scholarly journals Veillonella montpellierensis sp. nov., a novel, anaerobic, Gram-negative coccus isolated from human clinical samples

2004 ◽  
Vol 54 (4) ◽  
pp. 1311-1316 ◽  
Author(s):  
Estelle Jumas-Bilak ◽  
Jean-Philippe Carlier ◽  
Hélène Jean-Pierre ◽  
Corinne Teyssier ◽  
Bernard Gay ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rdna ◽  
Type Strain ◽  
Novel Species ◽  
Rdna Sequence ◽  
Animal Origin ◽  
Clinical Samples ◽  
16S Rdna Sequence ◽  
Gram Negative ◽  
Human Samples

Three strains of a hitherto unknown, Gram-negative, anaerobic coccus were isolated from human samples. At the phenotypic level, the isolates displayed all the characteristics of bacteria belonging to the genus Veillonella. Sequence analysis revealed that the three strains shared >99·5 % similarity in 16S rDNA sequence and >98·4 % similarity in dnaK sequence. The three unknown strains formed a separate subclade that was clearly remote from Veillonella species of human and animal origin. Based on these results, the three strains were considered to represent a novel species within the genus Veillonella, for which the name Veillonella montpellierensis is proposed. The type strain of the species is ADV 281.99T (=CIP 107992T=CCUG 48299T).

Sphingomonas yabuuchiae sp. nov. and Brevundimonas nasdae sp. nov., isolated from the Russian space laboratory Mir

2004 ◽  
Vol 54 (3) ◽  
pp. 819-825 ◽  
Author(s):  
Ying Li ◽  
Yoshiaki Kawamura ◽  
Nagatoshi Fujiwara ◽  
Takashi Naka ◽  
Hongsheng Liu ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rdna ◽  
Related Species ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Biochemical Properties ◽  
Rdna Sequence ◽  
Rrna Gene ◽  
16S Rdna Sequence

On the basis of phenotypic and genotypic characteristics and 16S rRNA gene sequence analysis, novel species belonging to the genera Sphingomonas and Brevundimonas were identified from samples taken from the Russian space laboratory Mir. Strain A1-18T was isolated from the air. 16S rDNA sequence analysis showed that strain A1-18T formed a coherent cluster with Sphingomonas sanguinis, Sphingomonas parapaucimobilis, Sphingomonas paucimobilis and Sphingomonas roseiflava with sequence similarity of 97·5–98·6 %. Similar to other Sphingomonas species, the G+C content was 66·1 mol%, but DNA–DNA hybridization rates at optimal temperatures among these related species were only 24·7–51·7 %. Strain A1-18T can be differentiated biochemically from related species. Strain W1-2BT was isolated from condensation water. It forms a distinct lineage within the genus Brevundimonas, forming a coherent cluster with Brevundimonas vesicularis, Brevundimonas aurantiaca and Brevundimonas intermedia. 16S rDNA sequence similarities were 98·6–99·5 % and the G+C content was 66·5 mol%, similar to other Brevundimonas species, but DNA–DNA relatedness was only 50·2–54·8 %. Strain W1-2BT also showed some differential biochemical properties from its related species. A series of polyphasic taxonomic studies led to the proposal of two novel species, Sphingomonas yabuuchiae sp. nov. (type strain A1-18T=GTC 868T=JCM 11416T=DSM 14562T) and Brevundimonas nasdae sp. nov. (type strain W1-2BT=GTC 1043T=JCM 11415T=DSM 14572T).

scholarly journals Bacillus novalis sp. nov., Bacillus vireti sp. nov., Bacillus soli sp. nov., Bacillus bataviensis sp. nov. and Bacillus drentensis sp. nov., from the Drentse A grasslands

2004 ◽  
Vol 54 (1) ◽  
pp. 47-57 ◽  
Author(s):  
Jeroen Heyrman ◽  
Bram Vanparys ◽  
Niall A. Logan ◽  
An Balcaen ◽  
Marina Rodríguez-Díaz ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rdna ◽  
Type Strain ◽  
Biochemical Characterization ◽  
Agricultural Research ◽  
Research Area ◽  
Fatty Acid Analysis ◽  
Rdna Sequence ◽  
16S Rdna Sequence ◽  
16S Rdna Sequence Analysis

A group of 42 isolates were isolated from the soil of several disused hay fields, in the Drentse A agricultural research area (The Netherlands), that were taken out of production at different times. The group represents hitherto-uncultured Bacillus lineages that have previously been found, by a non-cultural method, to be predominant in soil. The strains were subjected to a polyphasic taxonomic study, including (GTG)5-PCR, 16S rDNA sequence analysis, DNA–DNA hybridizations, DNA base-ratio determination, fatty acid analysis and morphological and biochemical characterization. By comparing the groupings obtained by (GTG)5-PCR and 16S rDNA sequence analysis, six clusters of similar strains could be recognized. A DNA–DNA relatedness study showed that these clusters represented five novel genospecies. Further analysis supported the proposal of five novel species in the genus Bacillus, namely Bacillus novalis sp. nov. (type strain IDA3307T=R-15439T=LMG 21837T=DSM 15603T), Bacillus vireti sp. nov. (type strain IDA3632T=R-15447T=LMG 21834T=DSM 15602T), Bacillus soli sp. nov. (type strain IDA0086T=R-16300T=LMG 21838T=DSM 15604T), Bacillus bataviensis sp. nov. (type strain IDA1115T=R-16315T=LMG 21833T=DSM 15601T) and Bacillus drentensis sp. nov. (type strain IDA1967T=R-16337T=LMG 21831T=DSM 15600T).

Nocardia asiatica sp. nov., isolated from patients with nocardiosis in Japan and clinical specimens from Thailand

2004 ◽  
Vol 54 (1) ◽  
pp. 125-130 ◽  
Author(s):  
Akiko Kageyama ◽  
Natteewan Poonwan ◽  
Katsukiyo Yazawa ◽  
Yuzuru Mikami ◽  
Kazuko Nishimura
Keyword(s):  
Sequence Analysis ◽  
16S Rdna ◽  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Clinical Samples ◽  
Asian Countries ◽  
Clinical Specimens

Five strains isolated from two patients with nocardiosis in Japan and three clinical samples from Thailand were found to have morphological, biochemical and chemotaxonomic properties consistent with their classification in the genus Nocardia. DNA–DNA hybridization, coupled with sequence analysis of 16S rDNA, indicated that these strains belong to a novel species of the genus Nocardia, named Nocardia asiatica sp. nov. because the isolation sites were in Asian countries; the type strain is IFM 0245T (=NBRC 100129T=JCM 11892T=DSM 44668T).

scholarly journals Prevotella nanceiensis sp. nov., isolated from human clinical samples

2007 ◽  
Vol 57 (10) ◽  
pp. 2216-2220 ◽  
Author(s):  
C. Alauzet ◽  
F. Mory ◽  
J.-P. Carlier ◽  
H. Marchandin ◽  
E. Jumas-Bilak ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
16S Rrna ◽  
Type Strain ◽  
Novel Species ◽  
Clinical Samples ◽  
The Novel ◽  
Gram Negative ◽  
End Products ◽  
Type Strains

Three strains of anaerobic, non-pigmented, Gram-negative bacilli isolated from various human clinical samples were characterized in terms of phenotypic and genotypic tests, including sequence analysis of 16S rRNA and rpoB genes. The strains were most closely related to the type strains of Prevotella marshii and Prevotella shahii on the basis of both 16S rRNA (89.8 and 89.0 % identity, respectively) and rpoB gene sequences (83.1 and 82.8 % identity, respectively). Phylogenetic analysis showed that the isolates constituted a robust homogeneous group distinct from known species in the genus Prevotella. The rrn skeleton (as determined by PFGE) and the DNA G+C content, determined to be 39.4 mol% for strain LBN 293T, distinguished the novel isolates from the type strains of P. marshii and P. shahii. The three strains were saccharolytic and produced acetic, lactic and succinic acids as major metabolic end products. Polyphasic investigations supported the proposal of a novel species, Prevotella nanceiensis sp. nov., with LBN 293T (=AIP 261.03T =CIP 108993T =CCUG 54409T) as the type strain.

scholarly journals Salegentibacter holothuriorum sp. nov., isolated from the edible holothurian Apostichopus japonicus

2004 ◽  
Vol 54 (4) ◽  
pp. 1107-1110 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Makoto Suzuki ◽  
Marc Vancanneyt ◽  
Ilse Cleenwerck ◽  
Natalia V. Zhukova ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Type Strain ◽  
Novel Species ◽  
Apostichopus Japonicus ◽  
The Sea Of Japan ◽  
Strictly Aerobic ◽  
Dna Homology ◽  
16S Rdna Sequence ◽  
Gram Negative ◽  
16S Rdna Sequence Analysis

Strain KMM 3524T was isolated from the holothurian Apostichopus japonicus living in the Sea of Japan. The bacterial strain was pigmented, non-motile, Gram-negative, strictly aerobic and oxidase-, catalase- and β-galactosidase-positive. From the results of 16S rDNA sequence analysis, strain KMM 3524T was found to be related closely to Salegentibacter salegens (98·1 %). DNA–DNA homology between strains KMM 3524T and S. salegens DSM 5424T was 38 %; this showed clearly that the holothurian isolate KMM 3524T belongs to a novel species of the genus Salegentibacter for which the name Salegentibacter holothuriorum sp. nov. is proposed, with KMM 3524T (=NBRC 100249T=LMG 21968T) as the type strain.

scholarly journals Erratum to: Deodorization of pig slurry and characterization of bacterial diversity using 16S rDNA sequence analysis

2014 ◽  
Vol 52 (12) ◽  
pp. 1056-1056
Author(s):  
Ok-Hwa Hwang ◽  
Sebastian Raveendar ◽  
Young-Ju Kim ◽  
Ji-Hun Kim ◽  
Tae-Hun Kim ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Bacterial Diversity ◽  
16S Rdna ◽  
Rdna Sequence ◽  
Pig Slurry ◽  
16S Rdna Sequence ◽  
16S Rdna Sequence Analysis

scholarly journals Detection and 16S rDNA Sequence Analysis of a Bloom-forming Cyanobacterial Genus Microcystis

1998 ◽  
Vol 64 (5) ◽  
pp. 840-841 ◽  
Author(s):  
Ryuji Kondo ◽  
Manabu Komura ◽  
Shingo Hiroishi ◽  
Yoshihiko Hata
Keyword(s):  
Sequence Analysis ◽  
16S Rdna ◽  
Rdna Sequence ◽  
16S Rdna Sequence ◽  
16S Rdna Sequence Analysis ◽  
Cyanobacterial Genus

scholarly journals Identification of Genomic Heterogeneity among Lactococcus lactis Strains by Plasmid Profiling, PFGE and 16S rDNA Sequence Analysis

2014 ◽  
Vol 63 (2) ◽  
pp. 157-166 ◽  
Author(s):  
OZLEM GUNAY-ESIYOK ◽  
NEFISE AKCELIK ◽  
MUSTAFA AKCELIK
Keyword(s):  
Sequence Analysis ◽  
16S Rdna ◽  
Lactococcus Lactis ◽  
Molecular Size ◽  
Rdna Sequence ◽  
16S Rdna Sequence ◽  
16S Rdna Sequence Analysis ◽  
Major Cluster ◽  
Cluster A ◽  
Plasmid Profiling

Lactococcus lactis strains are used commonly as starters, which contribute to desirable flavour and texture properties known as strain-specific, in dairy industry. Genomic heterogeneity of 30 L. lactis strains originating from Turkey and characterized phenotypically were investigated in this study. Plasmid profiling, PFGE and 16S rDNA sequence analyses were performed to determine the genetic variability of strains. High degree of heterogeneity was detected among the L. lactis strains. Plasmid profiles of strains showed that compared to the plasmid free control strains, namely; L. lactis subsp. lactis IL1403 and L. lactis subsp. cremoris MG1614, all tested strains carried one to ten plasmids with molecular size ranging from 1.5 to 41.5kb. The fingerprints of strains obtained by PFGE from digestion with ApaI, SmaI and I-CeuI restriction endonucleases of chromosomal DNA's were compared with each other. All strains out of four were grouped into a large cluster A with at least 44% similarity level. The other four strains formed a minor duster B, distinctively different from major cluster A. PFGE results were confirmed by 16S rDNA sequence analysis and strains included in cluster B were identified as members of different species. These results suggested that morphologic and biochemical methods should be verified by reliable molecular approaches for the purpose of strain typing. Also, PFGE was found suitable to determine genomic differentiations among inter- and intra species.

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