scholarly journals Ancylobacter rudongensis sp. nov., isolated from roots of Spartina anglica

2004 ◽  
Vol 54 (2) ◽  
pp. 385-388 ◽  
Author(s):  
Yu Hua Xin ◽  
Yu Guang Zhou ◽  
Hui Ling Zhou ◽  
Wen Xin Chen
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Binding ◽  
16S Rdna ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Spartina Anglica ◽  
Phenotypic Data ◽  
16S Rdna Sequence ◽  
Bacterium Strain

A curved, ring-like bacterium, strain AS 1.1761T, isolated from the roots of Spartina anglica, was studied by a polyphasic approach. According to phylogenetic analysis, strain AS 1.1761T belongs to the genus Ancylobacter, with 99·21 % 16S rDNA sequence similarity to Ancylobacter aquaticus, the only species described so far in this genus. However, strain AS 1.1761T had no significant DNA–DNA binding with the type strain of A. aquaticus. In addition, strain AS 1.1761T differed from A. aquaticus in many phenotypic features. Based on molecular and phenotypic data, a novel species, Ancylobacter rudongensis sp. nov., is proposed. The type strain is AS 1.1761T (=JCM 11671T).

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 Bifidobacterium psychraerophilum sp. nov. and Aeriscardovia aeriphila gen. nov., sp. nov., isolated from a porcine caecum

2004 ◽  
Vol 54 (2) ◽  
pp. 401-406 ◽  
Author(s):  
Paul J. Simpson ◽  
R. Paul Ross ◽  
Gerald F. Fitzgerald ◽  
Catherine Stanton
Keyword(s):  
16S Rdna ◽  
Type Strain ◽  
Growth Parameters ◽  
Novel Species ◽  
Growth Conditions ◽  
Heat Shock Protein 60 ◽  
Gene Sequences ◽  
Phenotypic Data ◽  
Hsp60 Gene ◽  
Rdna Sequencing

In a previous study that was based primarily on 16S rDNA sequencing, two groups of bifidobacteria that had been recovered from a pig caecum were proposed to belong to two novel species, termed ‘Bifidobacterium pyschroaerophilum’ and ‘Bifidobacterium aerophilum’. In this study, based on DNA G+C content and partial heat-shock protein 60 (HSP60) gene sequences, the assignment of ‘B. pyschroaerophilum’, corrected to Bifidobacterium pyschraerophilum, to the genus Bifidobacterium was confirmed. The DNA G+C content of ‘B. aerophilum’ was relatively low, which was consistent with its segregation into subcluster II of the 16S rDNA phylogenetic tree. Based on partial 16S rDNA and HSP60 gene sequences, the species was transferred to a novel genus and reclassified as Aeriscardovia aeriphila gen. nov., sp. nov. Biochemical profiles and growth parameters were established for both novel species. Interestingly, each had a high tolerance to oxygen and grew on agar media under aerobic conditions, a trait that may relate to their caecal habitat. Under aerobic growth conditions, the short-rod morphology of A. aeriphila lengthened considerably. This appeared to arise from incomplete cell division. In addition, B. pyschraerophilum was unusual in that it grew at temperatures as low as 4 °C. On the basis of genetic, phylogenetic and phenotypic data, the identities of Bifidobacterium pyschraerophilum sp. nov. (type strain, T16T=LMG 21775T=NCIMB 13940T) and Aeriscardovia aeriphila gen. nov., sp. nov. (type strain, T6T=LMG 21773T=NCIMB 13939T) are confirmed.

scholarly journals Lactobacillus farraginis sp. nov. and Lactobacillus parafarraginis sp. nov., heterofermentative lactobacilli isolated from a compost of distilled shochu residue

2007 ◽  
Vol 57 (4) ◽  
pp. 708-712 ◽  
Author(s):  
Akihito Endo ◽  
Sanae Okada
Keyword(s):  
Phylogenetic Analysis ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Dna Relatedness ◽  
Clear Separation ◽  
Micro Organisms

Five strains of lactic acid bacteria were isolated from a compost of distilled shochu residue in Japan. The isolates were separated into two groups on the basis of 16S rRNA gene sequence similarity, and two subclusters were formed that comprised micro-organisms closely related to Lactobacillus buchneri, L. diolivorans, L. hilgardii, L. kefiri, L. parabuchneri and L. parakefiri. DNA–DNA relatedness results revealed that the isolates could be separated into two groups, and these groups correlated well with the subclusters generated using the phylogenetic analysis. Moreover, the levels of DNA–DNA relatedness showed clear separation of the two groups from their phylogenetic relatives. Therefore, the two groups represent two novel species, for which the names Lactobacillus farraginis sp. nov. (type strain NRIC 0676T=JCM 14108T=DSM 18382T) and Lactobacillus parafarraginis sp. nov. (type strain NRIC 0677T=JCM 14109T=DSM 18390T) are proposed.

Lacibacter daechungensis sp. nov., isolated from deep freshwater of a reservoir

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4519-4523 ◽  
Author(s):  
Long Jin ◽  
Sang-Yoon Shin ◽  
Hyung-Gwan Lee ◽  
Chi-Yong Ahn ◽  
Hee-Mock Oh
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Whole Cells ◽  
Link Type ◽  
The 16S Rrna Gene ◽  
Motile By Gliding

A Gram-stain-negative, aerobic, motile by gliding, non-spore-forming, rod-shaped, orange-pigmented bacterium, designated strain H32-4T, was isolated from 32 m deep water of Daechung reservoir in Daejeon, Republic of Korea. Based on the nucleotide sequence of the 16S rRNA gene, the closest neighbouring type strain was Lacibacter cauensis NJ-8T with which strain H32-4T shared 98.9 % sequence similarity. The most abundant fatty acids in whole cells of strain H32-4T were C15 : 0 iso (40.6 %), C17 : 0 iso 3-OH (22.4 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 9.3 %) and C15 : 0 (6.6 %). The predominant menaquinone was MK-7. The G+C content of the genomic DNA of strain H32-4T was 45.7 mol%. Thus, these combined genotypic and phenotypic data supported the conclusion that strain H32-4T represents a novel species of the genus Lacibacter , for which the name Lacibacter daechungensis sp. nov. is proposed. The type strain is H32-4T ( = KCTC 32395T = JCM 19172T).

scholarly journals Lactobacillus paracollinoides sp. nov., isolated from brewery environments

2004 ◽  
Vol 54 (1) ◽  
pp. 115-117 ◽  
Author(s):  
Koji Suzuki ◽  
Wataru Funahashi ◽  
Masahiro Koyanagi ◽  
Hiroshi Yamashita
Keyword(s):  
Phylogenetic Analysis ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Dna Relatedness ◽  
Beer Spoilage

Three novel strains isolated from brewery environments are described. These strains were Gram-positive, facultatively anaerobic, heterofermentative rods that did not exhibit catalase activity. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that these strains belong to the genus Lactobacillus and are most closely related to Lactobacillus collinoides (approximately 99 % similarity). The novel strains could be differentiated from L. collinoides on the basis of DNA–DNA relatedness, differences in beer-spoilage ability and the inability to utilize d-fructose. These isolates represent a novel species, for which the name Lactobacillus paracollinoides sp. nov. is proposed. The type strain is LA2T (=DSM 15502T=JCM 11969T).

scholarly journals Streptomyces hyderabadensis sp. nov., an actinomycete isolated from soil

2011 ◽  
Vol 61 (1) ◽  
pp. 76-80 ◽  
Author(s):  
T. V. K. Reddy ◽  
Shaik Mahmood ◽  
Laskaris Paris ◽  
Y. Harish Kumar Reddy ◽  
E. M. H. Wellington ◽  
...  
Keyword(s):  
Type Strain ◽  
Andhra Pradesh ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Dna Relatedness ◽  
Streptomyces Olivaceus ◽  
Type Strains

A novel actinomycete, designated strain OU-40T, was isolated from farm soil collected from the Hyderabad region of Andhra Pradesh, southern India. The strain was found to have morphological and chemotaxonomic characteristics typical of species of the genus Streptomyces. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain OU-40T belonged to the genus Streptomyces, and was related most closely to Streptomyces pactum NBRC 13433T (99.0 % sequence similarity), Streptomyces olivaceus NBRC 12805T (99.0 %) and Streptomyces parvulus NBRC 13193T (98.8 %). Strain OU-40T could be distinguished from the type strains of its closest phylogenetic relatives based on levels of DNA–DNA relatedness and comparison of morphological and phenotypic data. It is therefore concluded that strain OU-40T represents a novel species of the genus Streptomyces, for which the name Streptomyces hyderabadensis sp. nov. is proposed. The type strain is OU-40T (=CCTCC AA 209024T =PCM 2692T).

scholarly journals Paenibacillus sputi sp. nov., isolated from the sputum of a patient with pulmonary disease

2010 ◽  
Vol 60 (10) ◽  
pp. 2371-2376 ◽  
Author(s):  
Kwang Kyu Kim ◽  
Keun Chul Lee ◽  
Heekyung Yu ◽  
Sungweon Ryoo ◽  
Youngkil Park ◽  
...  
Keyword(s):  
Pulmonary Disease ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Diamino Acid

Strain KIT 00200-70066-1T was isolated from the sputum of a patient with pulmonary disease. Cells of the strain were Gram-variable, facultatively anaerobic, motile, spore-forming rods and formed colourless to white colonies on tryptic soy agar at 30 °C and pH 7. The pathogenicity of the strain is not known. The strain contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, MK-7 as the predominant menaquinone, anteiso-C15 : 0, iso-C16 : 0 and C16 : 0 as the major fatty acids and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unknown lipids in the polar lipid profile. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belongs to the genus Paenibacillus, sharing the highest levels of sequence similarity with Paenibacillus nanensis MX2-3T, Paenibacillus agaridevorans DSM 1355T and Paenibacillus alkaliterrae KSL-134T (95.4, 95.2 and 94.8 %, respectively), and that it occupied a distinct position within this genus. Combined phylogenetic and phenotypic data supported the conclusion that strain KIT 00200-70066-1T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus sputi sp. nov. is proposed; the type strain is KIT 00200-70066-1T (=KCTC 13252T =DSM 22699T).

Lentibacillus jeotgali sp. nov., a halophilic bacterium isolated from traditional Korean fermented seafood

2010 ◽  
Vol 60 (5) ◽  
pp. 1017-1022 ◽  
Author(s):  
Mi-Ja Jung ◽  
Seong Woon Roh ◽  
Min-Soo Kim ◽  
Jin-Woo Bae
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Halophilic Bacterium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Moderately Halophilic Bacterium ◽  
Bacterium Strain

A novel, Gram-positive, non-motile, endospore-forming and moderately halophilic bacterium, strain GrbiT, was isolated from a traditional Korean fermented seafood. The organism grew optimally in the presence of 10–15 % NaCl, at 37 °C and pH 8.0. The peptidoglycan of the cell wall consisted of meso-diaminopimelic acid, and the predominant menaquinone was MK-7. The major fatty acids of strain GrbiT were iso-C16 : 0 (36.4 %), anteiso-C15 : 0 (30.3 %) and iso-C14 : 0 (18.2 %). The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. The genomic DNA G+C content was 42.5 mol%. Strain GrbiT was most closely related to the type strain Lentibacillus kapialis JCM 12580T, with which it shared 97.5 % 16S rRNA gene sequence similarity. The DNA–DNA hybridization value between strains GrbiT and L. kapialis JCM 12580T was 8 %. Based on phenotypic, genotypic and phylogenetic data, strain GrbiT should be classified as a novel species within the genus Lentibacillus, for which the name Lentibacillus jeotgali sp. nov. is proposed. The type strain is GrbiT (=KCTC 13300T=JCM 15795T).

Novosphingobium lindaniclasticum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2160-2167 ◽  
Author(s):  
Anjali Saxena ◽  
Shailly Anand ◽  
Ankita Dua ◽  
Naseer Sangwan ◽  
Fazlurrahman Khan ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Phylogenetic Analysis ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium

A yellow-pigmented, Gram-negative, aerobic, non-motile, non-spore-forming, rod-shaped-bacterium, LE124T, was isolated from a hexachlorocyclohexane (HCH) dumpsite located in Lucknow, India. The type strain LE124T grew well with hexachlorocyclohexane as a sole carbon source, degrading it within 24 h of incubation. Phylogenetic analysis of strain LE124T showed highest 16S rRNA gene sequence similarity to Novosphingobium barchaimii LL02T (98.5 %), Novosphingobium panipatense SM16T (98.1 %), Novosphingobium soli CC-TPE-1T (97.9 %), Novosphingobium naphthalenivorans TUT562T (97.6 %), Novosphingobium mathurense SM117T (97.5 %) and Novosphingobium resinovorum NCIMB 8767T (97.5 %) and lower sequence similarity (<97 %) to all other members of the genus Novosphingobium . The DNA–DNA relatedness between strain LE124T and N. barchaimii LL02T and other related type strains was found to vary from 15 % to 45 % confirming that it represents a novel species. The genomic DNA G+C content of strain LE124T was 60.7 mol%. The predominant fatty acids were summed feature 8 (C18 : 1ω7c, 49.1 %), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c, 19.9 %), C16 : 0 (6.7 %), C17 : 1ω6c (4.9 %) and a few hydroxyl fatty acids, C14 : 0 2-OH (9.4 %) and C16 : 0 2-OH (2.1 %). Polar lipids consisted mainly of phosphatidyldimethylethanolamine, phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, sphingoglycolipid and some unidentified lipids. The major respiratory quinone was ubiquinone Q-10. Spermidine was the major polyamine observed. Phylogenetic analysis, DNA–DNA hybridization, chemotaxonomic and phenotypic analysis support the conclusion that strain LE124T represents a novel species within the genus Novosphingobium for which we propose the name Novosphingbium lindaniclasticum sp. nov. The type strain is LE124T ( = CCM 7976T = DSM 25409T).

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).

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