scholarly journals Nocardia grenadensis sp. nov., isolated from sand of the Caribbean Sea

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 693-697 ◽  
Author(s):  
Peter Kämpfer ◽  
Nicole Lodders ◽  
Iris Grün-Wollny ◽  
Karin Martin ◽  
Hans-Jürgen Busse
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Caribbean Sea ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
The Caribbean

A Gram-stain-positive, non-spore-forming bacterium (GW5-5797T) was isolated on soil extract agar from sand collected at a depth of 5 m in the Caribbean Sea near Grenada. 16S rRNA gene sequence analysis and similarity studies showed that strain GW5-5797T belongs to the genus Nocardia, and is most closely related to Nocardia speluncae N2-11T (99.2 % similarity) and Nocardia jinanensis 04-5195T (99.2 %) and more distantly related to Nocardia rhamnosiphila 202GMOT (98.6 %) and other Nocardia species. Strain GW5-5797T could be distinguished from all other recognized Nocardia species by sequence similarity values less than 98.5 %. The peptidoglycan diamino acid was meso-diaminopimelic acid. Strain GW5-5797T exhibited a quinone system with the predominant compounds MK-8(H4ω-cyclo) and MK-8(H2). The polar lipid profile of GW5-5797T consisted of the major compounds diphosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid, moderate amounts of phosphatidylinositol and a phosphatidylinositol mannoside and minor amounts of several lipids including a second phosphatidylinositol mannoside. The polyamine pattern contained the major compound spermine and moderate amounts of spermidine. The major fatty acids were C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0. These chemotaxonomic traits are in excellent agreement with those of other Nocardia species. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain GW5-5797T from the most closely related species, showing 16S rRNA gene sequence similarities >98.5 %. Strain GW5-5797T therefore merits separate species status, and we propose the name Nocardia grenadensis sp. nov., with the type strain GW5-5797T ( = CCUG 60970T  = CIP 110294T).

scholarly journals Paenibacillus xinjiangensis sp. nov., isolated from Xinjiang province in China

2006 ◽  
Vol 56 (11) ◽  
pp. 2579-2582 ◽  
Author(s):  
Jee-Min Lim ◽  
Che Ok Jeon ◽  
Dong-Jin Park ◽  
Li-Hua Xu ◽  
Cheng-Lin Jiang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Sequence Similarities

Strain B538T is a Gram-positive, motile, rod-shaped bacterium, which was isolated from Xinjiang province in China. This organism grew optimally at 30–35 °C and pH 8.0–8.5. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B538T belonged to the genus Paenibacillus and chemotaxonomic data (DNA G+C content, 47.0 mol%; major isoprenoid quinone, MK-7; cell wall type, A1γ meso-diaminopimelic acid; major fatty acids, anteiso-C15 : 0 and C16 : 0) supported affiliation of the isolate with the genus Paenibacillus. Comparative 16S rRNA gene sequence analyses showed that the isolate was most closely related to Paenibacillus glycanilyticus DS-1T, with 16S rRNA gene sequence similarity of 98.1 %; sequence similarities to other members of the genus Paenibacillus used in the phylogenetic tree were less than 96.5 %. The DNA–DNA relatedness between strain B538T and P. glycanilyticus DS-1T was about 8.0 %. On the basis of physiological and molecular properties, strain B538T (=KCTC 3952T=DSM 16970T) is proposed as the type strain of a novel species within the genus Paenibacillus, for which the name Paenibacillus xinjiangensis sp. nov. is proposed.

scholarly journals Bacillus thermolactis sp. nov., isolated from dairy farms, and emended description of Bacillus thermoamylovorans

2011 ◽  
Vol 61 (8) ◽  
pp. 1954-1961 ◽  
Author(s):  
An Coorevits ◽  
Niall A. Logan ◽  
Anna E. Dinsdale ◽  
Gillian Halket ◽  
Patsy Scheldeman ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Emended Description

A polyphasic taxonomic study was performed on 22 thermotolerant, aerobic, endospore-forming bacteria from dairy environments. Seventeen isolates were retrieved from raw milk, one from a filter cloth and four from grass, straw or milking equipment. These latter four isolates (R-6546, R-7499, R-7764 and R-7440) were identified as Bacillus thermoamylovorans based on DNA–DNA hybridizations (values above 70 % with Bacillus thermoamylovorans LMG 18084T) but showed discrepancies in characteristics with the original species description, so an emended description of this species is given. According to 16S rRNA gene sequence analysis and DNA–DNA hybridization experiments, the remaining 18 isolates (R-6488T, R-28193, R-6491, R-6492, R-7336, R-33367, R-6486, R-6770, R-31288, R-28160, R-26358, R-7632, R-26955, R-26950, R-33520, R-6484, R-26954 and R-7165) represented one single species, most closely related to Bacillus thermoamylovorans (93.9 % 16S rRNA gene sequence similarity), for which the name Bacillus thermolactis is proposed. Cells were Gram-stain-positive, facultatively anaerobic, endospore-forming rods that grew optimally at 40–50 °C. The cell wall peptidoglycan type of strain R-6488T, the proposed type strain, was A1γ based on meso-diaminopimelic acid. Major fatty acids of the strains were C16 : 0 (28.0 %), iso-C16 : 0 (12.1 %) and iso-C15 : 0 (12.0 %). MK-7 was the predominant menaquinone, and major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and some unidentified phospholipids. DNA G+C content was 35.0 mol%. Phenotypic properties allowed discrimination from other thermotolerant species of the genus Bacillus and supported the description of the novel species Bacillus thermolactis, with strain R-6488T ( = LMG 25569T  = DSM 23332T) as the proposed type strain.

scholarly journals Oceanobacillus luteolus sp. nov., isolated from soil

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1495-1500 ◽  
Author(s):  
Min Wu ◽  
Guiqin Yang ◽  
Zhen Yu ◽  
Li Zhuang ◽  
Yingqiang Jin ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Two Gram-stain-positive, rod-shaped and endospore-forming bacteria, designated WM-1T and WM-4, were isolated from a paddy soil and a forest soil, respectively, in South China. Comparative 16S rRNA gene sequence analyses showed that both strains were members of the genus Oceanobacillus and most closely related to Oceanobacillus chironomi LMG 23627T with pairwise sequence similarity of 96.0 %. The isolates contained menaquinone-7 (MK-7) as the respiratory quinone and anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0 as the major fatty acids (>10 %). Polar lipids consisted of a predominance of diphosphatidylglycerol and moderate to minor amounts of phosphatidylglycerol and phosphatidylinositol. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The DNA G+C content was 38.6–39.2 mol%. The 16S rRNA gene sequence of strain WM-1T displayed 99.7 % similarity to that of strain WM-4, and DNA–DNA hybridization between the two strains showed a relatedness value of 91 %. Based on the results of this polyphasic study, strains WM-1T and WM-4 represent a novel species in the genus Oceanobacillus , for which the name Oceanobacillus luteolus sp. nov. is proposed. The type strain is WM-1T ( = KCTC 33119T = CGMCC 1.12406T).

scholarly journals Streptomyces coacervatus sp. nov., isolated from the intestinal tract of Armadillidium vulgare

2011 ◽  
Vol 61 (5) ◽  
pp. 1073-1077 ◽  
Author(s):  
Azusa Shibazaki ◽  
Yuta Omoto ◽  
Takuji Kudo ◽  
Takashi Yaguchi ◽  
Akihiro Saito ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Intestinal Tract ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Armadillidium Vulgare

A Gram-staining-positive bacterium, designated AS-0823T, which formed spiral spore chains on the aerial mycelium, was isolated from the intestinal tract of Armadillidium vulgare, a small terrestrial crustacean commonly found on the ground around houses in Japan. 16S rRNA gene sequence analysis showed that the isolate belonged to the genus Streptomyces and was most closely related to Streptomyces longisporus ISP 5166T (98.6 % 16S rRNA gene sequence similarity), Streptomyces curacoi NBRC 12761T (98.4 %) and Streptomyces griseoruber NBRC 12873T (98.4 %). The affiliation of strain AS-0823T to the genus Streptomyces was supported by chemotaxonomic data: iso-C16 : 0, anteiso-C15 : 0, C16 : 0, iso-C15 : 0 and anteiso-C17 : 0 as the major cellular fatty acids, ll-diaminopimelic acid as the characteristic diamino acid in the peptidoglycan and the absence of mycolic acids. DNA–DNA hybridization and physiological and biochemical analysis supported the differentiation of strain AS-0823T from S. longisporus JCM 4395T. Therefore, strain AS-0823T represents a novel species, for which the name Streptomyces coacervatus sp. nov. is proposed. The type strain is AS-0823T ( = IFM 11055T  = DSM 41983T  = JCM 17138T).

scholarly journals Marinobacterium halophilum sp. nov., a marine bacterium isolated from the Yellow Sea

2007 ◽  
Vol 57 (1) ◽  
pp. 77-80 ◽  
Author(s):  
Ho-Won Chang ◽  
Young-Do Nam ◽  
Hyuk-Yong Kwon ◽  
Ja Ryeong Park ◽  
Jung-Sook Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
The Yellow Sea ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Type Strains

A moderately halophilic, aerobic, Gram-negative bacterium was isolated from a tidal flat area of Dae-Chun, Chung-Nam, Korea. The strain, designated mano11T, comprised rod-shaped cells that were motile by means of polar flagella. It grew with 3–12 % NaCl and at 4–37 °C and pH 5.3–9.3. The predominant menaquinone present in this strain was MK-7 and diaminopimelic acid was not found in the cell-wall peptidoglycan. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain mano11T belongs to the genus Marinobacterium. Strain mano11T exhibited 92.8–98.3 % 16S rRNA gene sequence similarity when compared with the type strains of three other species of the genus Marinobacterium. DNA–DNA hybridization between strain mano11T and Marinobacterium georgiense DSM 11526T, its closest relative in terms of 16S rRNA gene sequence similarity, was 13 %. On the basis of the phenotypic, genetic and phylogenetic data, strain mano11T represents a novel species of the genus Marinobacterium, for which the name Marinobacterium halophilum sp. nov. is proposed. The type strain is mano11T (=KCTC 12240T=DSM 17586T).

scholarly journals Paenibacillus jilunlii sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Begonia semperflorens

2011 ◽  
Vol 61 (6) ◽  
pp. 1350-1355 ◽  
Author(s):  
Hao-Jie Jin ◽  
Yu-Guang Zhou ◽  
Hong-Can Liu ◽  
San-Feng Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Rrna Gene Sequence ◽  
Begonia Semperflorens

A nitrogen-fixing bacterium, designated strain Be17T, was isolated from rhizosphere soil of Begonia semperflorens planted in Beijing Botanical Garden, PR China. Phylogenetic analyses based on a segment of the nifH gene sequence and a full-length 16S rRNA gene sequence revealed that strain Be17T was a member of the genus Paenibacillus. High levels of 16S rRNA gene sequence similarity were found between strain Be17T and Paenibacillus graminis RSA19T (97.9 %), Paenibacillus sonchi LMG 24727T (97.8 %), Paenibacillus riograndensis CECT 7330T (96.2 %) and Paenibacillus borealis DSM 13188T (96.1 %), respectively. Levels of 16S rRNA gene sequence similarity between strain Be17T and the type strains of other recognized members of the genus Paenibacillus were below 96.0 %. However, the DNA–DNA hybridization values between strain Be17T and P. graminis RSA19T, P. sonchi LMG 24727T and P. riograndensis CECT 7330T were 47.9 %, 38.7 % and 37.5 %, respectively. The DNA G+C content of strain Be17T was 52.9 mol%. The major fatty acid component of strain Be17T was anteiso-branched C15 : 0 (30.92 %). The major isoprenoid quinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. On the basis of its phenotypic characteristics, 16S rRNA gene sequences, DNA G+C content, DNA–DNA relatedness, chemotaxonomic properties and nifH gene sequence, strain Be17T represents a nitrogen-fixing strain of a novel species of the genus Paenibacillus, for which the name Paenibacillus jilunlii sp. nov. is proposed. The type strain is Be17T ( = CGMCC 1.10239T = DSM 23019T).

scholarly journals Saccharopolyspora phatthalungensis sp. nov., isolated from rhizosphere soil of Hevea brasiliensis

2010 ◽  
Vol 60 (8) ◽  
pp. 1904-1908 ◽  
Author(s):  
Kannika Duangmal ◽  
Ratchanee Mingma ◽  
Arinthip Thamchaipenet ◽  
Atsuko Matsumoto ◽  
Yoko Takahashi
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Rhizosphere Soil ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties

The taxonomic position of a rhizosphere soil isolate, designated strain SR8.15T, was determined by using a polyphasic approach. Phylogenetic analysis based on an almost-complete 16S rRNA gene sequence of the strain showed that it formed a well-separated sub-branch within the radiation encompassing the genus Saccharopolyspora. Highest levels of 16S rRNA gene sequence similarity were found between strain SR8.15T and Saccharopolyspora shandongensis CGMCC 4.3530T (98.9 %) and Saccharopolyspora spinosa DSM 44228T (98.5 %). However, these strains shared low levels of DNA–DNA relatedness (<26 %). Strain SR8.15T had chemical characteristics consistent with its classification in the genus Saccharopolyspora. It contained meso-diaminopimelic acid as the diagnostic diamino acid. Whole-cell hydrolysates contained arabinose and galactose. The diagnostic phospholipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol. The main menaquinone was MK-9(H4). No mycolic acid was detected. The predominant cellular fatty acid was iso-C16 : 0. The G+C content of the genomic DNA of strain SR8.15T was 70.3 mol%. Strain SR8.15T had a phenotypic profile that readily distinguished it from recognized representatives of the genus Saccharopolyspora. It is evident from its combined genotypic and phenotypic properties that strain SR8.15T represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora phatthalungensis sp. nov. is proposed. The type strain is SR8.15T (=TISTR 1921T=BCC 35844T=NRRL B-24798T).

scholarly journals Pseudonocardia adelaidensis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of a grey box tree (Eucalyptus microcarpa)

2010 ◽  
Vol 60 (12) ◽  
pp. 2818-2822 ◽  
Author(s):  
Onuma Kaewkla ◽  
Christopher M. M. Franco
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Endophytic Actinobacterium

An aerobic, actinobacterial strain with rod-shaped spores, EUM 221T, which was isolated from the surface-sterilized stem of a grey box tree (Eucalyptus microcarpa), is described. Phylogenetic evaluation based on 16S rRNA gene sequence similarity showed that this isolate belongs to the family Pseudonocardiaceae, with the closest neighbour being Pseudonocardia zijingensis 6330T (98.7 %). The level of 16S rRNA gene sequence similarity between the isolate and species of the genus Pseudonocardia with validly published names ranged from 95 to 98 %. Chemotaxonomic data (meso-diaminopimelic acid; major menaquinone MK-8(H4); major fatty acid iso-C16 : 0) confirmed the affiliation of strain EUM 221T to the genus Pseudonocardia. The results of the phylogenetic analysis, including physiological and biochemical studies in combination with DNA–DNA hybridization, allowed the genotypic and phenotypic differentiation of strain EUM 221T from the closest described species. Therefore, this strain represented a novel species and the name proposed is Pseudonocardia adelaidensis sp. nov. The type strain is EUM 221T (=DSM 45352T =ACM 5286T).

scholarly journals Bacillus crescens sp. nov., isolated from soil

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2531-2536 ◽  
Author(s):  
Y. Shivani ◽  
Y. Subhash ◽  
P. Dave. Bharti ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Rrna Gene Sequence ◽  
Bacterial Strains

Two bacterial strains (JC247T and JC248) were isolated from soil samples collected from Rann of Kutch, Gujarat, India. Colonies of both strains were creamy white. Cells were Gram-stain-positive, rods-to-curved rods (crescent-shaped), and produced centrally located oval-shaped endospores. Major (>5 %) fatty acids of both strains were iso-C16  :  0, iso-C14  :  0, iso-C15  :  0, C16  :  1ω11c and C16  :  0, with minor ( < 5 but >1 %) amounts of anteiso-C15  :  0, anteiso-C17  :  0, iso-C16  :  1 H, iso-C17  :  0, iso-C18  :  0, C14  :  0, C17  :  0, C18  :  0, C18  :  1ω9c, iso-C17  :  1ω10c and anteiso-C17  :  0B/isoI. Diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids of both strains. Cell-wall amino acids were l-alanine, d-alanine, d-glutamic acid and meso-diaminopimelic acid. The genomic DNA G+C content of strains JC247T and JC248 was 48.2 and 48.1 mol%, respectively. Both strains were closely related with mean DNA–DNA hybridization >90 %. 16S rRNA gene sequence analysis of both strains indicated that they are members of the genus Bacillus within the family Bacillaceae of the phylum Firmicutes. Both strains had a 16S rRNA gene sequence similarity of 96.93 % with Bacillus firmus NCIMB 9366T and < 96.92 % with other members of the genus Bacillus. Sequence similarity between strain JC247T and JC248 was 100 %. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strains JC247T and JC248 as representatives of a novel species of the genus Bacillus, for which the name Bacillus crescens sp. nov. is proposed. The type strain is JC247T ( = KCTC 33627T = LMG 28608T).

scholarly journals Nocardioides daedukensis sp. nov., a halotolerant bacterium isolated from soil

2010 ◽  
Vol 60 (6) ◽  
pp. 1334-1338 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Sooyeon Park ◽  
So-Jung Kang ◽  
Jung-Sook Lee ◽  
Keun Chul Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties

A Gram-positive, non-motile and rod- or coccoid-shaped bacterial strain, MDN22T, was isolated from a soil sample from Korea. Strain MDN22T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 0–0.5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain MDN22T was phylogenetically most closely related to the genera Nocardioides and Marmoricola. In the neighbour-joining phylogenetic tree, strain MDN22T was most closely related to Nocardioides jensenii KCTC 9134T, with which it exhibited 98.3 % 16S rRNA gene sequence similarity. The strain exhibited 93.1–96.9 % and 95.3–95.9 % 16S rRNA gene sequence similarities to the type strains of other species of the genera Nocardioides and Marmoricola, respectively. The chemotaxonomic properties of strain MDN22T were consistent with those of the genus Nocardioides; the cell-wall peptidoglycan type was based on ll-2,6-diaminopimelic acid, the predominant menaquinone was MK-8(H4) and the major fatty acids were iso-C16 : 0 and C17 : 1. The DNA G+C content was 68.7 mol%. DNA–DNA relatedness data and differential phenotypic properties suggested that strain MDN22T could be differentiated from N. jensenii and Nocardioides dubius. On the basis of the data obtained, strain MDN22T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides daedukensis sp. nov., is proposed. The type strain is MDN22T (=KCTC 19601T=CCUG 57505T).

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