scholarly journals Acinetobacter bereziniae sp. nov. and Acinetobacter guillouiae sp. nov., to accommodate Acinetobacter genomic species 10 and 11, respectively

2010 ◽  
Vol 60 (4) ◽  
pp. 896-903 ◽  
Author(s):  
Alexandr Nemec ◽  
Martin Musílek ◽  
Ondrej Šedo ◽  
Thierry De Baere ◽  
Martina Maixnerová ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Restriction Analysis ◽  
Aflp Analysis ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Phenotypic Analysis ◽  
Genomic Species ◽  
Dna Reassociation ◽  
Acinetobacter Guillouiae

Acinetobacter genospecies (genomic species) 10 and 11 were described by Bouvet and Grimont in 1986 on the basis of DNA–DNA reassociation studies and comprehensive phenotypic analysis. In the present study, the names Acinetobacter bereziniae sp. nov. and Acinetobacter guillouiae sp. nov., respectively, are proposed for these genomic species based on the congruence of results of polyphasic analysis of 33 strains (16 and 17 strains of genomic species 10 and 11, respectively). All strains were investigated by selective restriction fragment amplification (i.e. AFLP) analysis rpoB sequence analysis, amplified rDNA restriction analysis and tDNA intergenic length polymorphism analysis, and their nutritional and physiological properties were determined. Subsets of the strains were studied by 16S rRNA gene sequence analysis and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS or had been classified previously by DNA–DNA reassociation. Results indicate that A. bereziniae and A. guillouiae represent two phenetically and phylogenetically distinct groups within the genus Acinetobacter. Based on the comparative analysis of housekeeping genes (16S rRNA and rpoB genes), these species together represent a monophyletic branch within the genus. Despite their overall phenotypic similarity, the ability to oxidize d-glucose and to grow at 38 °C can be used in the presumptive differentiation of these two species from each other: with the exception of three strains that were positive for only one test, A. bereziniae strains were positive for both tests, whereas A. guillouiae strains were negative in these tests. The strains of A. bereziniae originated mainly from human clinical specimens, whereas A. guillouiae strains were isolated from different environmental sources in addition to human specimens. The type strain of A. bereziniae sp. nov. is LMG 1003T (=CIP 70.12T =ATCC 17924T) and that of A. guillouiae sp. nov. is LMG 988T (=CIP 63.46T =ATCC 11171T =CCUG 2491T).

scholarly journals Cronobacter condimenti sp. nov., isolated from spiced meat, and Cronobacter universalis sp. nov., a species designation for Cronobacter sp. genomospecies 1, recovered from a leg infection, water and food ingredients

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1277-1283 ◽  
Author(s):  
Susan Joseph ◽  
Esin Cetinkaya ◽  
Hana Drahovska ◽  
Arturo Levican ◽  
Maria J. Figueras ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
Phenotypic Analysis ◽  
Content Type ◽  
Link Type ◽  
Dna Reassociation

A re-evaluation of the taxonomic position of five strains, one assigned to Cronobacter sakazakii (strain 1330T, isolated from spiced meat purchased in Slovakia), two previously assigned to Cronobacter genomospecies 1 (strains NCTC 9529T and 731, isolated from water and a leg infection, respectively) and two previously assigned to Cronobacter turicensis (strains 96 and 1435, isolated from onion powder and rye flour, respectively) was carried out. The analysis included phenotypic characterization, 16S rRNA gene sequencing and multilocus sequence analysis (MLSA) of seven housekeeping genes (atpD, fusA, glnS, gltB, gyrB, infB, ppsA; 3036 bp). 16S rRNA gene sequence analysis and MLSA showed that strain 1330T formed an independent phylogenetic lineage in the MLSA, with Cronobacter dublinensis LMG 23823T as the closest neighbour. DNA–DNA reassociation and phenotypic analysis revealed that strain 1330T represented a novel species, for which the name Cronobacter condimenti sp. nov. is proposed (type strain 1330T = CECT 7863T = LMG 26250T). Strains NCTC 9529T, 731, 96 and 1435 clustered together within an independent phylogenetic lineage, with C. turicensis LMG 23827T as the closest neighbour in the MLSA. DNA–DNA reassociation and phenotypic analysis confirmed that these strains represent a novel species, for which the name Cronobacter universalis sp. nov. is proposed (type strain NCTC 9529T = CECT 7864T = LMG 26249T).

scholarly journals Taxonomic evaluation of the Streptomyces griseus clade using multilocus sequence analysis and DNA–DNA hybridization, with proposal to combine 29 species and three subspecies as 11 genomic species

2010 ◽  
Vol 60 (3) ◽  
pp. 696-703 ◽  
Author(s):  
Xiaoying Rong ◽  
Ying Huang
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Streptomyces Griseus ◽  
Multilocus Sequence Analysis ◽  
Rrna Gene ◽  
Good Resolution ◽  
Species Definition ◽  
Genomic Species

Streptomyces griseus and related species form the biggest but least well-defined clade in the whole Streptomyces 16S rRNA gene tree. Multilocus sequence analysis (MLSA) has shown promising potential for refining Streptomyces systematics. In this investigation, strains of 18 additional S. griseus clade species were analysed and data from a previous pilot study were integrated in a larger MLSA phylogeny. The results demonstrated that MLSA of five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) is better than the previous six-gene scheme, as it provides equally good resolution and stability and is more cost-effective; MLSA using three or four of the genes also shows good resolution and robustness for differentiating most of the strains and is therefore of value for everyday use. MLSA is more suitable for discriminating strains that show >99 % 16S rRNA gene sequence similarity. DNA–DNA hybridization (DDH) between strains with representative MLSA distances revealed a strong correlation between the data of MLSA and DDH. The 70 % DDH value for current species definition corresponds to a five-gene MLSA distance of 0.007, which could be considered as the species cut-off for the S. griseus clade. It is concluded that the MLSA procedure can be a practical, reliable and robust alternative to DDH for the identification and classification of streptomycetes at the species and intraspecies levels. Based on the data from MLSA and DDH, as well as cultural and morphological characteristics, 18 species and three subspecies of the S. griseus clade are considered to be later heterotypic synonyms of 11 genomic species: Streptomyces griseinus and Streptomyces mediolani as synonyms of Streptomyces albovinaceus; Streptomyces praecox as a synonym of Streptomyces anulatus; Streptomyces olivoviridis as a synonym of Streptomyces atroolivaceus; Streptomyces griseobrunneus as a synonym of Streptomyces bacillaris; Streptomyces cavourensis subsp. washingtonensis as a synonym of Streptomyces cyaneofuscatus; Streptomyces acrimycini, Streptomyces baarnensis, Streptomyces caviscabies and Streptomyces flavofuscus as synonyms of Streptomyces fimicarius; Streptomyces flavogriseus as a synonym of Streptomyces flavovirens; Streptomyces erumpens, ‘Streptomyces ornatus’ and Streptomyces setonii as synonyms of Streptomyces griseus; Streptomyces graminofaciens as a synonym of Streptomyces halstedii; Streptomyces alboviridis, Streptomyces griseus subsp. alpha, Streptomyces griseus subsp. cretosus and Streptomyces luridiscabiei as synonyms of Streptomyces microflavus; and Streptomyces californicus and Streptomyces floridae as synonyms of Streptomyces puniceus.

scholarly journals Pantoea allii sp. nov., isolated from onion plants and seed

2011 ◽  
Vol 61 (4) ◽  
pp. 932-937 ◽  
Author(s):  
Carrie L. Brady ◽  
Teresa Goszczynska ◽  
Stephanus N. Venter ◽  
Ilse Cleenwerck ◽  
Paul De Vos ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Rrna Gene Sequence

Eight yellow-pigmented, Gram-negative, rod-shaped, oxidase-negative, motile, facultatively anaerobic bacteria were isolated from onion seed in South Africa and from an onion plant exhibiting centre rot symptoms in the USA. The isolates were assigned to the genus Pantoea on the basis of phenotypic and biochemical tests. 16S rRNA gene sequence analysis and multilocus sequence analysis (MLSA), based on gyrB, rpoB, infB and atpD sequences, confirmed the allocation of the isolates to the genus Pantoea. MLSA further indicated that the isolates represented a novel species, which was phylogenetically most closely related to Pantoea ananatis and Pantoea stewartii. Amplified fragment length polymorphism analysis also placed the isolates into a cluster separate from P. ananatis and P. stewartii. Compared with type strains of species of the genus Pantoea that showed >97 % 16S rRNA gene sequence similarity with strain BD 390T, the isolates exhibited 11–55 % whole-genome DNA–DNA relatedness, which confirmed the classification of the isolates in a novel species. The most useful phenotypic characteristics for the differentiation of the isolates from their closest phylogenetic neighbours are production of acid from amygdalin and utilization of adonitol and sorbitol. A novel species, Pantoea allii sp. nov., is proposed, with type strain BD 390T ( = LMG 24248T).

scholarly journals Use of the novel phylogenetic marker dnaJ and DNA–DNA hybridization to clarify interrelationships within the genus Aeromonas

2007 ◽  
Vol 57 (6) ◽  
pp. 1232-1237 ◽  
Author(s):  
Pham Hong Nhung ◽  
Hiroyuki Hata ◽  
Kiyofumi Ohkusu ◽  
Makiko Noda ◽  
Mohammad Monir Shah ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Dna Relatedness ◽  
Aeromonas Veronii ◽  
Dna Reassociation ◽  
Sequence Similarities

The interrelationships of 27 Aeromonas strains were investigated using dnaJ sequences and DNA–DNA hybridization. dnaJ sequence similarities showed a stronger relationship with DNA–DNA relatedness values than did 16S rRNA gene sequence similarities. Additionally, dnaJ sequence analysis, with interspecies divergence over 5.2 % in most cases, gave better resolution than 16S rRNA gene sequences for the differentiation of strains at the species level. Relationships among Aeromonas species were therefore elucidated on the basis of dnaJ sequences and DNA–DNA reassociation. Strains of Aeromonas encheleia and Aeromonas sp. HG11 were unquestionably grouped in the same genetic species, since they shared 98.7 % dnaJ sequence similarity and 82–85 % genomic relatedness. The phylogenetically close relationships obtained from dnaJ sequence analysis (1.7–3.3 % genetic distance) were corroborated by high DNA–DNA relatedness (73–97 %) to support the previous suggestion that Aeromonas culicicola and Aeromonas allosaccharophila are later heterotypic synonyms of Aeromonas veronii. Our findings will contribute to the clarification of controversial relationships in the genus Aeromonas and also demonstrate that analysis of dnaJ sequences can be a powerful tool for interspecies study of the genus.

scholarly journals First Report of Group 16SrXII Phytoplasma Associated with Papaya Yellows in Taiwan

Plant Disease ◽  
2011 ◽  
Vol 95 (12) ◽  
pp. 1581-1581 ◽  
Author(s):  
H. J. Bau ◽  
S. C. Hung ◽  
W. C. Chang ◽  
Y. K. Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Viral Infections ◽  
Restriction Analysis ◽  
Disease Incidence ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Universal Primer ◽  
First Report ◽  
Sequence Identity

Phytoplasmas have been reported to cause various disorders in papaya (Carica papaya L.), including dieback, mosaic, and yellow crinkle in Australia, Nivun Haamir dieback in Israel, and bunchy top-like disease in Cuba (1). Papaya is an economically important crop in Taiwan, and therefore, is monitored for viral infections. In 2005, papaya plants showing chlorosis, yellows and shriveling of leaves, dieback and lateral growth of branches, bending of apical branches, latexosis of fruits, and brown necrosis in phloem tissues were observed in southern Taiwan. Examination by an electron microscope revealed the presence of pleomorphic phytoplasma cells in sieve tubes of the phloem of petioles and leaf veins of diseased plants. Total DNA was extracted individually from at least three diseased plants at each location with a commercial DNA preparation kit (Axygen Scientific, Union City, CA) and used for amplification of the phytoplasma 16S rRNA gene in PCR with universal primer pairs P1 and Tint (3). The full-length 16S rRNA gene has been amplified and cloned. Sequence analysis revealed that the fragment was 1,581 bp long (GenBank Accession No. AJ919994) and shared 99.6% sequence identity with that of the ‘Candidatus Phytoplasma solani’ reference strain (GenBank Accession No. AF248959). A virtual restriction fragment length polymorphism analysis of the 16S rDNA sequence amplified from the R16F2n/R16R2 primers (2) was performed with iPhyClassifier (4) and pDRAW32. In silico restriction analysis identified the studied papaya phytoplasma as a subgroup 16SrXII-A strain. The sequence had 97 to 98% sequence identity with papaya phytoplasmas of the 16SrXII group in Australia (GenBank Accession No. Y10095), Israel (GenBank Accession No. AY903951), and Cuba (GenBank Accession No. AY725234). The disease incidence was 30 to 35% during the 2006 to 2010 growing seasons, and field surveys indicated that the disease has spread to central Taiwan with sporadic occurrence in recent years. To our knowledge, this is the first report of phytoplasma associated with papaya yellows in Taiwan. References: (1) Y. Arocha et al. Int. J. Syst. Evol. Microbiol. 55:2451, 2005. (2) I. M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (3) C. D. Smart et al. Appl. Environ. Microbiol. 62:2988, 1996. (4) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.

scholarly journals Multilocus sequence analysis of the genus Kurthia, and a description of Kurthia populi sp. nov.

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3788-3793 ◽  
Author(s):  
Wei Fang ◽  
Min-wei Guo ◽  
Zhi-yong Ruan ◽  
Han Xue ◽  
Lai-fa Wang ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Analyses ◽  
Hybrid Poplar ◽  
Multilocus Sequence Analysis ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Dna Base Composition ◽  
Dna Reassociation

Four novel bacterial strains belonging to the genus Kurthia were isolated from the surface of a weevil of the family Curculionidae (strain 10y-14T), and from bark samples of hybrid poplar, Populus × euramericana (strains 6-3, 2-5 and 06C10-3-14), in Puyang, Henan Province, China. Phylogenetic analyses of the 16S rRNA gene and multilocus sequence analysis (MLSA) data showed that the four strains form a distinct cluster in the genus Kurthia, indicating that they all belong to a single taxon within the genus. DNA–DNA hybridization levels between strain 10y-4T and Kurthia huakuii LAM0618T and Kurthia massiliensis DSM 24639T were 58.31 and 53.92 %, respectively. This indicates that the four novel strains represent a species distinct from these two closely related species. The DNA G+C content of the novel strains was 42.1–42.6 %. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0.The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unknown phospholipid and unidentified aminophospholipids. The predominant menaquinones were MK-7 (90 %) and MK-6 (10 %). The major cell-wall amino acids were lysine, alanine, glutamic acid and glycine. On the basis of the MLSA and 16S rRNA gene sequence phylogenetic analyses, DNA–DNA reassociation values, DNA base composition, and biochemical and phenotypic characteristics, the four strains are considered to represent a novel species within the genus Kurthia, for which the name Kurthia populi sp. nov. is proposed. The type strain is 10y-14T ( = CFCC 11600T = KCTC 33522T).

scholarly journals Diagnosis of Fulminant Pneumonia Caused by Legionella pneumophila Serogroup 8 with the Sequence Analysis of the 16S rRNA Gene

2011 ◽  
Vol 225 (1) ◽  
pp. 65-69 ◽  
Author(s):  
Toshinori Kawanami ◽  
Kazuhiro Yatera ◽  
Kazumasa Fukuda ◽  
Kei Yamasaki ◽  
Masamizu Kunimoto ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Legionella Pneumophila ◽  
Rrna Gene ◽  
The 16S Rrna Gene

scholarly journals Kaistia terrae sp. nov., isolated from a wetland in Korea

2010 ◽  
Vol 60 (4) ◽  
pp. 949-952 ◽  
Author(s):  
Soo-Jin Kim ◽  
Hang-Yeon Weon ◽  
Yi-Seul Kim ◽  
Rangasamy Anandham ◽  
Seung-Hee Yoo ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

An ivory-coloured bacterium, designated strain 5YN7-3T, was isolated from a wetland, Yongneup, Korea. Cells of the strain were aerobic, Gram-stain-negative, non-motile and short rods. 16S rRNA gene sequence analysis demonstrated that strain 5YN7-3T belongs to the order Rhizobiales of the class Alphaproteobacteria and is closely related to Kaistia soli 5YN9-8T (97.8 %), Kaistia granuli Ko04T (97.6 %) and Kaistia adipata Chj404T (97.4 %). Strain 5YN7-3T showed DNA–DNA hybridization values of 28, 22 and 35 % with K. granuli Ko04T, K. soli 5YN9-8T and K. adipata Chj404T, respectively. The major fatty acids were C18 : 1 ω7c (51.2 %), C19 : 0 cyclo ω8c (25.0 %), C18 : 0 (12.9 %) and C16 : 0 (10.8 %) (>10 % of total fatty acids). Ubiquinone-10 was the major isoprenoid quinone and the DNA G+C content was 66.5 mol%. The phenotypic characteristics in combination with 16S rRNA gene sequence analysis and DNA–DNA hybridization data clearly define strain 5YN7-3T as a novel species of the genus Kaistia, for which the name Kaistia terrae sp. nov. is proposed. The type strain is 5YN7-3T (=KACC 12910T =DSM 21341T).

scholarly journals Parabacteroides johnsonii sp. nov., isolated from human faeces

2007 ◽  
Vol 57 (2) ◽  
pp. 293-296 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Maki Kitahara ◽  
Yoshimi Benno
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Human Faeces ◽  
Gene Sequence Analysis

A bacterial strain isolated from human faeces, M-165T, was characterized in terms of its phenotypic and biochemical features, cellular fatty acid profile, menaquinone profile and phylogenetic position (based on 16S rRNA gene sequence analysis). A 16S rRNA gene sequence analysis showed that the isolate was a member of the genus Parabacteroides. Strain M-165T was closely related to Parabacteroides merdae strains, showing 98 % sequence similarity. The strain was obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative, rod-shaped and was able to grow on media containing 20 % bile. Although the phenotypic characteristics of the strain M-165T were similar to those of P. merdae, the isolate could be differentiated from P. merdae by means of API 20A tests for l-arabinose and l-rhamnose fermentation. DNA–DNA hybridization experiments revealed the genomic distinctiveness of the novel strain with respect to P. merdae JCM 9497T (⩽60 % DNA–DNA relatedness). The DNA G+C content of the strain is 47.6 mol%. On the basis of these data, strain M-165T represents a novel species of the genus Parabacteroides, for which the name Parabacteroides johnsonii sp. nov. is proposed. The type strain is M-165T (=JCM 13406T=DSM 18315T).

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