scholarly journals Shimia isoporae sp. nov., isolated from the reef-building coral Isopora palifera

2011 ◽  
Vol 61 (4) ◽  
pp. 823-827 ◽  
Author(s):  
Ming-Hui Chen ◽  
Shih-Yi Sheu ◽  
Chaolun Allen Chen ◽  
Jih-Terng Wang ◽  
Wen-Ming Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Respiratory Quinone ◽  
Isopora Palifera

A bacterial strain, designated SW6T, was isolated from the reef-building coral Isopora palifera, collected from seawater off the coast of southern Taiwan, and characterized using a polyphasic taxonomic approach. Strain SW6T was Gram-negative, aerobic, beige coloured, rod-shaped and motile by monopolar flagella. 16S rRNA gene sequence studies showed that the strain clustered closely with Shimia marina JCM 13038T (97.9 % 16S rRNA gene sequence similarity). Strain SW6T required NaCl for growth and exhibited optimal growth at 25–30 °C and 3–4 % NaCl. The predominant cellular fatty acid was summed feature 8 (C18 : 1ω7c/C18 : 1ω6c; 64.1 %). The major respiratory quinone was ubiquinone Q-10 and the DNA G+C content was 54.9 mol%. The results of physiological and biochemical tests allowed clear phenotypic differentiation of this isolate from previously described species of the genus Shimia. It is evident from the genotypic, phenotypic and chemotaxonomic data that the new strain should be classified as a representative of a novel species in the genus Shimia. The name proposed for this taxon is Shimia isoporae sp. nov.; the type strain is SW6T ( = LMG 25377T = BCRC 80085T).

scholarly journals Effusibacillus dendaii sp. nov. isolated from farm soil

2021 ◽  
Author(s):  
Tomoyuki Konishi ◽  
Tomohiko Tamura ◽  
Toru Tobita ◽  
Saori Sakai ◽  
Namio Matsuda ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Genome Analyses

Abstract Gram-positive, rod-shaped, spore-forming, thermophilic, acidophilic bacterium, designated strain skT53T, was isolated from farm soil in Tokyo, Japan. The strain grew aerobically at 37–55°C (optimum 50°C) and pH 4.0–6.0 (optimum 5.0). Phylogenetic analysis of the 16S rRNA gene sequence showed that the isolate was most closely related to the type strain of Effusibacillus consociatus (94.3% similarity). The G + C content of the genomic DNA was 48.22 mol%. MK-7 was the predominant respiratory quinone. The major fatty acids were anteiso-C15:0, iso-C15:0, iso-C16:0 and C18:3ω6c. The results of phenotypic and chemotaxonomic, 16S rRNA gene sequence similarity, and whole genome analyses support strain skT53T as representing a novel species of Effusibacillus dendaii sp. nov. is proposed. The type strain is strain skT53T (= NBRC 114101T = TBRC 11241T).

scholarly journals Flavisolibacter ginsengiterrae gen. nov., sp. nov. and Flavisolibacter ginsengisoli sp. nov., isolated from ginseng cultivating soil

2007 ◽  
Vol 57 (8) ◽  
pp. 1834-1839 ◽  
Author(s):  
Min-Ho Yoon ◽  
Wan-Taek Im
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Separate Species

Two strains (Gsoil 492T and Gsoil 643T) isolated in Pocheon Province, South Korea, from soil used for ginseng cultivation were characterized using a polyphasic approach. Both isolates comprised Gram-negative, aerobic, non-motile, rod-shaped bacteria. They had similar chemotaxonomic characteristics, e.g. containing MK-7 as the major quinone, having a DNA G+C content in the range 42.5–43.3 mol% and possessing iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. A phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates formed a tight cluster with several uncultured bacterial clones and with the established genera Terrimonas, Niastella and Chitinophaga in the phylum Bacteroidetes but were clearly separate from these genera. The levels of 16S rRNA gene sequence similarity between the isolates and type strains of related genera ranged from 87.5 to 92.4 %. Furthermore, the results of physiological and biochemical tests allowed phenotypic differentiation of the isolates from phylogenetically closely related species with validly published names. The level of 16S rRNA gene sequence similarity between the two strains was 99.5 %, whereas the DNA–DNA relatedness value was 44 %, indicating that they represent separate species. On the basis of the polyphasic evidence, a novel genus, Flavisolibacter gen. nov., and two novel species, Flavisolibacter ginsengiterrae sp. nov. (type strain Gsoil 492T=KCTC 12656T=DSM 18136T) and Flavisolibacter ginsengisoli sp. nov. (type strain Gsoil 643T=KCTC 12657T=DSM 18119T), are proposed. Flavisolibacter ginsengiterrae is the type species of the genus.

Terrabacter terrae sp. nov., a novel actinomycete isolated from soil in Spain

2005 ◽  
Vol 55 (6) ◽  
pp. 2491-2495 ◽  
Author(s):  
Marta Montero-Barrientos ◽  
Raúl Rivas ◽  
Encarna Velázquez ◽  
Enrique Monte ◽  
Manuel G. Roig
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Bacterium Strain

A Gram-positive, aerobic, long-rod-shaped, non-spore-forming bacterium (strain PPLBT) was isolated from soil mixed with Iberian pig hair. This actinomycete showed keratinase activity in vitro when chicken feathers were added to the culture medium. Strain PPLBT was oxidase-negative and catalase-positive and produced lipase and esterase lipase. This actinomycete grew at 40 °C on nutrient agar and in the same medium containing 5 % (w/v) NaCl. Growth was observed with many different carbohydrates as the sole carbon source. On the basis of 16S rRNA gene sequence similarity, strain PPLBT was shown to belong to the genus Terrabacter of the family Intrasporangiaceae. Strain PPLBT showed 98·8 % 16S rRNA gene sequence similarity to Terrabacter tumescens. Chemotaxonomic data, such as the main ubiquinone (MK-8), the main polar lipids (phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylinositol) and the main fatty acids (i-C15 : 0, ai-C15 : 0, i-C16 : 0 and ai-C17 : 0) supported the affiliation of strain PPLBT to the genus Terrabacter. The G+C content of the DNA was 71 mol%. The results of DNA–DNA hybridization (36·6 % relatedness between Terrabacter tumescens and strain PPLBT) and physiological and biochemical tests suggested that strain PPLBT belongs to a novel species of the genus Terrabacter, for which the name Terrabacter terrae sp. nov. is proposed. The type strain is PPLBT (=CECT 3379T=LMG 22921T).

scholarly journals Sediminicola luteus gen. nov., sp. nov., a novel member of the family Flavobacteriaceae

2006 ◽  
Vol 56 (4) ◽  
pp. 841-845 ◽  
Author(s):  
Shams Tabrez Khan ◽  
Yasuyoshi Nakagawa ◽  
Shigeaki Harayama
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Golden Yellow ◽  
The Family

The taxonomic position of four Gram-negative, rod-shaped, golden-yellow-coloured bacteria isolated from marine sediments was determined. Analysis of the almost complete 16S rRNA gene sequences indicated that these isolates belong to the family Flavobacteriaceae. An unclassified bacterium, NBRC 15975, was found to be the closest relative, showing 16S rRNA gene sequence similarity of 93 %; other related genera shared only 87·9–90·5 % similarity. In contrast, the four isolates shared high levels of 16S rRNA gene sequence similarity (99·3–99·7 %) and high DNA–DNA reassociation values (93–104 %). The isolates could be differentiated phenotypically from other genera by the abilities to reduce nitrate and to degrade gelatin, casein and starch. The only respiratory quinone was MK-6, and the major fatty acids were iso-C15 : 0, iso-C15 : 1, anteiso-C15 : 0, iso-C17 : 1 ω9c and iso-C17 : 0 3-OH. The DNA G+C content was 38–40 mol%. Differentiating phenotypic characteristics and large phylogenetic distances between the isolates and previously published genera indicated that the isolates constitute a novel genus, for which the name Sediminicola gen. nov. is proposed. The type species is Sediminicola luteus sp. nov. (type strain CNI-3T=NBRC 100966T=LMG 23246T).

Actinoplanes couchii sp. nov.

2007 ◽  
Vol 57 (4) ◽  
pp. 721-724 ◽  
Author(s):  
Peter Kämpfer ◽  
Birgit Huber ◽  
Kathrin Thummes ◽  
Iris Grün-Wollny ◽  
Hans-Jürgen Busse
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Closely Related Species ◽  
Bacterium Strain

A Gram-positive bacterium, strain GW8-1761T, was isolated from soil close to the Marmore waterfalls, Terni, Italy. 16S rRNA gene sequence similarity studies showed that strain GW8-1761T belonged to the genus Actinoplanes, being most closely related to Actinoplanes italicus JCM 3165T (98.9 %), A. rectilineatus IFO 13941T (98.5 %), A. palleronii JCM 7626T (97.8 %), A. utahensis IFO 13244T (97.6 %) and A. cyaneus DSM 46137T (97.6 %). Strain GW8-1761T could be distinguished from any other Actinoplanes species with validly published names by 16S rRNA gene sequence similarity values of less than 97.5 %. Chemotaxonomic data [major menaquinone MK-9(H4); major polar lipids diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol, with phosphatidylcholine and aminoglycolipids absent; major fatty acids C15 : 0, C16 : 0, C16 : 0 iso, C17 : 1 ω8c and summed feature 3 (C16 : 1 ω7c and/or C15 : 0 iso 2-OH)] supported the affiliation of strain GW8-1761T to the genus Actinoplanes. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain GW8-1761T from the most closely related species. Strain GW8-1761T therefore merits species status, and we propose the name Actinoplanes couchii sp. nov., with the type strain GW8-1761T (=DSM 45050T=CIP 109316T).

scholarly journals Gracilibacillus ureilyticus sp. nov., a halotolerant bacterium from a saline–alkaline soil

2010 ◽  
Vol 60 (6) ◽  
pp. 1383-1386 ◽  
Author(s):  
Ying-Yi Huo ◽  
Xue-Wei Xu ◽  
Heng-Lin Cui ◽  
Min Wu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Alkaline Soil ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone

A Gram-stain-positive, halotolerant, neutrophilic, rod-shaped bacterium, strain MF38T, was isolated from a saline–alkaline soil in China and subjected to a polyphasic taxonomic characterization. The isolate grew in the presence of 0–15 % (w/v) NaCl and at pH 6.5–8.5; optimum growth was observed with 3.0 % (w/v) NaCl and at pH 7.0. Chemotaxonomic analysis showed menaquinone MK-7 as the predominant respiratory quinone and anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, C17 : 0 and C16 : 0 as major fatty acids. The genomic DNA G+C content was 35.3 mol%. 16S rRNA gene sequence similarities of strain MF38T with type strains of described Gracilibacillus species ranged from 95.3 to 97.7 %. Strain MF38T exhibited the closest phylogenetic affinity to the type strain of Gracilibacillus dipsosauri, with 97.7 % 16S rRNA gene sequence similarity. The DNA–DNA reassociation between strain MF38T and G. dipsosauri DSM 11125T was 45 %. On the basis of phenotypic and genotypic data, strain MF38T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus ureilyticus sp. nov. (type strain MF38T =CGMCC 1.7727T =JCM 15711T) is proposed.

scholarly journals Paenibacillus humicus sp. nov., isolated from poultry litter compost

2007 ◽  
Vol 57 (10) ◽  
pp. 2267-2271 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
Cátia Faria ◽  
M. Fernanda Nobre ◽  
Peter Schumann ◽  
Olga C. Nunes ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Poultry Litter ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Respiratory Quinone

Two bacterial strains, PC-142 and PC-147T, isolated from poultry litter compost, were characterized with respect to their phenetic and phylogenetic characteristics. The isolates were endospore-forming rods that were reddish in colour after Gram staining. They were catalase- and oxidase-positive, were able to degrade starch and gelatin and grew at 15–40 °C and pH 5.5–10.0. The predominant fatty acids were anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0, the major respiratory quinone was menaquinone MK-7, the cell-wall peptidoglycan was of the A1γ type and the G+C content of the DNA was 58 mol%. The 16S rRNA gene sequence analysis and phenetic characterization indicated that these organisms belong to the genus Paenibacillus, with Paenibacillus pasadenensis SAFN-007T as the closest phylogenetic neighbour (97.5 %). Strains PC-142, PC-147T and P. pasadenensis SAFN-007T represent a novel lineage within the genus Paenibacillus, characterized by a high DNA G+C content (58–63 mol%). The low levels of 16S rRNA gene sequence similarity with respect to other taxa with validly published names and the identification of distinctive phenetic features in the two isolates indicate that strains PC-142 and PC-147T represent a novel species of the genus Paenibacillus, for which the name Paenibacillus humicus sp. nov. is proposed. The type strain is PC-147T (=DSM 18784T =NBRC 102415T =LMG 23886T).

scholarly journals Streptococcus rupicaprae sp. nov., isolated from a Pyrenean chamois (Rupicapra pyrenaica)

2011 ◽  
Vol 61 (8) ◽  
pp. 1989-1993 ◽  
Author(s):  
A. I. Vela ◽  
G. Mentaberre ◽  
I. Marco ◽  
R. Velarde ◽  
S. Lavín ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Pyrenean Chamois

Biochemical and molecular genetic studies were performed on an unknown Gram-stain-positive, catalase-negative, coccus-shaped organism isolated from clinical samples of a Pyrenean chamois. The micro-organism was identified as a streptococcal species based on its cellular morphological and biochemical tests. 16S rRNA gene sequence comparison studies confirmed its identification as a member of the genus Streptococcus, but the organism did not correspond to any species of this genus. The nearest phylogenetic relative of the unknown coccus from chamois was Streptococcus ovis (95.9 % 16S rRNA gene sequence similarity). The rpoB and sodA sequence analysis showed sequence similarity values of less than 85.7 % and 83.0 %, respectively, with the currently recognized species of the genus Streptococcus. The novel bacterial isolate was distinguished from S. ovis and other species of the genus Streptococcus using biochemical tests. Based on both phenotypic and phylogenetic findings, it is proposed that the unknown bacterium be classified as a novel species of the genus Streptococcus, Streptococcus rupicaprae sp. nov., with the type strain 2777-2-07T ( = CECT 7718T  = CCUG 59652T).

scholarly journals Gulbenkiania mobilis gen. nov., sp. nov., isolated from treated municipal wastewater

2007 ◽  
Vol 57 (5) ◽  
pp. 1108-1112 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
M. Fernanda Nobre ◽  
Olga C. Nunes ◽  
Célia M. Manaia
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Municipal Wastewater ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Treated Municipal Wastewater

A bacterial strain (E4FC31T) isolated from treated municipal wastewater was characterized phenotypically and phylogenetically. Cells were Gram-negative, curved rods with a polar flagellum. The isolate was catalase-, oxidase- and arginine dihydrolase-positive, and able to grow between 15 and 45 °C and between pH 5.5 and 9.0. The predominant fatty acids were C16 : 1/iso-C15 : 0 2-OH and C16 : 0, the major respiratory quinone was ubiquinone 8 and the G+C content of the genomic DNA was 63 mol%. 16S rRNA gene sequence analysis indicated that strain E4FC31T belonged to the class Betaproteobacteria and was a member of the family Neisseriaceae. Its closest phylogenetic neighbours were Aquitalea magnusonii and Chromobacterium violaceum (<94 % 16S rRNA gene sequence similarity). Phylogenetic analysis and phenotypic characteristics of strain E4FC31T suggest that it represents a novel species of a new genus, for which the name Gulbenkiania mobilis gen. nov., sp. nov. is proposed. The type strain of Gulbenkiania mobilis is E4FC31T (=DSM 18507T=LMG 23770T).

scholarly journals Hansschlegelia zhihuaiae sp. nov., isolated from a polluted farmland soil

2011 ◽  
Vol 61 (5) ◽  
pp. 1114-1117 ◽  
Author(s):  
Ya Wen ◽  
Xing Huang ◽  
Yu Zhou ◽  
Qing Hong ◽  
Shunpeng Li
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Farmland Soil

A novel Gram-negative, aerobic, coccoid-shaped strain designated S 113T was isolated from a polluted-soil sample collected in Jiangsu Province, China. A polyphasic taxonomic study including phylogenetic analysis based on the 16S rRNA gene sequence and determination of phenotypic characteristics was performed on the new isolate. The highest 16S rRNA gene sequence similarity was 96.8 %, with Hansschlegelia plantiphila S1 T. The predominant respiratory quinone was ubiquinone 10 (Q-10). The major fatty acids were C18 : 1ω7c and C16 : 0. The G+C content of the DNA was about 65.7 mol%. DNA–DNA hybridization experiments showed 44.9 % relatedness for strain S 113T with its closest relative, H. plantiphila NCIMB 14035T. The dominant phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and phosphatidylcholine. The results of our polyphasic taxonomic analysis indicate that strain S 113T represents a novel species within the genus Hansschlegelia, for which the name Hansschlegelia zhihuaiae sp. nov. is proposed. The type strain is S 113T ( = DSM 18984T  = CCTCC AB 206143T  = KCTC 12880T).

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