affiliation of strain MJ07T to the genus Pusillimonas. Strain MJ07T exhibited relatively low levels of DNA–DNA relatedness with respect to P. ginsengisoli KCTC 22046T (50±8 %) and P. noertemannii KACC 13183T (18±7 %). On the basis of its phenotypic and genotypic properties together with its phylogenetic distinctiveness, strain MJ07T (=KCTC 22455T =JCM 16386T) should be classified in the genus Pusillimonas as the type strain of a novel species, for which the name Pusillimonas soli sp. nov. is proposed.

scholarly journals Barnesiella viscericola gen. nov., sp. nov., a novel member of the family Porphyromonadaceae isolated from chicken caecum

2007 ◽  
Vol 57 (2) ◽  
pp. 342-346 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Pham Thi Ngoc Lan ◽  
Yoshimi Benno
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family

Two bacterial strains isolated from chicken caecum, C46T and C47, were characterized using a polyphasic taxonomic approach that included analysis of the phenotypic and biochemical features, cellular fatty acid profiles, menaquinone profiles and phylogenetic position (using 16S rRNA gene sequence analysis). The 16S rRNA gene sequence analysis showed that these strains belonged to the family Porphyromonadaceae. These strains shared 100 % 16S rRNA gene sequence similarity with each other and were related to Parabacteroides distasonis (showing 86 % sequence similarity). The strains were found to be obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative rods. Growth of the strains was inhibited on medium containing 20 % bile. The major menaquinones of the isolates were MK-11 and MK-12. This menaquinone composition was different from those of other genera of the family Porphyromonadaceae, such as Parabacteroides (in which the predominant menaquinones are MK-9 and MK-10), Porphyromonas (MK-9 and MK-10) and Tannerella (MK-10 and MK-11). This is an important chemotaxonomic characteristic of these micro-organisms. The DNA G+C content of strain C46T is 52.0 mol%. On the basis of these data, strains C46T and C47 represent a novel genus and species, for which the name Barnesiella viscericola gen. nov., sp. nov. is proposed. The type strain of Barnesiella viscericola is C46T (=JCM 13660T=DSM 18177T).

Lysobacter dokdonensis sp. nov., isolated from soil

2011 ◽  
Vol 61 (5) ◽  
pp. 1089-1093 ◽  
Author(s):  
Ki-Hoon Oh ◽  
So-Jung Kang ◽  
Yong-Taek Jung ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Closely Related Species ◽  
The Family ◽  
Type Strains

A Gram-negative, non-motile, rod-shaped bacterial strain, DS-58T, was isolated from a soil sample from Dokdo, an island of Korea, and its taxonomic position was investigated. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-58T fell within the family Xanthomonadaceae. The isolate showed 96.9 % 16S rRNA gene sequence similarity with its closest phylogenetic neighbour, Lysobacter niastensis GH41-7T, and 93.4–95.7 % 16S rRNA gene sequence similarity with other members of the genus Lysobacter. Strain DS-58T contained Q-8 as the predominant ubiquinone and iso-C16 : 0, iso-C15 : 0 and iso-C17 : 1ω9c as the major fatty acids. The DNA G+C content was 68.1 mol%. Strain DS-58T could be distinguished phenotypically from type strains of closely related species of the genus Lysobacter and phylogenetically from all members of the genus Lysobacter. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain DS-58T is considered to represent a novel species of the genus Lysobacter, for which the name Lysobacter dokdonensis sp. nov. is proposed. The type strain is DS-58T ( = KCTC 12822T  = DSM 17958T).

scholarly journals Flavobacterium nitrogenifigens sp. nov., isolated from switchgrass (Panicum virgatum)

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2803-2809 ◽  
Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
Jia Xu ◽  
Stefanie P. Glaeser
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Panicum Virgatum ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Type Strains ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

A yellow, nitrogen-fixing bacterial strain, NXU-44T, isolated from the rhizosphere of switchgrass (Panicum virgatum) in Auburn, Alabama, USA, was studied to determine its taxonomic position. Cells of the isolate were rod-shaped and Gram-stain-negative. A comparison of the 16S rRNA gene sequence with the sequences of the type strains of the most closely related species showed that the strain belongs to the genus Flavobacterium with highest sequence similarities to the type strains of Flavobacterium ginsenosidimutans (97.9 %), Flavobacterium phragmitis (97.6 %) and Flavobacterium anhuiense (97.5 %). The 16S rRNA gene sequence similarities to all other species of the genus Flavobacterium were below 97.5 %. The fatty acid profile of strain NXU-44T consisted of the major fatty acids iso-C15 : 0, iso-C15 : 0 2-OH/C16 : 1ω7c and iso-C17 : 0 3-OH. The major compounds in the polar lipid profile were phosphatidylethanolamine, phosphatidylserine, one aminolipid and two polar lipids. The quinone system was composed exclusively of menaquinone MK-6. The polyamine pattern contained the major compound sym-homospermidine and only minor amounts of other polyamines. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. These data and the differential biochemical and chemotaxonomic properties show that strain NXU-44T represents a novel species of the genus Flavobacterium for which the name Flavobacterium nitrogenifigens sp. nov. is proposed. The type strain is NXU-44T ( = LMG 28694T = CIP 110894T).

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