Roseomonas riguiloci sp. nov., isolated from wetland freshwater

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 3024-3029 ◽  
Author(s):  
Keun Sik Baik ◽  
Seong Chan Park ◽  
Han Na Choe ◽  
Se Na Kim ◽  
Jae-Hak Moon ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Approach

A non-motile, coccobacillus-shaped and pink pigmented bacterium, designated strain 03SU10-PT, was isolated from wetland freshwater (Woopo wetland, Republic of Korea). Cells were Gram reaction-negative and catalase- and oxidase-positive. The major fatty acids (>10 % of total) were C18 : 1ω7c and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). The predominant respiratory lipoquinone was Q-10. The DNA G+C content was 68 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine and an unknown aminolipid. Spermidine, putrescine and 1,3-diaminopropane were the major polyamines. A phylogenetic tree based on 16S rRNA gene sequence comparisons showed that strain 03SU10-PT formed an evolutionary lineage within the radiation enclosing the members of the genus Roseomonas . The nearest neighbour to the novel strain was Roseomonas stagni HS-69T (96.3 % gene sequence similarity). The evidence provided by the polyphasic taxonomic approach used in this study indicated that strain 03SU10-PT could not be assigned to any recognized species; therefore a novel species is proposed, Roseomonas riguiloci sp. nov., with 03SU10-PT ( = KCTC 23339T = JCM 17520T) as the type strain.

Rhodococcus spelaei sp. nov., isolated from a cave, and proposals that Rhodococcus biphenylivorans is a later synonym of Rhodococcus pyridinivorans, Rhodococcus qingshengii and Rhodococcus baikonurensis are later synonyms of Rhodococcus erythropolis, and Rhodococcus percolatus and Rhodococcus imtechensis are later synonyms of Rhodococcus opacus

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Soon Dong Lee ◽  
In Seop Kim
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rhodococcus Erythropolis ◽  
Rhodococcus Opacus ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Two novel actinobacterial strains, designated C9-5T and C3-43, were isolated from soil samples of a cave in Jeju Island, Republic of Korea, and subjected to taxonomic study by a polyphasic approach. The organisms exhibited a typical rod–coccus developmental cycle during growth and grew at 10–30 °C, pH 5–9 and 0–3 % (w/v) NaCl. In 92 single-copy core gene sequence analysis, strain C9-5T was loosely associated with Rhodococcus tukisamuensis , albeit sharing low 16S rRNA gene sequence similarity (97.4 %). A combination of morphological and chemotaxonomic characteristics supported assignment with the genus Rhodococcus . With respect to 16S rRNA gene sequence similarity, the novel isolates showed the highest identity to the type strain of Rhodococcus subtropicus (98.7 % sequence similarity), followed by Rhodococcus olei (98.5 %) and Rhodococcus pedocola (98.4 %).The average nucleotide identity and digital DNA–DNA hybridization values between strain C9-5T and members of the genus Rhodococcus were ≤81.5 and ≤37.1 %, respectively. A set of physiological and chemotaxonomic properties together with overall genomic relatedness differentiated the novel isolates from members of the genus Rhodococcus , for which the name Rhodococcus spelaei sp. nov. is proposed. The type strain is C9-5T (=KACC 19822T=DSM 107558T). Based on genome analysis performed here, it is also proposed that Rhodococcus biphenylivorans Su et al. 2015 is a later heterotypic synonym of Rhodococcus pyridinivorans Yoon et al. 2000, Rhodococcus qingshengii Xu et al. 2007 and Rhodococcus baikonurensis Li et al. 2004 are later heterotypic synonyms of Rhodococcus erythropolis (Gray and Thornton 1928) Goodfellow and Alderson 1979 (Approved Lists 1980), and Rhodococcus percolatus Briglia et al. 1996 and Rhodococcus imtechensis Ghosh et al. 2006 are later heterotypic synonyms of Rhodococcus opacus Klatte et al. 1995.

scholarly journals Phenylobacterium kunshanense sp. nov., isolated from the sludge of a pesticide manufacturing factory

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 325-330 ◽  
Author(s):  
Cuiwei Chu ◽  
Cansheng Yuan ◽  
Xin Liu ◽  
Li Yao ◽  
Jianchun Zhu ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Ubiquinone 10 ◽  
Sequence Similarities

A novel aerobic, Gram-stain-negative, motile bacterium, designated strain BUT-10T, was isolated from the sludge of a pesticide manufacturing factory in Kunshan, China. Cells were rod-shaped (0.4–0.45×0.9–1.4 µm) and colonies were white, circular with entire edges and had a smooth surface. The strain grew at 25–37 °C, at pH 6.0–8.0 and with 0–0.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain BUT-10T was a member of the genus Phenylobacterium , and showed highest sequence similarities to Phenylobacterium muchangponense A8T (97.49 %), Phenylobacterium immobile DSM 1986T (97.14 %) and Phenylobacterium lituiforme FaiI3T (96.34 %). Major fatty acids (>5 %) were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The major isoprenoid quinone was ubiquinone-10. The DNA G+C content was 71.85 mol%. Strain BUT-10T showed low DNA–DNA relatedness with P. muchangponense A8T (15.7±2.9 %) and P. immobile DSM 1986T (12.8±1.1 %). On the basis of the phenotypic, phylogenetic and genotypic data, strain BUT-10T is considered to represent a novel species of the genus Phenylobacterium , for which the name Phenylobacterium kunshanense sp. nov. is proposed. The type strain is BUT-10T ( = CCTCC AB 2013085T = KCTC 42014T).

Rhodanobacter denitrificans sp. nov., isolated from nitrate-rich zones of a contaminated aquifer

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2457-2462 ◽  
Author(s):  
Om Prakash ◽  
Stefan J. Green ◽  
Puja Jasrotia ◽  
Will A. Overholt ◽  
Andy Canion ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Contaminated Aquifer ◽  
Content Type ◽  
Link Type ◽  
Characteristic Features

Bacterial strains 2APBS1T and 116-2 were isolated from the subsurface of a nuclear legacy waste site where the sediments are co-contaminated with large amounts of acids, nitrate, metal radionuclides and other heavy metals. A combination of physiological and genetic assays indicated that these strains represent the first member of the genus Rhodanobacter shown to be capable of complete denitrification. Cells of strain 2APBS1T and 116-2 were Gram-negative, non-spore-forming rods, 3–5 µm long and 0.25–0.5 µm in diameter. The isolates were facultative anaerobes, and had temperature and pH optima for growth of 30 °C and pH 6.5; they were able to tolerate up to 2.0 % NaCl, although growth improved in its absence. Strains 2APBS1T and 116-2 contained fatty acid and quinone (ubiquinone-8; 100 %) profiles that are characteristic features of the genus Rhodanobacter . Although strains 2APBS1T and 116-2 shared high 16S rRNA gene sequence similarity with Rhodanobacter thiooxydans LCS2T (>99 %), levels of DNA–DNA relatedness between these strains were substantially below the 70 % threshold used to designate novel species. Thus, based on genotypic, phylogenetic, chemotaxonomic and physiological differences, strains 2APBS1T and 116-2 are considered to represent a single novel species of the genus Rhodanobacter , for which the name Rhodanobacter denitrificans sp. nov. is proposed. The type strain is 2APBS1T ( = DSM 23569T = JCM 17641T).

Chitinophaga cymbidii sp. nov., isolated from Cymbidium goeringii roots

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1800-1804 ◽  
Author(s):  
Lubin Li ◽  
Lei Sun ◽  
Nan Shi ◽  
Lin Liu ◽  
Huijuan Guo ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Cellular Fatty Acids ◽  
Link Type ◽  
Gram Staining ◽  
Cymbidium Goeringii

Two Gram-staining-negative, aerobic, non-spore-forming rod-shaped, non-motile bacteria, designated strains R156-2T and T58-2 were isolated from the roots of Cymbidium goeringii. The colonies were yellow-pigmented. On the basis of 16S rRNA gene sequence similarity, strains R156-2T and T58-2 were shown to be members of the genus Chitinophaga . Strains R156-2T and T58-2 showed the greatest level of sequence similarity with Chitinophaga niabensis (96.0–96.3 %). The major menaquinone was MK-7. The main cellular fatty acids were iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. Phenotypic and genotypic analyses indicated that strains R156-2T and T58-2 could not be assigned to any recognized species. Therefore, strains R156-2T and T58-2 represent a novel species of the genus Chitinophaga , for which the name Chitinophaga cymbidii sp. nov. is proposed. The type strain is R156-2T ( = ACCC 05363T = KCTC 23738T). The DNA G+C content of this strain is 51.9 mol%.

scholarly journals Ochrobactrum teleogrylli sp. nov., a pesticide-degrading bacterium isolated from the insect Teleogryllus occipitalis living in deserted cropland

2020 ◽  
Vol 70 (4) ◽  
pp. 2217-2225 ◽  
Author(s):  
Mengyao Hu ◽  
Xiaoguang Li ◽  
Zhenjiang Li ◽  
Bo Liu ◽  
Zhigang Yang ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium ◽  
A Genome ◽  
Pr China

A Gram-stain-negative, non-spore-forming, motile, aerobic, rod-shaped bacteria strain, designated LCB8T, was isolated from the insect Teleogryllus occipitalis captured from a deserted cropland in Shuangliu district, Chengdu, PR China. Phylogenetic analysis on the basis of 16S rRNA gene sequence indicated that the strain represented a member of the genus Ochrobactrum , family Brucellaceae , class Alphaproteobacteria. Ochrobactrum pecoris CCUG 60088T (97.9 %) and Ochrobactrum haematophilum CCUG 38531T (98.8 %) were identified as the most closely related phylogenetic neighbours of strain LCB8T. The novel strain was able to grow at salt concentrations of 0–4.5 % (w/v), pH 5–9 and temperatures of 20–42 °C. The major quinone system was ubiquinone Q-10, the major fatty acids were C18 : 1ω7c, C16 : 0 and C18 : 0. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol and four undefined aminolipids. The major polyamines were putrescine and spermidine. Genome sequencing revealed a genome size of 4.76 Mbp and a DNA G+C content of 57.1 mol%. These phenotypic, genotypic and chemotaxonomic traits excellently supported the affiliation of LCB8T to the genus Ochrobactrum . Pairwise determined whole-genome average nucleotide identity (ANI) values indicated that strain LCB8T represents a novel species, for which we propose the name Ochrobactrum teleogrylli sp. nov. with the type strain LCB8T (=KCTC 72031T=CGMCC 1.13984T).

Sneathia vaginalis sp. nov. (Fusobacteriales, Leptotrichiaceae) as a replacement of the species ‘Sneathia amnii’ Harwich et al. 2012 and ‘Leptotrichia amnionii’ Shukla et al. 2002, and emended description of Sneathia Collins et al. 2001

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Tobias Eisenberg ◽  
Sabine Gronow ◽  
Jane Falgenhauer ◽  
Can Imirzalioglu ◽  
Kristin Mühldorfer ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Members of the genus Sneathia are fastidious bacteria that predominantly colonise the female genital tract and are significantly associated with reproductive disorders and genital and neonatal disease. From a taxonomical perspective, the genus only comprises the species Sneathia sanguinegens . Numerous reports on a second species, ‘Sneathia amnii’, have been published, but the name has never been validated. The same is the case for ‘Leptotrichia amnionii’, which was previously shown to belong to the same species as ‘Sneathia amnii’. We studied strains DSM 16631T and DSM 16630, which have been identified and deposited as ‘Leptotrichia amnionii’ previously. At the time of isolation, these strains were found to be most closely related to, but clearly different from, Sneathia sanguinegens based on 16S rRNA gene sequence similarities. Both strains proved to be almost indistinguishable from ‘Sneathia amnii’ based on molecular, morphological and physiological traits. The 16S rRNA gene sequence analysis revealed that strain DSM 16631T was assigned to the genus Sneathia with a sequence similarity of 95.47 % to Sneathia sanguinegens CCUG 41628T, followed by type strains of Caviibacter abscessus (93.03 %), Oceanivirga salmonicida (92.68 %) and Oceanivirga miroungae (91.97 %) as the next closely related members of the Leptotrichiaceae . The novel species was also clearly differentiated from other related taxa by core genome phylogeny, average nucleotide and amino acid identities, in silico DNA–DNA hybridization and MALDI-TOF MS. With respect to chemotaxonomic and physiological patterns, strains DSM 16631T and DSM 16630 were again highly similar to Sneathia sanguinegens . On the basis of these data, we propose the novel species Sneathia vaginalis sp. nov. with the type strain DSM 16631T (=CCUG 52977T=CCUG 52889AT) and a second strain DSM 16630 (=CCUG 52976=CCUG 52888) that were both isolated from bloodstream infections in women with puerperal fever in France. The G+C content of the DNA of the type strain is 28.4 mol% and the genome size is 1.28 Mbp. Based on the observed extremely high similarities of genotypic and phenotypic traits of the novel proposed species to those reported for ‘Sneathia amnii’, we recommend using this new name in all further publications on this taxon.

scholarly journals Lysobacter terrae sp. nov. isolated from Aglaia odorata rhizosphere soil

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 587-592 ◽  
Author(s):  
Hien T. T. Ngo ◽  
KyungHwa Won ◽  
Juan Du ◽  
Heung-Min Son ◽  
YongJin Park ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Rhizosphere Soil ◽  
Novel Species ◽  
Rrna Gene ◽  
Gram Stain ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type

A Gram-stain negative, facultatively anaerobic, non-motile, rod-shaped bacterium, designated strain THG-A13T, was isolated from Aglaia odorata rhizosphere soil in Gyeonggi-do, Republic of Korea. Based on 16S rRNA gene sequence comparisons, strain THG-A13T had close similarity with Lysobacter niabensis GH34-4T (98.5 %), Lysobacter oryzae YC6269T (97.9 %) and Lysobacter yangpyeongensis GH19-3T (97.3 %). Chemotaxonomic data revealed that strain THG-A13T possesses ubiquinone-8 (Q8) as the predominant isoprenoid quinone and iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1ω9c as the major fatty acids. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol) and diphosphatidylglycerol. The G+C content was 66.3 mol%. The DNA–DNA relatedness values between strain THG-A13T and its closest phylogenetic neighbours were below 18.0 %. These data corroborated the affiliation of strain THG-A13T to the genus Lysobacter . These data suggest that the isolate represents a novel species for which the name Lysobacter terrae sp. nov. is proposed, with THG-A13T as the type strain ( = KACC 17646T = JCM 19613T).

scholarly journals Actinoplanes abujensis sp. nov., isolated from Nigerian arid soil

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 960-965 ◽  
Author(s):  
Anil Sazak ◽  
Nevzat Sahin ◽  
Mustafa Camas
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Arid Soil ◽  
Link Type ◽  
Type Strains

A novel actinobacterial strain, A4029T, isolated from arid soil of Abuja, Nigeria, and provisionally assigned to the genus Actinoplanes , was subjected to a polyphasic taxonomic study. 16S rRNA gene sequence similarity studies showed that strain A4029T belonged to the genus Actinoplanes , being most closely related to Actinoplanes brasiliensis DSM 43805T (98.9 %) and Actinoplanes deccanensis DSM 43806T (98.0 %); similarity to other type strains of the genus Actinoplanes ranged from 96.2 to 97.9 %. Chemotaxonomic data [major menaquinone MK-9(H4); major polar lipids phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol; characteristic sugars arabinose and xylose; major fatty acids iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, C17 : 1ω9c and iso-C14 : 0] confirmed the affiliation of strain A4029T to the genus Actinoplanes . The results of DNA–DNA hybridizations and phylogenetic analysis, together with phenotypic and biochemical test data, allowed strain A4029T to be differentiated from strains of other Actinoplanes species. Therefore, strain A4029T represents a novel species, for which the name Actinoplanes abujensis sp. nov. is proposed, with A4029T ( = DSM 45518T = NRRL B-24835T = KCTC 19984T) as the type strain.

scholarly journals Actinoplanes lutulentus sp. nov., isolated from mucky soil in China

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1782-1788 ◽  
Author(s):  
Ruixia Gao ◽  
Chongxi Liu ◽  
Junwei Zhao ◽  
Feiyu Jia ◽  
Chuang Li ◽  
...  
Keyword(s):  
Type Species ◽  
North China ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type

A novel actinomycete, designated strain NEAU-GRX6T, was isolated from mucky soil collected from a stream of Jinlong Mountain in Harbin, Heilongjiang Province, north China, and characterized using a polyphasic approach. The isolate formed irregular sporangia containing motile sporangiospores on the substrate mycelium. The whole-cell sugars were xylose, glucose and galactose. The predominant menaquinones were MK-9(H6), MK-10(H4) and MK-9(H4). The major fatty acids were C16 : 0, C15 : 0, C18 : 1ω9c, C17 : 1ω7c and C18 : 0. The phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol. The DNA G+C content was 67 mol%. 16S rRNA gene sequence similarity studies showed that strain NEAU-GRX6T belonged to the genus Actinoplanes , being most closely related to Actinoplanes palleronii IFO 14916T (97.80 % similarity) and Actinoplanes missouriensis NBRC 102363T (97.76 %). However, the low observed levels of DNA–DNA relatedness allowed the isolate to be differentiated from the above-mentioned species of the genus Actinoplanes . Moreover, strain NEAU-GRX6T could also be distinguished from A. palleronii IFO 14916T and A. missouriensis NBRC 102363T by phenotypic characteristics. Therefore, it is proposed that strain NEAU-GRX6T represents a novel species of the genus Actinoplanes , for which the name Actinoplanes lutulentus sp. nov. is proposed. The type strain is strain NEAU-GRX6T ( = CGMCC 4.7090T = DSM 45883T).

Bombella favorum sp. nov. and Bombella mellum sp. nov., two novel species isolated from the honeycombs of Apis mellifera

2021 ◽  
Author(s):  
Maik Hilgarth ◽  
Johannes Redwitz ◽  
Matthias A. Ehrmann ◽  
Rudi F. Vogel ◽  
Frank Jakob
Keyword(s):  
Apis Mellifera ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

As part of a study investigating the microbiome of bee hives and honey, two novel strains (TMW 2.1880T and TMW 2.1889T) of acetic acid bacteria were isolated and subsequently taxonomically characterized by a polyphasic approach, which revealed that they cannot be assigned to known species. The isolates are Gram-stain-negative, aerobic, pellicle-forming, catalase-positive and oxidase-negative. Cells of TMW 2.1880T are non-motile, thin/short rods, and cells of TMW 2.1889T are motile and occur as rods and long filaments. Morphological, physiological and phylogenetic analyses revealed a distinct lineage within the genus Bombella . Strain TMW 2.1880T is most closely related to the type strain of Bombella intestini with a 16S rRNA gene sequence similarity of 99.5 %, and ANIb and in silico DDH values of 94.16 and 56.3 %, respectively. The genome of TMW 2.1880T has a size of 1.98 Mb and a G+C content of 55.3 mol%. Strain TMW 2.1889T is most closely related to the type strain of Bombella apis with a 16S rRNA gene sequence similarity of 99.5 %, and ANIb and in silico DDH values of 85.12 and 29.5 %, respectively. The genome of TMW 2.1889T has a size of 2.07 Mb and a G+C content of 60.4 mol%. Ubiquinone analysis revealed that both strains contained Q-10 as the main respiratory quinone. Major fatty acids for both strains were C16 : 0, C19 : 0 cyclo ω8c and summed feature 8, respectively, and additionally C14 : 0 2-OH only for TMW 2.1880T and C14 : 0 only for TMW 2.1889T. Based on polyphasic evidence, the two isolates from honeycombs of Apis mellifera represent two novel species of the genus Bombella , for which the names Bombella favorum sp. nov and Bombella mellum sp. nov. are proposed. The designated respective type strains are TMW 2.1880T (=LMG 31882T=CECT 30114T) and TMW 2.1889T (=LMG 31883T=CECT 30113T).

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