scholarly journals Dietzia timorensis sp. nov., isolated from soil

2010 ◽  
Vol 60 (2) ◽  
pp. 451-454 ◽  
Author(s):  
Hideki Yamamura ◽  
Puspita Lisdiyanti ◽  
Roni Ridwan ◽  
Shanti Ratnakomala ◽  
Rasti Sarawati ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequencing ◽  
Treatment Method ◽  
Rrna Gene ◽  
The Novel ◽  
Sequencing Studies ◽  
Actinomycete Strain ◽  
Pre Treatment ◽  
Rrna Gene Sequencing ◽  
Taxonomic Approach

An actinomycete strain, ID05-A0528T, was isolated using the SDS-yeast extract pre-treatment method from soil under mahogany (Swietenia mahogani) trees in West Timor, Indonesia, and was examined by using a polyphasic taxonomic approach. Chemotaxonomic and phylogenetic characterizations demonstrated that the novel strain belongs to the genus Dietzia. 16S rRNA gene sequencing studies showed that the strain was related to Dietzia cinnamea (97.2 %). Results of phenotypic and phylogenetic analyses determined that strain ID05-A0528T is different from the known species of the genus Dietzia. It is proposed that the isolate should be classified as a representative of a novel species of the genus Dietzia, with the name Dietzia timorensis sp. nov. The type strain is ID05-A0528T (=BTCC B-560T =NBRC 104184T).

scholarly journals Nocardia amamiensis sp. nov., isolated from a sugar-cane field in Japan

2007 ◽  
Vol 57 (7) ◽  
pp. 1599-1602 ◽  
Author(s):  
Hideki Yamamura ◽  
Tomohiko Tamura ◽  
Yayoi Sakiyama ◽  
Shigeaki Harayama
Keyword(s):  
Sugar Cane ◽  
16S Rrna Gene Sequencing ◽  
Treatment Method ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Sequencing Studies ◽  
Actinomycete Strain ◽  
Pre Treatment ◽  
Rrna Gene Sequencing ◽  
Type Strains

An actinomycete, strain TT 00-78T, was isolated from soil from a sugar-cane field on Amami Island in Japan, using an SDS/yeast extract pre-treatment method, and the taxonomy was studied using a polyphasic approach. The chemotaxonomic and morphological characterizations clearly demonstrated that the strain belongs to the genus Nocardia. 16S rRNA gene sequencing studies showed that the strain was closely related to the type strains of Nocardia pneumoniae (98.6 %), Nocardia araoensis (98.1 %), Nocardia arthritidis (97.9 %) and Nocardia beijingensis (97.7 %). However, the results of DNA–DNA hybridization and physiological and biochemical tests showed that strain TT 00-78T could be differentiated from its closest phylogenetic relatives both genotypically and phenotypically. Therefore this strain represents a novel species of the genus Nocardia, for which the name Nocardia amamiensis sp. nov. is proposed. The type strain is TT 00-78T (=NBRC 102102T=DSM 45066T=KCTC 19208T).

scholarly journals Streptococcus ursoris sp. nov., isolated from the oral cavities of bears

2011 ◽  
Vol 61 (1) ◽  
pp. 40-44 ◽  
Author(s):  
Noriko Shinozaki-Kuwahara ◽  
Kazuko Takada ◽  
Masatomo Hirasawa
Keyword(s):  
Type Strain ◽  
16S Rrna Gene Sequencing ◽  
Extracellular Polysaccharide ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Sequencing Studies ◽  
Streptococcal Species ◽  
Rrna Gene Sequencing ◽  
Streptococcus Ratti

Three Gram-positive, catalase-negative, coccus-shaped organisms were isolated from the oral cavities of bears. The isolates were tentatively identified as a streptococcal species based on the results of biochemical tests. Comparative 16S rRNA gene sequencing studies confirmed that the organisms were members of the genus Streptococcus, but they did not correspond to any recognized species of the genus. The nearest phylogenetic relative of the new isolates was Streptococcus ratti ATCC 19645T (98.6 %), however, DNA–DNA hybridization analysis showed that the isolates displayed less than 15 % DNA–DNA relatedness with the type strain of S. ratti. Colonies of the novel strains grown on mitis salivarius agar showed an extracellular polysaccharide-producing colony morphology. Based on phenotypic and phylogenetic evidence, it is proposed that the novel isolates are classified in the genus Streptococcus as Streptococcus ursoris sp. nov. The type strain of S. ursoris is NUM 1615T (=JCM 16316T=DSM 22768T).

scholarly journals Pseudomonas simiae sp. nov., isolated from clinical specimens from monkeys (Callithrix geoffroyi)

2006 ◽  
Vol 56 (11) ◽  
pp. 2671-2676 ◽  
Author(s):  
Ana I. Vela ◽  
María C. Gutiérrez ◽  
Enevold Falsen ◽  
Eduardo Rollán ◽  
Isabel Simarro ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Molecular Genetic ◽  
16S Rrna Gene Sequencing ◽  
Clinical Samples ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Sequencing Studies ◽  
Rrna Gene Sequencing ◽  
Callithrix Geoffroyi

An unusual Gram-negative, catalase- and oxidase-positive, rod-shaped bacterium isolated from different clinical samples from two monkeys (Callithrix geoffroyi) was characterized by phenotypic and molecular genetic methods. The micro-organism was tentatively identified as a Pseudomonas species on the basis of the results of cellular morphological and biochemical tests. Fatty acid studies confirmed this generic placement and comparative 16S rRNA gene sequencing studies demonstrated that the unknown isolates were phylogenetically closely related to each other (100 % sequence similarity) and were part of the ‘Pseudomonas fluorescens intrageneric cluster’. The novel bacterium, however, was distinguished from other phylogenetically related species of Pseudomonas by DNA–DNA hybridization studies and biochemical tests. On the basis of both phenotypic and phylogenetic findings, it is proposed that the novel Pseudomonas isolates are classified as Pseudomonas simiae sp. nov. The type strain of P. simiae is OLiT (=CCUG 50988T=CECT 7078T).

scholarly journals Rubritalea halochordaticola sp. nov., a carotenoid-producing verrucomicrobial species isolated from a marine chordate

2011 ◽  
Vol 61 (7) ◽  
pp. 1515-1520 ◽  
Author(s):  
Jaewoo Yoon ◽  
Satoru Matsuda ◽  
Kyoko Adachi ◽  
Hiroaki Kasai ◽  
Akira Yokota
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Sea Squirt ◽  
Cell Biomass ◽  
Taxonomic Approach

A Gram-negative-staining, obligately aerobic, non-motile, rod-shaped and chemoheterotrophic bacterium, designated strain MN1-1006T, was isolated from an ascidian (sea squirt) sample, and was studied using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the new isolate shared approximately 93–99% sequence similarity with recognized species of the genus Rubritalea within the phylum ‘Verrucomicrobia’. DNA–DNA hybridization values between strain MN1-1006T and Rubritalea squalenifaciens HOact23T and Rubritalea sabuli YM29-052T were 57% and 14.5%, respectively. Strain MN1-1006T produced carotenoid compounds that rendered the cell biomass a reddish pink colour. The strain also contained squalene. The cell-wall peptidoglycan of the novel strain contained muramic acid and meso-diaminopimelic acid. The DNA G+C content of strain MN1-1006T was 51.4 mol%. The major cellular fatty acids were iso-C14:0, iso-C16:0 and anteiso-C15:0. The major isoprenoid quinone was MK-9. On the basis of these data, it was concluded that strain MN1-1006T represents a novel species of the genus Rubritalea, for which the name Rubritalea halochordaticola sp. nov. is proposed. The type strain is MN1-1006T ( = KCTC 23186T = NBRC 107102T).

scholarly journals Campylobacter insulaenigrae sp. nov., isolated from marine mammals

2004 ◽  
Vol 54 (6) ◽  
pp. 2369-2373 ◽  
Author(s):  
Geoffrey Foster ◽  
Barry Holmes ◽  
Arnold G. Steigerwalt ◽  
Paul A. Lawson ◽  
Petra Thorne ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Marine Mammals ◽  
16S Rrna Gene Sequencing ◽  
Single Species ◽  
Rrna Gene ◽  
Campylobacter Coli ◽  
Phylogenetic Studies ◽  
Sequencing Studies ◽  
Rrna Gene Sequencing ◽  
Campylobacter Lari

Phenotypic and phylogenetic studies were performed on four Campylobacter-like organisms recovered from three seals and a porpoise. Comparative 16S rRNA gene sequencing studies demonstrated that the organisms represent a hitherto unknown subline within the genus Campylobacter, associated with a subcluster containing Campylobacter jejuni, Campylobacter coli and Campylobacter lari. DNA–DNA hybridization studies confirmed that the bacteria belonged to a single species, for which the name Campylobacter insulaenigrae sp. nov. is proposed. The type strain of Campylobacter insulaenigrae sp. nov. is NCTC 12927T (=CCUG 48653T).

scholarly journals Citroniella saccharovorans gen. nov. sp. nov., a member of the family Peptoniphilaceae isolated from a human fecal sample from a coastal traditional community member

2019 ◽  
Vol 69 (4) ◽  
pp. 1142-1148 ◽  
Author(s):  
Nisha B. Patel ◽  
Alexandra J. Obregón-Tito ◽  
Raul Y. Tito ◽  
Omar Trujillo-Villaroel ◽  
Luis Marin-Reyes ◽  
...  
Keyword(s):  
Fecal Sample ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Novel Bacterium ◽  
The Family ◽  
Diamino Acid ◽  
Rrna Gene Sequencing

A novel Gram-stain-positive, non-motile, non-spore-forming coccus-shaped obligately anaerobic bacterium was recovered from a fecal sample obtained from an individual from a traditional community located on the southern coast of Peru. The results of analysis based on 16S rRNA gene sequencing indicated the novel bacterium to be phylogenetically distinct from other genera of members of the Peptoniphilaceae family, sharing a loose affinity with the genera Ezakiella , Finegoldia , Gallicola and Parvimonas . The major cellular fatty acids of the novel isolate were determined to be C16:0, C17:1ω8c, and C18:1ω9c. The DNA G+C content was 29.9 mol%. End products of metabolism from peptone yeast glucose broth (PYG) were determined to be acetate and methyl succinate. The diagnostic diamino acid present in the cell wall was lysine. On the basis of the phenotypic, chemotaxonomic and phylogenetic results the organism is a member of a novel genus belonging to the family Peptoniphilaceae for which the name Citroniella saccharovorans gen nov. sp. nov., is proposed. The type strain is M6.X9T (DSM 29873T=CCUG 66799T).

scholarly journals Blastococcus jejuensis sp. nov., an actinomycete from beach sediment, and emended description of the genus Blastococcus Ahrens and Moll 1970

2006 ◽  
Vol 56 (10) ◽  
pp. 2391-2396 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
The Novel ◽  
Separate Species ◽  
Beach Sediment ◽  
Actinomycete Strain ◽  
Type Strains

A novel actinomycete, strain KST3-10T, was isolated from sand sediment of a beach in Jeju, Korea, and was subjected to polyphasic taxonomic characterization. The organism produced circular, smooth, translucent, apricot-coloured colonies comprising coccoid- or rod-shaped cells. Phylogenetic analyses based on 16S rRNA gene sequences showed that the organism belonged to the family Geodermatophilaceae and consistently formed a distinct sub-branch outside the radiation of the genus Blastococcus. The organism showed 16S rRNA gene sequence similarity values of 98.2 % with respect to Blastococcus aggregatus DSM 4725T and 98.1 % with respect to Blastococcus saxobsidens BC444T. The type strains of the two Blastococcus species shared 98.2 % sequence similarity with respect to each other, whereas the levels of sequence similarity between the novel organism and the type strains of the less closely related neighbours, Modestobacter multiseptatus and Geodermatophilus obscurus, were in the range 96.2–96.9 %. The physiological, biochemical and chemotaxonomic data revealed that the novel organism can be readily differentiated from members of the genus Blastococcus and that it merits separate species status. On the basis of the phenotypic and genotypic evidence, strain KST3-10T represents a novel species of the genus Blastococcus, for which the name Blastococcus jejuensis sp. nov. is proposed. The type strain is KST3-10T (=NRRL B-24440T=KCCM 42251T).

scholarly journals Nocardiopsis arvandica sp. nov., isolated from sandy soil

2011 ◽  
Vol 61 (5) ◽  
pp. 1189-1194 ◽  
Author(s):  
Javad Hamedi ◽  
Fatemeh Mohammadipanah ◽  
Gabriele Pötter ◽  
Cathrin Spröer ◽  
Peter Schumann ◽  
...  
Keyword(s):  
Sandy Soil ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Aerial Mycelium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Hybridization Data ◽  
Actinomycete Strain ◽  
Taxonomic Approach

An actinomycete strain, HM7T, was isolated from sandy soil from the banks of the Arvand River, Khoramshahr, Iran. In a study conducted using a polyphasic taxonomic approach, it was found that this strain represented a novel species in the genus Nocardiopsis. Strain HM7T had long, branched substrate mycelia and the aerial mycelium completely fragmented to long chains of rod-shaped spores. The cell wall of strain HM7T contained meso-diaminopimelic acid, galactose and ribose. The predominant phospholipids were phosphatidylglycerol, phosphatidylethanolamine diphosphatidylglycerol, and phosphatidylcholine. The main menaquinones were MK-10(H2), MK-10(H4), MK-10(H0) and MK-9(H2). Strain HM7T showed the highest degree of 16S rRNA gene sequence similarity with Nocardiopsis sinuspersici UTMC 00102T (99.8 %) and Nocardiopsis quinghaiensis YIM 28A4T (99.3 %), but differed significantly from these type strains based on DNA–DNA hybridization data (37.6 and 38.9 % relatedness, respectively). Physiological, biochemical and phenotypic characteristics allowed strain HM7T to be differentiated from related species. On the basis of results from phenotypic and phylogenetic analyses, strain HM7T is considered to represent a novel species of the genus Nocardiopsis, for which the name Nocardiopsis arvandica sp. nov. is proposed; the type strain of this species is HM7T ( = UTMC 00103T = DSM 45278T = CCUG 58831T).

scholarly journals The archives are half-empty: an assessment of the availability of microbial community sequencing data

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Stephanie D. Jurburg ◽  
Maximilian Konzack ◽  
Nico Eisenhauer ◽  
Anna Heintz-Buschart
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rrna Gene Sequencing ◽  
Data Reuse ◽  
Data Availability ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Data Archiving ◽  
Sequencing Studies ◽  
Rrna Gene Sequencing

AbstractAs DNA sequencing has become more popular, the public genetic repositories where sequences are archived have experienced explosive growth. These repositories now hold invaluable collections of sequences, e.g., for microbial ecology, but whether these data are reusable has not been evaluated. We assessed the availability and state of 16S rRNA gene amplicon sequences archived in public genetic repositories (SRA, EBI, and DDJ). We screened 26,927 publications in 17 microbiology journals, identifying 2015 16S rRNA gene sequencing studies. Of these, 7.2% had not made their data public at the time of analysis. Among a subset of 635 studies sequencing the same gene region, 40.3% contained data which was not available or not reusable, and an additional 25.5% contained faults in data formatting or data labeling, creating obstacles for data reuse. Our study reveals gaps in data availability, identifies major contributors to data loss, and offers suggestions for improving data archiving practices.

scholarly journals Loktanella koreensis sp. nov., isolated from sea sand in Korea

2006 ◽  
Vol 56 (9) ◽  
pp. 2199-2202 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Seung-Hee Yoo ◽  
Jong-Shik Kim ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sand Sample ◽  
Sea Sand ◽  
Sequencing Studies ◽  
Rrna Gene Sequencing ◽  
Taxonomic Characterization

A bacterial strain, GA2-M3T, isolated from a sea-sand sample in Korea, was subjected to polyphasic taxonomic characterization. Cells of strain GA2-M3T were Gram-negative, non-motile, non-spore-forming and short rod- to ovoid-shaped. Comparative 16S rRNA gene sequencing studies confirmed that the bacterium fell within the radiation of the genus Loktanella. Similarity levels between the 16S rRNA gene sequence of strain GA2-M3T and those of type strains of Loktanella species with validly published names were 93.5–96.1 %; highest sequence similarity was with Loktanella rosea. The G+C content of the genomic DNA of strain GA2-M3T was 60.0 mol% and the predominant ubiquinone was Q-10. Major fatty acids were 18 : 1ω7c, 18 : 0 and 18 : 1ω7c 11-methyl. On the basis of the evidence presented, it is proposed that strain GA2-M3T represents a novel species, for which the name Loktanella koreensis sp. nov. is proposed. The type strain is GA2-M3T (=KACC 11519T=DSM 17925T).

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