scholarly journals Methylobacterium variabile sp. nov., a methylotrophic bacterium isolated from an aquatic environment

2005 ◽  
Vol 55 (4) ◽  
pp. 1429-1433 ◽  
Author(s):  
Virginia Gallego ◽  
Maria Teresa García ◽  
Antonio Ventosa
Keyword(s):  
Dna Hybridization ◽  
Distribution System ◽  
Bacterial Population ◽  
Sequence Similarity ◽  
Methylotrophic Bacterium ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Natural Habitats ◽  
Hybridization Data ◽  
The 16S Rrna Gene

Strain GR3T was isolated from drinking water during a screening programme to monitor the bacterial population present in the distribution system of Seville (Spain), and it was studied phenotypically, genotypically and phylogenetically. This pink-pigmented bacterium was identified as a Methylobacterium sp. Members of this genus are distributed in a wide variety of natural habitats, including soil, dust, air, freshwater and aquatic sediments. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain GR3T was closely related to Methylobacterium aquaticum (97·4 % sequence similarity), whereas sequence similarity values with respect to the rest of the species belonging to this genus were lower than 96 %. Furthermore, the DNA–DNA hybridization data and its phenotypic characteristics clearly indicate that the isolate represents a novel Methylobacterium species, for which the name Methylobacterium variabile sp. nov. is proposed. GR3T (=DSM 16961T=CCM 7281T=CECT 7045T) is the type strain; the DNA G+C content of this strain is 69·2 mol%.

scholarly journals Chryseobacterium hispanicum sp. nov., isolated from the drinking water distribution system of Sevilla, Spain

2006 ◽  
Vol 56 (7) ◽  
pp. 1589-1592 ◽  
Author(s):  
Virginia Gallego ◽  
Maria Teresa García ◽  
Antonio Ventosa
Keyword(s):  
Drinking Water ◽  
Distribution System ◽  
Water Distribution ◽  
Bacterial Population ◽  
Water Distribution System ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Drinking Water Distribution ◽  
Type Strains ◽  
The 16S Rrna Gene

Strain VP48T was isolated from drinking water during a screening programme to monitor the bacterial population present in the water distribution system of Sevilla (Spain). A polyphasic taxonomic study of the isolate resulted in its identification as a member of the genus Chryseobacterium, members of which are widely distributed in soil, water and clinical sources. However, the 16S rRNA gene sequence similarity values of strain VP48T to the type strains of Chryseobacterium species were 96 % or lower. Furthermore, phenotypic characteristics clearly indicated that the isolate represents a novel Chryseobacterium species, for which the name Chryseobacterium hispanicum sp. nov. is proposed; strain VP48T (=CECT 7129T=CCM 7359T=JCM 13554T) is the type strain. The DNA G+C content of this strain is 34.3 mol%.

scholarly journals Luteipulveratus halotolerans sp. nov., an actinobacterium (Dermacoccaceae) from forest soil

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4113-4120 ◽  
Author(s):  
Holed Juboi ◽  
Ann Anni Basik ◽  
Sunita Sara Gill Shamsul ◽  
Phil Arnold ◽  
Esther K. Schmitt ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Monophyletic Clade ◽  
Phenotypic Characteristics ◽  
Pacbio Rs Ii ◽  
The Family ◽  
The 16S Rrna Gene

The taxonomic position of an actinobacterium strain, C296001T, isolated from a soil sample collected in Sarawak, Malaysia, was established using a polyphasic approach. Phylogenetically, strain C296001T was closely associated with the genus Luteipulveratus and formed a distinct monophyletic clade with the only described species, Luteipulveratus mongoliensis NBRC 105296T. The 16S rRNA gene sequence similarity between strain C296001T and L. mongoliensis was 98.7 %. DNA–DNA hybridization results showed that the relatedness of strain C296001T to L. mongoliensis was only 21.5 %. The DNA G+C content of strain C296001T was 71.7 mol%. Using a PacBio RS II system, whole genome sequences for strains C296001T and NBRC 105296T were obtained. The genome sizes of 4.5 Mbp and 5.4 Mbp determined were similar to those of other members of the family Dermacoccaceae. The cell-wall peptidoglycan contained lysine, alanine, aspartic acid, glutamic acid and serine, representing the peptidoglycan type A4α l-Lys-l-Ser-d-Asp. The major menaquinones were MK-8(H4), MK-8 and MK-8(H2). Phosphatidylglycerol, phosphatidylinositol, diphosphatidylglycerol and phosphoglycolipid were the polar lipids, while the whole-cell sugars were glucose, fucose and lesser amounts of ribose and galactose. The major fatty acids were iso-C16 : 0, anteiso-C17 : 0, iso-C16 : 1 H, anteiso-C17 : 1ω9c, iso-C18 : 0 and 10-methyl C17 : 0. Chemotaxonomic analyses showed that C296001T had typical characteristics of members of the genus Luteipulveratus, with the main differences occurring in phenotypic characteristics. On the basis of the phenotypic and chemotaxonomic evidence, it is proposed that strain C296001T be classified as a representative of a novel species in the genus Luteipulveratus, for which the name Luteipulveratus halotolerans sp. nov. is recommended. The type strain is C296001T ( = ATCC TSD-4T = JCM 30660T).

Reclassification of Herbaspirillum putei as a later heterotypic synonym of Herbaspirillum huttiense, with the description of H. huttiense subsp. huttiense subsp. nov. and H. huttiense subsp. putei subsp. nov., comb. nov., and description of Herbaspirillum aquaticum sp. nov.

2010 ◽  
Vol 60 (6) ◽  
pp. 1418-1426 ◽  
Author(s):  
Anatoly P. Dobritsa ◽  
M. C. S. Reddy ◽  
Mansour Samadpour
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Phenotypic Characteristics ◽  
Phylogenetic Relatedness ◽  
The 16S Rrna Gene

Resequencing of the 16S rRNA gene of the type strain of Herbaspirillum putei Ding and Yokota 2004 revealed 99.9 % sequence similarity to that of the type strain of Herbaspirillum huttiense (Leifson 1962) Ding and Yokota 2004. This high phylogenetic relatedness of H. putei and H. huttiense was confirmed by the results of DNA–DNA hybridization between H. huttiense DSM 10281T and H. putei ATCC BAA-806T (reassociation value 96 %). Therefore, it is proposed to reclassify the type strain of H. putei as a strain of H. huttiense. However, the genome of the type strain of H. putei is about 0.9 Mb larger than that of the H. huttiense type strain. This results in a decrease in the reassociation value in the reciprocal DNA–DNA hybridization to 72 %, a level slightly above the threshold for delineating bacterial species. These data and distinctive phenotypic characteristics indicate that the name Herbaspirillum putei is a later heterotypic synonym of Herbaspirillum huttiense and permit the description of two novel subspecies, Herbaspirillum huttiense subsp. huttiense subsp. nov. (type strain ATCC 14670T =JCM 21423T =DSM 10281T) and Herbaspirillum huttiense subsp. putei subsp. nov., comb. nov. (type strain 7-2T =JCM 21495T =ATCC BAA-806T). Three bacterial strains, IEH 4430T, IEH 4515 and IEH 8757, isolated from water were found to be the closest relatives of these strains. Strain IEH 8757 was classified as a strain of H. huttiense subsp. putei. Studies of genotypic and phenotypic features of strains IEH 4430T and IEH 4515 showed that the strains represent a novel species, which is most closely related to H. huttiense and for which the name Herbaspirillum aquaticum sp. nov. is proposed (type strain IEH 4430T =DSM 21191T =ATCC BAA-1628T).

scholarly journals Shewanella haliotis sp. nov., isolated from the gut microflora of abalone, Haliotis discus hannai

2007 ◽  
Vol 57 (12) ◽  
pp. 2926-2931 ◽  
Author(s):  
Duwoon Kim ◽  
Keun Sik Baik ◽  
Mi Sun Kim ◽  
Bok-Mi Jung ◽  
Tai-Sun Shin ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gut Microflora ◽  
Phenotypic Characteristics ◽  
Shewanella Algae ◽  
South Sea ◽  
Haliotis Discus ◽  
Abalone Haliotis Discus ◽  
The 16S Rrna Gene

A motile, rod-shaped, pink–orange pigmented bacterium, designated strain DW01T, was isolated from the gut microflora of abalone collected from the South Sea (Republic of Korea). Cells were Gram-negative, facultatively anaerobic, catalase- and oxidase-positive. The major fatty acids were iso-C15 : 0 (17.7 %), C16 : 0 (13.4 %), iso-C15 : 0 2-OH and/or C16 : 1 ω7c (12.5 %) and C17 : 1 ω8c (10.7 %). The DNA G+C content was 53.7 mol%. A phylogenetic tree based on the 16S rRNA gene sequences showed that strain DW01T forms a lineage of the genus Shewanella and is closely related to Shewanella algae ATCC 51192T (98.3 % sequence similarity) and to other members of the genus Shewanella (91.0–94.9 %). The phenotypic characteristics and DNA–DNA hybridization relatedness data indicate that strain DW01T should be distinguished from S. algae ATCC 51192T. On the basis of the data presented in this study, strain DW01T represents a novel species, for which the name Shewanella haliotis sp. nov. is proposed. The type strain is DW01T (=KCTC 12896T=JCM 14758T).

Pandoraea oxalativorans sp. nov., Pandoraea faecigallinarum sp. nov. and Pandoraea vervacti sp. nov., isolated from oxalate-enriched culture

2011 ◽  
Vol 61 (9) ◽  
pp. 2247-2253 ◽  
Author(s):  
Nurettin Sahin ◽  
Akio Tani ◽  
Recep Kotan ◽  
Ivo Sedláček ◽  
Kazuhide Kimbara ◽  
...  
Keyword(s):  
16S Rrna ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Fatty Acid Profiles ◽  
Potassium Oxalate ◽  
Phenotypic Characteristics ◽  
B Subunit

Five isolates, designated TA2, TA4, TA25T, KOxT and NS15T were isolated in previous studies by enrichment in mineral medium with potassium oxalate as the sole carbon source and were characterized using a polyphasic approach. The isolates were Gram-reaction-negative, aerobic, non-spore-forming rods. Phylogenetic analyses based on 16S rRNA and DNA gyrase B subunit (gyrB) gene sequences confirmed that the isolates belonged to the genus Pandoraea and were most closely related to Pandoraea sputorum and Pandoraea pnomenusa (97.2–99.7 % 16S rRNA gene sequence similarity). The isolates could be differentiated from their closest relatives on the basis of several phenotypic characteristics. The major cellular fatty acid profiles of the isolates comprised C16 : 0, C18 : 1ω7c, C17 : 0 cyclo and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). On the basis of DNA–DNA hybridization studies and phylogenetic analyses, the isolates represent three novel species within the genus Pandoraea, for which the names Pandoraea oxalativorans sp. nov. (TA25T  = NBRC 106091T  = CCM 7677T  = DSM 23570T), Pandoraea faecigallinarum sp. nov. (KOxT  = NBRC 106092T  = CCM 2766T  = DSM 23572T) and Pandoraea vervacti sp. nov. (NS15T  = NBRC 106088T  = CCM 7667T  = DSM 23571T) are proposed.

scholarly journals Tetrathiobacter mimigardefordensis sp. nov., isolated from compost, a betaproteobacterium capable of utilizing the organic disulfide 3,3′-dithiodipropionic acid

2006 ◽  
Vol 56 (6) ◽  
pp. 1305-1310 ◽  
Author(s):  
Jan Hendrik Wübbeler ◽  
Tina Lütke-Eversloh ◽  
Stefanie Van Trappen ◽  
Peter Vandamme ◽  
Alexander Steinbüchel
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Alcaligenes Faecalis ◽  
Rrna Gene ◽  
Fatty Acid Profiles ◽  
Rrna Gene Sequence ◽  
Nearest Neighbours ◽  
The 16S Rrna Gene

In this study, a novel betaproteobacterium, strain DPN7T, was isolated under mesophilic conditions from compost because of its capacity to utilize the organic disulfide 3,3′-dithiodipropionic acid. Analysis of the 16S rRNA gene sequence of strain DPN7T revealed 98.5 % similarity to that of Tetrathiobacter kashmirensis LMG 22695T. Values for sequence similarity to members of the genera Alcaligenes, Castellaniella and Taylorella, the nearest neighbours of the genus Tetrathiobacter, were about 95 % or less. The DNA G+C content of strain DPN7T was 55.1 mol%. The level of DNA–DNA hybridization between strain DPN7T and T. kashmirensis LMG 22695T was 41 %, whereas it was much lower between strain DPN7T and Alcaligenes faecalis LMG 1229T (7 %) or Castellaniella defragrans LMG 18538T (5 %). This genotypic divergence was supported by differences in biochemical and chemotaxonomic characteristics. For this reason, and because of the differences in the protein and fatty acid profiles, strain DPN7T should be classified within a novel species of Tetrathiobacter, for which the name Tetrathiobacter mimigardefordensis sp. nov. is proposed. The type strain is strain DPN7T (=DSM 17166T=LMG 22922T).

scholarly journals Agromyces arachidissp. nov. Isolated from a Peanut (Arachis hypogaea) Crop Field

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Chandandeep Kaur ◽  
Anil Kumar Pinnaka ◽  
Nitin Kumar Singh ◽  
Monu Bala ◽  
Shanmugam Mayilraj
Keyword(s):  
Arachis Hypogaea ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Crop Field ◽  
Bacterium Strain ◽  
The 16S Rrna Gene

A Gram-positive, yellowish bacterium strain AK-1Twas isolated from soil sample collected from peanut (Arachis hypogaea) crop field and studied by using a polyphasic approach. The organism had morphological and chemotaxonomic properties consistent with its classification in the genusAgromyces. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain AK-1Twas closely related toAgromyces aurantiacus(98.6%) followed byAgromyces soli(98.3%),Agromyces tropicus(97.6%),Agromyces ulmi(97.3%),Agromyces flavus(97.2%), andAgromyces italicus(97.0%), whereas the sequence similarity values with respect to the otherAgromycesspecies with validly published names were between 95.3 and 96.7 %. However, the DNA-DNA hybridization values obtained between strain AK-1Tand other related strains were well below the threshold that is required for the proposal of a novel species. The DNAG+Ccontent of the strain is 71.8 mol%. The above data in combination with the phenotypic distinctiveness of AK-1Tclearly indicate that the strain represents a novel species, for which the nameAgromyces arachidissp. nov. is proposed. The type strain is AK-1T(=MTCC 10524T= JCM 19251T).

scholarly journals Rhodococcus kyotonensis sp. nov., a novel actinomycete isolated from soil

2007 ◽  
Vol 57 (9) ◽  
pp. 1956-1959 ◽  
Author(s):  
Bing Li ◽  
Keiko Furihata ◽  
Lin-Xian Ding ◽  
Akira Yokota
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Mycolic Acids ◽  
Rhodococcus Fascians ◽  
The 16S Rrna Gene ◽  
Is Strain

A polyphasic study was undertaken to establish the taxonomic position of an isolate, strain DS472T, from soil in Kyoto, Japan. Phylogenetic analysis, based on the 16S rRNA gene sequences, revealed that this strain constitutes a new subline within the genus Rhodococcus, with Rhodococcus yunnanensis YIM 70056T and Rhodococcus fascians DSM 20669T as its nearest phylogenetic neighbours (98.2 and 97.8 % sequence similarity, respectively). DNA–DNA hybridization experiments revealed 36 and 29 % relatedness between the isolate and its phylogenetic relatives, R. yunnanensis and R. fascians, respectively. Chemotaxonomic characteristics, including the major quinone MK-8(H2), predominant fatty acids C16 : 0, C18 : 1 ω9c and 10-methyl C18 : 0, the presence of cell-wall chemotype IV and mycolic acids, were consistent with the properties of members of the genus Rhodococcus. The DNA G+C content was 64.5 mol%. On the basis of both phenotypic and genotypic evidence, strain DS472T represents a novel species of the genus Rhodococcus, for which the name Rhodococcus kyotonensis sp. nov. is proposed. The type strain is strain DS472T (=IAM 15415T=CCTCC AB206088T).

scholarly journals Gemella parahaemolysans sp. nov. and Gemella taiwanensis sp. nov., isolated from human clinical specimens

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 2060-2065 ◽  
Author(s):  
Wei-Chun Hung ◽  
Hsiao-Jan Chen ◽  
Jui-Chang Tsai ◽  
Sung-Pin Tseng ◽  
Tai-Fen Lee ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Gram Staining

Four Gram-staining-positive, catalase-negative, coccoid isolates, designated NTUH_1465T, NTUH_2196, NTUH_4957 and NTUH_5572T, were isolated from human specimens. The four isolates displayed more than 99.6 % 16S rRNA gene sequence similarity with Gemella haemolysans ATCC 10379T, and 96.7 to 98.6 % similarity with Gemella sanguinis ATCC 700632T, Gemella morbillorum ATCC 27824T or Gemella cuniculi CCUG 42726T. However, phylogenetic analysis of concatenated sequences of three housekeeping genes, groEL, rpoB and recA, suggested that the four isolates were distinct from G. haemolysans ATCC 10379T and other species. Isolates NTUH_2196, NTUH_4957 and NTUH_5572T clustered together and formed a stable monophyletic clade. DNA–DNA hybridization values among strains NTUH_1465T and NTUH_5572T and their phylogenetically related neighbours were all lower than 49 %. The four isolates could be distinguished from G. haemolysans and other species by phenotypic characteristics. Based on the phylogenetic and phenotypic results, two novel species Gemella parahaemolysans sp. nov. (type strain NTUH_1465T = BCRC 80365T = JCM 18067T) and Gemella taiwanensis sp. nov. (type strain NTUH_5572T = BCRC 80366T = JCM 18066T) are proposed.

scholarly journals Glaciecola arctica sp. nov., isolated from Arctic marine sediment

2011 ◽  
Vol 61 (10) ◽  
pp. 2338-2341 ◽  
Author(s):  
Yan-Jiao Zhang ◽  
Xi-Ying Zhang ◽  
Zi-Hao Mi ◽  
Chun-Xiao Chen ◽  
Zhao-Ming Gao ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sediment ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Hybridization Data ◽  
Gene Sequence Analysis ◽  
Curved Rods ◽  
Type Strains

A Gram-negative, motile, psychrotolerant, oxidase- and catalase-positive bacterium, designated BSs20135T, was isolated from Arctic marine sediment. Cells were straight or slightly curved rods and formed circular, convex and yellowish-brown colonies. Buds and prosthecae could be produced. The strain grew at 4–28 °C (optimum 25 °C) and with 1–5 % (w/v) NaCl (optimum 2 %) and hydrolysed aesculin and DNA, but did not reduce nitrate to nitrite. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain BSs20135T belonged to the genus Glaciecola and shared 93.6–97.7 % sequence similarity with the type strains of known species of the genus Glaciecola. The major cellular fatty acids of strain BSs20135T were summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C17 : 1ω8c and C18 : 1ω7c. The genomic DNA G+C content was 40.3 mol%. Based on 16S rRNA gene sequence analysis, DNA–DNA hybridization data and phenotypic and chemotaxonomic characterization, strain BSs20135T represents a novel species, for which the name Glaciecola arctica sp. nov. is proposed. The type strain is BSs20135T ( = CCTCC AB 209161T  = KACC 14537T).

Sign in / Sign up

Export Citation Format

Share Document