scholarly journals Taxonomic variation in the Mycobacterium fortuitum third biovariant complex: description of Mycobacterium boenickei sp. nov., Mycobacterium houstonense sp. nov., Mycobacterium neworleansense sp. nov. and Mycobacterium brisbanense sp. nov. and recognition of Mycobacterium porcinum from human clinical isolates

2004 ◽  
Vol 54 (5) ◽  
pp. 1653-1667 ◽  
Author(s):  
Mark F. Schinsky ◽  
Roger E. Morey ◽  
Arnold G. Steigerwalt ◽  
Michael P. Douglas ◽  
Rebecca W. Wilson ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Respiratory Infections ◽  
Restriction Analysis ◽  
Rrna Gene ◽  
Mycobacterium Fortuitum ◽  
Genetic Groups ◽  
Gene Sequence Analysis ◽  
Pcr Rflp ◽  
Disseminated Disease ◽  
Type Strains

The Mycobacterium fortuitum third biovariant complex (sorbitol-negative and sorbitol-positive) contains unnamed taxa first characterized in 1991. These organisms can cause respiratory infections, a spectrum of soft tissue and skeletal infections, bacteraemia and disseminated disease. To evaluate this group of organisms, clinical reference isolates and the type strains of M. fortuitum third biovariant complex sorbitol-negative (n=21), M. fortuitum third biovariant complex sorbitol-positive (n=3), M. fortuitum (n=3), Mycobacterium peregrinum (pipemidic acid-susceptible) (n=1), Mycobacterium porcinum (n=1), Mycobacterium senegalense (n=2) and Mycobacterium septicum (n=1) were characterized by using conventional phenotypic (morphological, physiological and antimicrobial susceptibilities), chemotaxonomic (HPLC and cellular fatty acids) and genotypic [RFLP of the rRNA gene (ribotyping), PCR-RFLP of a 439 bp segment of the 65 kDa hsp gene (PCR restriction analysis) and 16S rRNA gene sequence] analysis, DNA G+C content and DNA–DNA relatedness analyses. The results of these studies indicated that the strains comprised M. porcinum (n=13), M. septicum (n=1) and four novel closely related genetic groups within the M. fortuitum third biovariant complex: Mycobacterium boenickei sp. nov. (n=6), Mycobacterium houstonense sp. nov. (n=2), Mycobacterium neworleansense sp. nov. (n=1) and Mycobacterium brisbanense sp. nov. (n=1), with type strains ATCC 49935T (=W5998T=DSM 44677T), ATCC 49403T (=W5198T=DSM 44676T) ATCC 49404T (=W6705T=DSM 44679T) and ATCC 49938T (=W6743T=DSM 44680T), respectively.

scholarly journals Novosphingobium gossypii sp. nov., isolated from Gossypium hirsutum

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2831-2837 ◽  
Author(s):  
Peter Kämpfer ◽  
Karin Martin ◽  
John A. McInroy ◽  
Stefanie P. Glaeser
Keyword(s):  
Gossypium Hirsutum ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
High Sequence Similarity ◽  
Polar Lipid Profile ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Type Strains ◽  
Sequence Similarities

A Gram-stain-negative, rod-shaped, non-spore-forming bacterium (strain JM-1396T) producing a yellow pigment, was isolated from the healthy internal stem tissue of post-harvest cotton (Gossypium hirsutum, cultivar ‘DES-119’) grown at the Plant Breeding Unit at the E. V. Smith Research Center in Tallassee (Macon county), AL, USA. 16S rRNA gene sequence analysis of strain JM-1396T showed high sequence similarity values to the type strains of Novosphingobium mathurense, Novosphingobium panipatense (both 98.6 %) and Novosphingobium barchaimii (98.5 %); sequence similarities to all other type strains of species of the genus Novosphingobium were below 98.3 %. DNA–DNA pairing experiments of the DNA of strain JM-1396T and N. mathurense SM117T, N. panipatense SM16T and N. barchaimii DSM 25411T showed low relatedness values of 8 % (reciprocal 7 %), 24 % (reciprocal 26 %) and 19 % (reciprocal 25 %), respectively. Ubiquinone Q-10 was detected as the dominant quinone; the fatty acids C18 : 1ω7c (71.0 %) and the typical 2-hydroxy fatty acid, C14 : 0 2-OH (11.7 %), were detected as typical components. The polar lipid profile contained the diagnostic lipids diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. The polyamine pattern contained the major compound spermidine and only minor amounts of other polyamines. All these data revealed that strain JM-1396T represents a novel species of the genus Novosphingobium. For this reason we propose the name Novosphingobium gossypii sp. nov. with the type strain JM-1396T ( = LMG 28605T = CCM 8569T = CIP 110884T).

Terrabacter carboxydivorans sp. nov., a carbon monoxide-oxidizing actinomycete

2011 ◽  
Vol 61 (3) ◽  
pp. 482-486 ◽  
Author(s):  
Sung M. Kim ◽  
Sae W. Park ◽  
Sang T. Park ◽  
Young M. Kim
Keyword(s):  
Carbon Monoxide ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Gene Sequence Analysis ◽  
Diamino Acid ◽  
Type Strains

A bacterial strain, PY2T, capable of oxidizing carbon monoxide, was isolated from a soil sample collected from a roadside at Yonsei University, Seoul, Korea. On the basis of 16S rRNA gene sequence analysis, strain PY2T was shown to belong to the genus Terrabacter and was most closely related to Terrabacter lapilli LR-26T (99.1 % similarity). Strain PY2T was characterized chemotaxonomically as having iso-C15 : 0 as the predominant fatty acid, MK-8(H4) as the major menaquinone, ll-diaminopimelic acid as the diagnostic diamino acid of the cell wall, as possessing a polar lipid profile that included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and unknown amino-containing phosphoglycolipids, and having a DNA G+C content of 75.6 mol%. DNA–DNA relatedness values between strain PY2T and the type strains of T. lapilli, Terrabacter tumescens, Terrabacter terrae and Terrabacter aerolatus were 20.0 %, 22.9 %, 35.9 % and 64.5 %, respectively. Based on the combined evidence from the phylogenetic analyses, chemotaxonomic data and DNA–DNA hybridization experiments, it is proposed that strain PY2T represents a novel species for which the name Terrabacter carboxydivorans sp. nov. is proposed. The type strain is PY2T (=KCCM 42922T=JCM 16259T).

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 Marinomonas ostreistagni sp. nov., isolated from a pearl-oyster culture pond in Sanya, Hainan Province, China

2006 ◽  
Vol 56 (10) ◽  
pp. 2271-2275 ◽  
Author(s):  
Ken W. K. Lau ◽  
Jianping Ren ◽  
Natalie L. M. Wai ◽  
Simon C. L. Lau ◽  
Pei-Yuan Qian ◽  
...  
Keyword(s):  
Marine Bacterium ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Pearl Oyster ◽  
Rrna Gene ◽  
Hainan Province ◽  
Oyster Culture ◽  
Gene Sequence Analysis ◽  
Type Strains

A Gram-negative, aerobic, halophilic, neutrophilic, rod-shaped, non-pigmented, polar-flagellated bacterium, UST010306-043T, was isolated from a pearl-oyster culture pond in Sanya, Hainan Province, China in January 2001. This marine bacterium had an optimum temperature for growth of between 33 and 37 °C. On the basis of 16S rRNA gene sequence analysis, the strain was closely related to Marinomonas aquimarina and Marinomonas communis, with 97.5–97.7 and 97.1 % sequence similarity, respectively. Levels of DNA–DNA relatedness to the type strains of these species were well below 70 %. Analyses of phylogenetic, phenotypic and chemotaxomonic characteristics showed that strain UST010306-043T was distinct from currently established Marinomonas species. A novel species with the name Marinomonas ostreistagni sp. nov. is proposed to accommodate this bacterium, with strain UST010306-043T (=JCM 13672T=NRRL B-41433T) as the type strain.

scholarly journals Paenibacillus chungangensis sp. nov., isolated from a tidal-flat sediment

2011 ◽  
Vol 61 (2) ◽  
pp. 281-285 ◽  
Author(s):  
Mi-Hak Park ◽  
Jitsopin Traiwan ◽  
Min Young Jung ◽  
Yun Sung Nam ◽  
Ji Hoon Jeong ◽  
...  
Keyword(s):  
Tidal Flat ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Tidal Flat Sediment ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Type Strains

A Gram-stain-positive, rod-shaped, endospore-forming bacterium, strain CAU 9038T, was isolated from a tidal-flat sediment of DaeYiJac Island, Republic of Korea, and its taxonomic position was investigated using a polyphasic approach. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol, the major isoprenoid quinone was MK-7 and the dominant cellular fatty acid was anteiso-C15 : 0. The DNA G+C content was 51.6 mol%. 16S rRNA gene sequence analysis showed that the strain belonged to the genus Paenibacillus, with <96.1 % sequence similarity to type strains of Paenibacillus species with validly published names. The most closely related type strains to CAU 9038T were Paenibacillus thailandensis S3-4AT (96.1 % similarity) and Paenibacillus agaridevorans DSM 1355T (95.3 %). The phenotypic, chemotaxonomic and genotypic data clearly indicated that strain CAU 9038T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus chungangensis sp. nov. is proposed. The type strain is CAU 9038T (=KCTC 13717T =CCUG 59129T).

scholarly journals Gordonia neofelifaecis sp. nov., a cholesterol side-chain-cleaving actinomycete isolated from the faeces of Neofelis nebulosa

2011 ◽  
Vol 61 (1) ◽  
pp. 165-169 ◽  
Author(s):  
Yuchang Liu ◽  
Fanglan Ge ◽  
Guiying Chen ◽  
Wei Li ◽  
Pingmei Ma ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Sequence Similarity ◽  
Side Chain ◽  
Rrna Gene ◽  
The Novel ◽  
Nearest Neighbours ◽  
Gene Sequence Analysis ◽  
Neofelis Nebulosa ◽  
Taxonomic Approach ◽  
Type Strains

A cholesterol side-chain-cleaving bacterial strain, AD-6T, was isolated from fresh faeces of a clouded leopard (Neofelis nebulosa) and was studied using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis showed that the novel strain formed a distinct subline within the genus Gordonia, its closest neighbours being the type strains of Gordonia cholesterolivorans, Gordonia sihwensis and Gordonia hydrophobica, with sequence similarity values of 98.2, 97.8 and 97.6 %, respectively. The gyrB gene sequence of strain AD-6T exhibited similarities of 77–91 % with those of the type strains of recognized species of the genus Gordonia, being most similar to the type strains of G. sihwensis, G. hydrophobica and Gordonia hirsuta (91, 87 and 84 % similarity, respectively). The results of whole-cell fatty acid analyses and DNA–DNA relatedness data readily distinguished the new isolate from its nearest neighbours. Strain AD-6T is therefore considered to represent a novel species of the genus Gordonia, for which the name Gordonia neofelifaecis sp. nov. is proposed. The type strain is AD-6T (=NRRL B-59395T=CCTCC AB-209144T).

scholarly journals Kocuria atrinae sp. nov., isolated from traditional Korean fermented seafood

2010 ◽  
Vol 60 (4) ◽  
pp. 914-918 ◽  
Author(s):  
Eun-Jin Park ◽  
Min-Soo Kim ◽  
Seong Woon Roh ◽  
Mi-Ja Jung ◽  
Jin-Woo Bae
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Cellular Fatty Acids ◽  
Gene Sequence Analysis ◽  
Kocuria Rosea ◽  
Type Strains ◽  
Kocuria Rhizophila

A novel actinobacterium, strain P30T, was isolated from jeotgal, a traditional Korean fermented seafood. Cells were aerobic, Gram-positive, non-motile and coccoid. Optimal growth occurred at 30–37 °C, at pH 8–9 and in the presence of 0–2 % (w/v) NaCl. Based on 16S rRNA gene sequence analysis, strain P30T was phylogenetically closely related to Kocuria carniphila, Kocuria gwangalliensis, Kocuria rhizophila, Kocuria marina, Kocuria rosea and K. varians with levels of similarity of 98.6, 98.2, 98.1, 97.4, 97.3 and 97.3 %, respectively, to the type strains of these species. Levels of DNA–DNA relatedness between strain P30T and the type strains of K. carniphila, K. rhizophila, K. marina, K. rosea and K. varians were 37, 43, 37, 25 and 17 %, respectively. The predominant menaquinone of strain P30T was MK-7. Major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0. The genomic DNA G+C content of strain P30T was 70.2 mol%. Based on these data, strain P30T is considered to represent a novel species of the genus Kocuria, for which the name Kocuria atrinae sp. nov. is proposed. The type strain is P30T (=KCTC 19594T=JCM 15914T).

scholarly journals Pseudomonas pohangensis sp. nov., isolated from seashore sand in Korea

2006 ◽  
Vol 56 (9) ◽  
pp. 2153-2156 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Seung-Hee Yoo ◽  
Youn-Kyung Baek ◽  
Seon-Young Lee ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Novel Bacterium ◽  
Gene Sequence Analysis ◽  
Seashore Sand ◽  
Type Strains ◽  
Sequence Similarities

A novel bacterium, designated strain H3-R18T, was isolated from seashore sand collected from Homi cape, Pohang city, Korea. Cells were Gram-negative, aerobic, non-motile, cream-coloured, mesophilic and slightly halotolerant. 16S rRNA gene sequence analysis indicated that the organism was a member of the genus Pseudomonas, but the sequence showed ⩽96.3 % sequence similarity to that of the type strains of all recognized Pseudomonas species. Highest sequence similarities were to Pseudomonas brenneri CFML 97-391T (96.3 %) and Pseudomonas migulae CIP 105470T (96.3 %). The major fatty acids were summed feature 3 and C16 : 0, with lesser amounts of C12 : 0, C12 : 0 3-OH, C18 : 1ω7c and C14 : 0. The major isoprenoid quinone was Q-9. The DNA G+C content was 64.0 mol%. The phylogenetic, phenotypic and genetic properties of strain H3-R18T suggest that it represents a novel species, for which the name Pseudomonas pohangensis sp. nov. is proposed. The type strain is H3-R18T (=KACC 11517T=DSM 17875T).

scholarly journals Lysinibacillus macroides sp. nov., nom. rev.

2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1121-1127 ◽  
Author(s):  
An Coorevits ◽  
Anna E. Dinsdale ◽  
Jeroen Heyrman ◽  
Peter Schumann ◽  
Anita Van Landschoot ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Cow Dung ◽  
Rrna Gene ◽  
Pairwise Similarity ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Type Strains

‘Bacillus macroides’ ATCC 12905T ( = DSM 54T = LMG 18474T), isolated in 1947 from cow dung, was not included in the Approved Lists of Bacterial Names and so it lost standing in bacteriological nomenclature. Reinvestigation of the strain, including DNA–DNA relatedness experiments, revealed that ‘Bacillus macroides’ is genomically distinct from its closest relatives Lysinibacillus xylanilyticus , Lysinibacillus boronitolerans and Lysinibacillus fusiformis (as determined by 16S rRNA gene sequence analysis, with pairwise similarity values of 99.2, 98.8 and 98.5 %, respectively, with the type strains of these species). Further analysis showed that ‘Bacillus macroides’ shares the A4α l-Lys–d-Asp peptidoglycan type with other members of the genus Lysinibacillus and can thus be attributed to this genus. These results, combined with additional phenotypic data, justify the description of strain LMG 18474T ( = DSM 54T = ATCC 12905T) as Lysinibacillus macroides sp. nov., nom. rev.

scholarly journals Flavobacterium algicola sp. nov., isolated from marine algae

2010 ◽  
Vol 60 (2) ◽  
pp. 344-348 ◽  
Author(s):  
Mika Miyashita ◽  
Shuki Fujimura ◽  
Yasuyoshi Nakagawa ◽  
Makoto Nishizawa ◽  
Noboru Tomizuka ◽  
...  
Keyword(s):  
Marine Algae ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Respiratory Quinone ◽  
Gram Staining ◽  
Gene Sequence Analysis ◽  
Major Respiratory Quinone ◽  
Type Strains ◽  
Sequence Similarities

A rod-shaped Gram-staining-negative, non-motile, aerobic and fucoidan-digesting strain, designated TC2T, was isolated from marine algae collected from the coast of the Sea of Okhotsk at Abashiri, Hokkaido, Japan. The bacterium formed yellow, translucent, circular and convex colonies. Comparative 16S rRNA gene sequence analysis indicated that the strain belonged to the genus Flavobacterium, with the highest sequence similarities of 97.1 to 97.3 % to the type strains of Flavobacterium frigidarium, Flavobacterium frigoris, Flavobacterium limicola and Flavobacterium psychrolimnae. DNA–DNA relatedness values between strain TC2T and the above-mentioned species were lower than 28 %. The genomic DNA G+C content was 33.9 mol%. The major respiratory quinone was menaquinone-6 and the predominant fatty acids were iso-C15 : 1 G, iso-C15 : 0, iso-C15 : 0 3-OH and summed feature 3 (which comprises iso-C15 : 0 2-OH and/or C16 : 1 ω7c). Strain TC2T could be differentiated from related species by several phenotypic characteristics. Thus, on the basis of these results, strain TC2T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium algicola sp. nov. is proposed. The type strain is TC2T (=NBRC 102673T =CIP 109574T).

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