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 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).

scholarly journals Pantoea coffeiphila sp. nov., cause of the ‘potato taste’ of Arabica coffee from the African Great Lakes region

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 23-29 ◽  
Author(s):  
Dominique Gueule ◽  
Gérard Fourny ◽  
Elisabeth Ageron ◽  
Anne Le Flèche-Matéos ◽  
Mathias Vandenbogaert ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Gene Sequencing ◽  
Great Lakes Region ◽  
The Novel ◽  
Content Type ◽  
African Great Lakes ◽  
Link Type

Six isolates recovered from coffee seeds giving off a potato-like flavour were studied. Gene sequencing (rrs and rpoB) showed they belong to the genus Pantoea . By DNA–DNA hybridization, the isolates constituted a genomic species with less than 17 % relatedness to 96 strains representing enterobacterial species. Multilocus sequence analysis (gyrB, rpoB, atpD and infB genes) showed the isolates to represent a discrete species of the genus Pantoea . Nutritional versatility of the novel species was poor. The novel species is proposed as Pantoea coffeiphila sp.nov. and its type strain is Ca04T ( = CIP 110718T = DSM 28482T).

scholarly journals Lactobacillus similis sp. nov., isolated from fermented cane molasses

2010 ◽  
Vol 60 (1) ◽  
pp. 187-190 ◽  
Author(s):  
Maki Kitahara ◽  
Mitsuo Sakamoto ◽  
Yoshimi Benno
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Cane Molasses ◽  
Gene Sequence Analysis

The taxonomic position of strain JCM 2765T isolated from fermented cane molasses in Thailand was reinvestigated. Strain JCM 2765T was originally identified as representing Lactobacillus buchneri on the basis of biochemical and physiological characteristics. In the present study, 16S rRNA gene sequence analysis of strain JCM 2765T demonstrated a low level of similarity with the type strain of L. buchneri (92.5 %) and high levels with those of Lactobacillus collinoides (97.6 %) and Lactobacillus paracollinoides (98.0 %). Ribotyping was applied to investigate the relationships between strain JCM 2765T, L. collinoides and L. paracollinoides. The dendrogram based on ribotyping patterns showed one cluster for six strains of L. paracollinoides, and that strain JCM 2765T and L. collinoides JCM 1123T were each independent. Based on additional phenotypic findings and DNA–DNA hybridization results, strain JCM 2765T is considered to represent a novel species of the genus Lactobacillus, for which the name Lactobacillus similis sp. nov. is proposed. The type strain is JCM 2765T (=LMG 23904T).

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 Nesterenkonia sandarakina sp. nov. and Nesterenkonia lutea sp. nov., novel actinobacteria, and emended description of the genus Nesterenkonia

2005 ◽  
Vol 55 (1) ◽  
pp. 463-466 ◽  
Author(s):  
Wen-Jun Li ◽  
Hua-Hong Chen ◽  
Chang-Jin Kim ◽  
Yu-Qin Zhang ◽  
Dong-Jin Park ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Gene Sequence Analysis ◽  
Emended Description

Two novel actinobacteria isolates, designated YIM 70009T and YIM 70081T, were characterized in order to determine their taxonomic position. Cells of strains YIM 70009T and YIM 70081T were cocci, although only the latter were motile. The G+C contents of their DNAs were 64·0 and 64·5 mol%, respectively. On the basis of chemotaxonomic characteristics and 16S rRNA gene sequence analysis, the two isolates were classified in the genus Nesterenkonia. DNA–DNA hybridization and comparison of phenotypic characteristics revealed that strains YIM 70009T and YIM 70081T differed from each other and from known species. Therefore, it is proposed that they represent two separate novel species of the genus Nesterenkonia: Nesterenkonia sandarakina sp. nov. (type strain, YIM 70009T=CCTCC AA 203007T=DSM 15664T=KCTC 19011T) and Nesterenkonia lutea sp. nov. (type strain, YIM 70081T=CCTCC AA 203010T=DSM 15666T=KCTC 19013T).

scholarly journals Leptospira mayottensis sp. nov., a pathogenic species of the genus Leptospira isolated from humans

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4061-4067 ◽  
Author(s):  
Pascale Bourhy ◽  
Louis Collet ◽  
Sylvain Brisse ◽  
Mathieu Picardeau
Keyword(s):  
Sequence Analysis ◽  
Dna Hybridization ◽  
Genomic Dna ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type ◽  
Leptospira Borgpetersenii

A group of strains representing species of the genus Leptospira, isolated from patients with leptospirosis in Mayotte (Indian Ocean), were previously found to be considerably divergent from other known species of the genus Leptospira . This was inferred from sequence analysis of rrs (16S rRNA) and other genetic loci and suggests that they belong to a novel species. Two strains from each serogroup currently identified within this novel species were studied. Spirochaete, aerobic, motile, helix-shaped strains grew well at 30–37 °C, but not at 13 °C or in the presence of 8-azaguanine. Draft genomes of the strains were also analysed to study the DNA relatedness with other species of the genus Leptospira . The new isolates formed a distinct clade, which was most closely related to Leptospira borgpetersenii , in multilocus sequence analysis using concatenated sequences of the genes rpoB, recA, fusA, gyrB, leuS and sucA. Analysis of average nucleotide identity and genome-to-genome distances, which have recently been proposed as reliable substitutes for classical DNA–DNA hybridization, further confirmed that these isolates should be classified as representatives of a novel species. The G+C content of the genomic DNA was 39.5 mol%. These isolates are considered to represent a novel species, for which the name Leptospira mayottensis sp. nov. is proposed, with 200901116T ( = CIP 110703T = DSM 28999T) as the type strain.

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 Corynebacterium hansenii sp. nov., an α-glucosidase-negative bacterium related to Corynebacterium xerosis

2007 ◽  
Vol 57 (5) ◽  
pp. 1113-1116 ◽  
Author(s):  
François N. R. Renaud ◽  
Alain Le Coustumier ◽  
Nathalie Wilhem ◽  
Dominique Aubel ◽  
Philippe Riegel ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Carbon Assimilation ◽  
Rrna Gene ◽  
Negative Bacterium ◽  
16S Rrna Gene Sequences ◽  
Glucose Fermentation ◽  
Biochemical Characteristics ◽  
Hybridization Data

A novel strain, C-138T, belonging to the genus Corynebacterium was isolated from a severe thigh liposarcoma infection and its differentiation from Corynebacterium xerosis and Corynebacterium freneyi is described. Analysis of 16S rRNA gene sequences, rpoB sequences and the PCR profile of the 16S–23S spacer regions was not conclusive enough to differentiate strain C-138T from C. xerosis and C. freneyi. However, according to DNA–DNA hybridization data, strain C-138T constitutes a member of a distinct novel species. It can be differentiated from strains of C. xerosis and C. freneyi by colony morphology, the absence of α-glucosidase and some biochemical characteristics such as glucose fermentation at 42 °C and carbon assimilation substrates. The name Corynebacterium hansenii sp. nov. is proposed for this novel species; the type strain is C-138T (=CIP 108444T=CCUG 53252T).

Ogataea kolombanensis sp. nov., Ogataea histrianica sp. nov. and Ogataea deakii sp. nov., three novel yeast species from plant sources

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3115-3123 ◽  
Author(s):  
Neža Čadež ◽  
Dénes Dlauchy ◽  
Peter Raspor ◽  
Gábor Péter
Keyword(s):  
Sequence Analysis ◽  
Olive Oil ◽  
Type Strain ◽  
Yeast Species ◽  
Novel Species ◽  
Large Subunit ◽  
Virgin Olive Oil ◽  
Rrna Gene ◽  
Internal Transcribed Spacer Region ◽  
Lsu Rrna

Nine methanol-assimilating yeast strains isolated from olive oil sediments in Slovenia, extra virgin olive oil from Italy and rotten wood collected in Hungary were found to form three genetically separated groups, distinct from the currently recognized yeast species. Sequence analysis from genes of the small subunit (SSU) rRNA, internal transcribed spacer region/5.8S rRNA, large subunit (LSU) rRNA D1/D2 domains and translational elongation factor-1α (EF-1α) revealed that the three closely related groups represent three different undescribed yeast species. Sequence analysis of the LSU rRNA gene D1/D2 domains placed the novel species in the Ogataea clade. The three novel species are designated as Ogataea kolombanensis sp. nov. (type strain: ZIM 2322T = CBS 12778T = NRRL Y-63657T), Ogataea histrianica sp. nov. (type strain: ZIM 2463T = CBS 12779T = NRRL Y-63658T) and Ogataea deakii sp. nov. (type strain: NCAIM Y.01896T = CBS 12735T = NRRL Y-63656T).

scholarly journals Pseudovibrio japonicus sp. nov., isolated from coastal seawater in Japan

2007 ◽  
Vol 57 (9) ◽  
pp. 1952-1955 ◽  
Author(s):  
Shoichi Hosoya ◽  
Akira Yokota
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Biochemical Characteristics ◽  
Boso Peninsula ◽  
Coastal Seawater ◽  
Definition Of ◽  
Type Strains

A Gram-negative, motile, rod-shaped bacterium (WSF2T) was isolated from coastal seawater of the Boso Peninsula in Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain WSF2T represented a separate lineage within the genus Pseudovibrio. The DNA G+C content of strain WSF2T was 51.7 mol%. DNA–DNA hybridization values between strain WSF2T and the type strains of Pseudovibrio species were significantly lower than those accepted as the phylogenetic definition of a species. Furthermore, some biochemical characteristics indicated that strain WSF2T differed from other Pseudovibrio species. Based on these characteristics, it is proposed that the isolate represents a novel species, Pseudovibrio japonicus sp. nov. The type strain is WSF2T (=IAM 15442T=NCIMB 14279T=KCTC 12861T).

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