scholarly journals Transfer of Pantoea citrea, Pantoea punctata and Pantoea terrea to the genus Tatumella emend. as Tatumella citrea comb. nov., Tatumella punctata comb. nov. and Tatumella terrea comb. nov. and description of Tatumella morbirosei sp. nov.

2010 ◽  
Vol 60 (3) ◽  
pp. 484-494 ◽  
Author(s):  
Carrie L. Brady ◽  
Stephanus N. Venter ◽  
Ilse Cleenwerck ◽  
Katrien Vandemeulebroecke ◽  
Paul De Vos ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Dna Hybridization ◽  
Type Strain ◽  
Branch Length ◽  
Rrna Gene ◽  
Phylogenetic Distance ◽  
Japanese Species ◽  
Separate Species ◽  
Hybridization Data ◽  
Phenotypic Tests

Pantoea citrea, Pantoea punctata and Pantoea terrea were described for strains isolated from fruit and soil originating in Japan. These three ‘Japanese’ species have been shown to be phylogenetically distant from other species of the genus Pantoea. It has been observed previously that, using multilocus sequence analysis (MLSA), the ‘Japanese’ species consistently formed a distinct clade with an extended branch length, casting doubt on the inclusion of these species within the genus Pantoea. Furthermore, the ‘Japanese’ species are closely related to Tatumella ptyseos, strains of which originate from human clinical specimens. DNA–DNA hybridization and phenotypic tests confirmed the observed phylogenetic distance of P. citrea, P. punctata and P. terrea from the genus Pantoea and the affiliation of these species with Tatumella. In addition, strains causing pink disease of pineapple, identified previously as P. citrea, were shown to represent a separate species by using 16S rRNA gene sequence analysis, and MLSA and DNA–DNA hybridization data. The name Tatumella morbirosei sp. nov. with the type strain LMG 23360T (=BD 878T=NCPPB 4036T=CMC6T) is proposed to accommodate these strains. The new combinations Tatumella citrea (Kageyama et al. 1992) comb. nov. (type strain, SHS 2003T=ATCC 31623T=BD 875T=CCUG 30156T=CIP 105599T=DSM 13699T=JCM 8882T=LMG 22049T), Tatumella punctata (Kageyama et al. 1992) comb. nov. (type strain, SHS 2006T=ATCC 31626T=BD 876T=CCUG 30159T=CIP 105598T=DSM 13700T=JCM 8885T=LMG 22050T) and Tatumella terrea (Kageyama et al. 1992) comb. nov. (type strain, SHS 2008T=ATCC 31628T=BD 877T=CCUG 30161T=CIP 105600T=DSM 13701T=JCM 8887T=LMG 22051T) are proposed for P. citrea, P. punctata and P. terrea, respectively.

Descriptions of Actinoplanes ianthinogenes nom. rev. and Actinoplanes octamycinicus corrig. comb. nov., nom. rev.

2011 ◽  
Vol 61 (12) ◽  
pp. 2916-2921 ◽  
Author(s):  
Tomohiko Tamura ◽  
Yuumi Ishida ◽  
Ken-ichiro Suzuki
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Separate Species ◽  
Hybridization Data ◽  
The Family ◽  
The Status ◽  
Rrna Gene Sequencing

Phylogenetic analysis of ‘Actinoplanes ianthinogenes’ Coronelli et al. 1974 and ‘Actinoplanes ianthinogenes subsp. octamycini’ Gauze et al. 1979 based on 16S rRNA gene sequencing data revealed that these organisms form a clade in the family Micromonosporaceae. Morphological and chemotaxonomic characteristics of strains of these species were consistent with those of members of the genus Actinoplanes. Morphological, DNA–DNA hybridization, physiological, biochemical and chemotaxonomic data showed that ‘A. ianthinogenes’ and ‘A. ianthinogenes subsp. octamycini’ can be easily differentiated from each other and that they merit separate species status. On the basis of morphological, physiological, biochemical, chemotaxonomic and DNA–DNA hybridization data, it is concluded that ‘A. ianthinogenes’ and ‘A. ianthinogenes subsp. octamycini’ should be assigned the status of two novel species: Actinoplanes ianthinogenes nom. rev. (type strain NBRC 13996T = A/1668T = ATCC 21884T = BCRC 13611T = DSM 43864T = IMSNU 20032T = JCM 3249T = KCTC 9347T = KCTC 9592T = NCIMB 12639T = NRRL B-16720T) and Actinoplanes octamycinicus corrig. comb. nov., nom. rev. (type strain NBRC 14524T = INA 4041T = ATCC 43632T = JCM 9649T = KCTC 9593T), respectively.

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).

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).

scholarly journals Emendation of the genus Flammeovirga and Flammeovirga aprica with the proposal of Flammeovirga arenaria nom. rev., comb. nov. and Flammeovirga yaeyamensis sp. nov.

2006 ◽  
Vol 56 (9) ◽  
pp. 2095-2100 ◽  
Author(s):  
Mai Takahashi ◽  
Ken-ichiro Suzuki ◽  
Yasuyoshi Nakagawa
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Sequence Analyses ◽  
Separate Species ◽  
Taxonomic Approach

The taxonomic positions of five bacterial strains isolated from the Yaeyama Islands of Japan and ‘Microscilla arenaria’ NBRC 15982 were determined using a polyphasic taxonomic approach. 16S rRNA gene sequence analyses placed all of the strains close to the genus Flammeovirga. DNA–DNA hybridization studies, biochemical and physiological characterizations and chemotaxonomic analyses suggested that ‘M. arenaria’ NBRC 15982 and the five novel isolates represented two separate species of the genus Flammeovirga. Emendation of the genus Flammeovirga Nakagawa et al. 1997 and the species Flammeovirga aprica (Reichenbach 1989) Nakagawa et al. 1997 is proposed. In addition, ‘Microscilla arenaria’ Lewin 1969 is proposed as Flammeovirga arenaria nom. rev., comb. nov. (with the type strain NBRC 15982T=CIP 109101T) and the novel isolates are proposed as Flammeovirga yaeyamensis sp. nov. (type strain IR25-3T=NBRC 100898T=CIP 109099T).

scholarly journals Niastella koreensis gen. nov., sp. nov. and Niastella yeongjuensis sp. nov., novel members of the phylum Bacteroidetes, isolated from soil cultivated with Korean ginseng

2006 ◽  
Vol 56 (8) ◽  
pp. 1777-1782 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Seung-Hee Yoo ◽  
Seon-Young Lee ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Separate Species ◽  
Phenotypic Data ◽  
Species Type ◽  
Korean Ginseng

Two novel strains, GR20-10T and GR20-13T, were isolated from soil using R2A medium. The soil sample was collected from a field in the Yeongju region of Korea that was cultivated with Korean ginseng. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains formed a cluster with several uncultured bacterial clones and with Flexibacter filiformis, Flexibacter sancti, Flexibacter japonensis, Cytophaga arvensicola and Flavobacterium ferrugineum (recently reclassified as Terrimonas ferruginea) in the phylum Bacteroidetes. The level of 16S rRNA gene sequence similarity between the two novel strains was 98.9 %. Isolates GR20-10T and GR20-13T showed the highest sequence similarities to Flexibacter japonensis IFO 16041T (91.8 and 91.9 %, respectively) and T. ferruginea ATCC 13524T (90.4 and 90.6 %, respectively). The whole-cell fatty acid profiles of the two isolates were similar and their major fatty acids were 15 : 0 iso, 17 : 0 iso 3-OH and 15 : 1 iso G. The major isoprenoid quinone of both strains was MK-7. The G+C contents of GR20-10T and GR20-13T were 45.8 and 44.3 mol%, respectively. DNA–DNA hybridization (57 % DNA–DNA hybridization value) and phenotypic data indicated that strains GR20-10T and GR20-13T each belong to a separate species. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, strains GR20-10T and GR20-13T represent two novel species in a novel genus in the phylum Bacteroidetes; the names Niastella koreensis gen. nov., sp. nov. (the type species; type strain GR20-10T=KACC 11465T=DSM 17620T) and Niastella yeongjuensis sp. nov. (type strain GR20-13T=KACC 11466T=DSM 17621T) are proposed.

scholarly journals Pseudonocardia mongoliensis sp. nov. and Pseudonocardia khuvsgulensis sp. nov., isolated from soil

2011 ◽  
Vol 61 (4) ◽  
pp. 747-756 ◽  
Author(s):  
Ismet Ara ◽  
Baljinova Tsetseg ◽  
Damdinsuren Daram ◽  
Manabu Suto ◽  
Katsuhiko Ando
Keyword(s):  
Related Species ◽  
Type Strain ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Whole Cell ◽  
Hybridization Data ◽  
Physiological And Biochemical Characteristics ◽  
Phenotypic Tests ◽  
Physiological And Biochemical

Two actinomycetes, designated MN08-A0270T and MN08-A0297T, were isolated from soil from the area around Khuvsgul Lake, Khuvsgul province, Mongolia, and subjected to phenotypic and genotypic characterization. They produced well-developed, branched substrate hyphae and, similar to closely related species of the genus Pseudonocardia, produced zigzag-shaped aerial hyphae by acropetal budding and blastospores. A comparative analysis of 16S rRNA gene sequences indicated that strains MN08-A0270T and MN08-A0297T formed two distinct clades within the genus Pseudonocardia and were respectively most closely related to Pseudonocardia yunnanensis NBRC 15681T (97.3 % similarity) and Pseudonocardia thermophila IMSNU 20112T (97.1 %). Chemotaxonomic characteristics, including cell-wall diaminopimelic acid, whole-cell sugars, fatty acid components and major menaquinones, suggested that the two organisms belonged to the genus Pseudonocardia. Strains MN08-A0270T and MN08-A0297T could be differentiated from each other and from closely related species of the genus Pseudonocardia by physiological and biochemical characteristics, predominant fatty acids, menaquinones and whole-cell sugar components. Combined with the results of a broad range of phenotypic tests and DNA–DNA hybridization data and phylogenetic analysis, these results support the conclusion that these strains represent two novel species of the genus Pseudonocardia, for which we propose the names Pseudonocardia mongoliensis sp. nov. (type strain MN08-A0270T  = NBRC 105885T  = VTCC D9-25T) and Pseudonocardia khuvsgulensis sp. nov. (type strain MN08-A0297T  = NBRC 105886T  = VTCC D9-26T).

scholarly journals Halomonas stevensii sp. nov., Halomonas hamiltonii sp. nov. and Halomonas johnsoniae sp. nov., isolated from a renal care centre

2010 ◽  
Vol 60 (2) ◽  
pp. 369-377 ◽  
Author(s):  
Kwang Kyu Kim ◽  
Keun Chul Lee ◽  
Hee-Mock Oh ◽  
Jung-Sook Lee
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Care Centre ◽  
Hybridization Data ◽  
Rrna Gene Sequencing

A total of 14 Halomonas strains were isolated from the blood of two patients and from dialysis machines of a renal care centre. The strains were Gram-negative, halophilic, motile and non-spore-forming rods. They produced cream-coloured colonies and contained Q-9 as the predominant ubiquinone and C18 : 1 ω7c and C16 : 0 as the major fatty acids. Phylogenetic analysis based on 16S rRNA gene sequencing showed that the 14 isolates were most closely related to Halomonas magadiensis 21 MIT with 98.1–98.9 % sequence similarity and that they formed three separate lineages among themselves. Combined phenotypic and DNA–DNA hybridization data support the conclusion that they represent three novel species of the genus Halomonas, for which the names Halomonas stevensii sp. nov. (type strain S18214T=KCTC 22148T=DSM 21198T), Halomonas hamiltonii sp. nov. (type strain W1025T=KCTC 22154T=DSM 21196T) and Halomonas johnsoniae sp. nov. (type strain T68687T=KCTC 22157T=DSM 21197T) are proposed.

Three novel species of the genus Catellatospora, Catellatospora chokoriensis sp. nov., Catellatospora coxensis sp. nov. and Catellatospora bangladeshensis sp. nov., and transfer of Catellatospora citrea subsp. methionotrophica Asano and Kawamoto 1988 to Catellatospora methionotrophica sp. nov., comb. nov.

2006 ◽  
Vol 56 (2) ◽  
pp. 393-400 ◽  
Author(s):  
Ismet Ara ◽  
Takuji Kudo
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Physiological Data ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Separate Species ◽  
Nearest Neighbours ◽  
Agar Media

Three Gram-positive, aerobic, non-motile, mesophilic strains, designated 2-25(1)T, 2-29(17)T and 2-70(23)T, were isolated from sandy soil from Chokoria, Cox's Bazar, Bangladesh. The organisms produce short chains of non-motile spores that emerge singly or in tufts from vegetative hyphae on the surface of agar media. A comparative phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolates formed a distinct clade within the evolutionary radiation of the family Micromonosporaceae and clustered with members of the genus Catellatospora. The nearest neighbours were Catellatospora citrea subsp. citrea and C. citrea subsp. methionotrophica. Chemotaxonomic data, such as the presence of meso- and 3-hydroxy-diaminopimelic acids, N-glycolyl type muramic acid, arabinose and xylose and glucose in whole-cell hydrolysates, phosphatidylethanolamine as a diagnostic phospholipid, a tetrahydrogenated menaquinone with 9 isoprene units as a major menaquinone and fatty acid profiles predominated by iso-branched hexadecanoic acid and iso-branched pentadecanoic acid, supported the affiliation of the novel isolates to the genus Catellatospora. The results of DNA–DNA hybridization and physiological and biochemical tests allowed the novel isolates to be differentiated genotypically and phenotypically from the three recognized Catellatospora species. The three isolates therefore represent novel species for which the names Catellatospora chokoriensis sp. nov. [type strain 2-25(1)T=JCM 12950T=DSM 44900T], Catellatospora coxensis sp. nov. [type strain 2-29(17)T=JCM 12951T=DSM 44901T] and Catellatospora bangladeshensis sp. nov. [type strain 2-70(23)T=JCM 12949T=DSM 44899T], are proposed. DNA–DNA hybridization tests with C. citrea subsp. citrea and C. citrea subsp. methionotrophica, in combination with chemotaxonomic and physiological data, demonstrated that C. citrea subsp. methionotrophica should be elevated to a separate species for which the name Catellatospora methionotrophica sp. nov., comb. nov. is proposed (type strain JCM 7543T=DSM 44098T).

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 Proposal for creation of a new genus Neomicrococcus gen. nov. to accommodate Zhihengliuella aestuarii Baik et al. 2011 and Micrococcus lactis Chittpurna et al. 2011 as Neomicrococcus aestuarii comb. nov. and Neomicrococcus lactis comb. nov.

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3771-3776 ◽  
Author(s):  
Om Prakash ◽  
Avinash Sharma ◽  
Yogesh Nimonkar ◽  
Yogesh S. Shouche
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
New Genus ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Separate Species ◽  
Low Concentrations ◽  
Zhihengliuella Aestuarii ◽  
Type Strains

Micrococcus lactis and Zhihengliuella aestuarii were described independently in 2011. Their type strains showed high levels of 16S rRNA gene sequence similarity (99.3 %). Phylogenetic analysis revealed that M. lactis MCC 2278T and Z. aestuarii JCM 16166T formed a monophyletic group and showed distant relationships to other members of closely related genera such as Micrococcus, Zhihengliuella, Arthrobacter and Citricoccus. The presence of large proportions of iso-C14 : 0 and iso-C16 : 0 with small amounts of iso-C15 : 0 distinguished M. lactis MCC 2278T and Z. aestuarii JCM 16166T from other members of the genera Micrococcus and Zhihengliuella. Unlike other members of the genera Zhihengliuella and Micrococcus, M. lactis MCC 2278T and Z. aestuarii JCM 16166T showed growth at low concentrations of NaCl. Thus, based on distinctive phylogenetic, chemotaxonomic and physiological features of these two organisms in comparison with other members of the genera Micrococcus and Zhihengliuella, it is clear that they do not fit within the existing classification and deserve separate status. DNA–DNA hybridization between the two type strains was 63 %, indicating that they represent separate species. In this study, we propose the creation of a novel genus, Neomicrococcus gen. nov., to accommodate the two species with Neomicrococcus aestuarii gen. nov., comb. nov. (type strain JCM 16166T = KCTC 19557T) as the type species. Neomicrococcus lactis comb. nov. (type strain MCC 2278T = DSM 23694T) is also proposed.

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