scholarly journals Description of Helicobacter valdiviensis sp. nov., an Epsilonproteobacteria isolated from wild bird faecal samples

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1913-1919 ◽  
Author(s):  
Luis Collado ◽  
Ronald Jara ◽  
Susana González
Keyword(s):  
16S Rrna ◽  
Related Species ◽  
Type Species ◽  
Wild Bird ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Faecal Samples ◽  
Study Results

Two Gram-stain-negative, gently curved rod-shaped isolates (WBE14T and WBE19), recovered from wild bird faecal samples in the city of Valdivia (Southern Chile) were subjected to a polyphasic taxonomic study. Results of a genus-specific PCR indicated that these isolates belonged to the genus Helicobacter . This was further confirmed by a phylogenetic analyses based on the 16S rRNA, 60 kDa heat-shock protein (cpn60) and gyrase subunit B (gyrB) genes, where both strains formed a novel phylogenetic line within this genus. The 16S rRNA gene sequence similarity of strain WBE14T to the type strains of all other species of the genus Helicobacter examined ranged from 89.4 to 97.0 %; Helicobacter brantae and Helicobacter pametensis were the most closely related species. However, on the basis of the protein-coding genes Helicobacter pullorum and Helicobacter canadensis are the most closely related species. These data, together with their different morphological and biochemical characteristics, revealed that these strains represent a novel species, for which the name Helicobacter valdiviensis sp. nov. is proposed, with the type strain WBE14T ( = CECT 8410T = LMG 27920T).

scholarly journals Pseudomonas yamanorum sp. nov., a psychrotolerant bacterium isolated from a subantarctic environment

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 424-431 ◽  
Author(s):  
Víctor Gonzalo Arnau ◽  
Leandro Arturo Sánchez ◽  
Osvaldo Daniel Delgado
Keyword(s):  
16S Rrna ◽  
Related Species ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Psychrotolerant Bacterium ◽  
Type Strains

A psychrotolerant strain, 8H1T, was isolated from soil samples collected in Isla de los Estados, Ushuaia, Argentina. Cells were Gram-negative, aerobic, straight rods, occurring singly or in pairs, non-spore-forming and motile by means of two polar flagella. The isolate was able to grow in the range 4–35 °C, with optimum growth at 28 °C. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The polar lipid pattern of strain 8H1T comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid. Ubiquinone 9 (Q-9) was the predominant lipoquinone. The DNA G+C content was 59.8 mol%. 16S rRNA gene sequence-based phylogeny suggested the affiliation of strain 8H1T to the ‘Pseudomonas fluorescens group’, displaying ≥98.5 % sequence similarity to 29 type strains. A multilocus sequence analysis (MLSA) study performed by concatenating 16S rRNA, gyrB, rpoD and rpoB gene sequences showed that isolate 8H1T could be discriminated from closely related species of the genus Pseudomonas and placed in the ‘Pseudomonas gessardii subgroup’, including the species with the highest MLSA sequence similarities: Pseudomonas brenneri (96.2 %), P. gessardii (96.1 %), P. proteolytica (96.0 %), P. meridiana (96.0 %) and P. mucidolens (95.4 %). DNA–DNA hybridization analysis between 8H1T and the type strains of these closely related species revealed relatedness values of 27.0, 8.8, 41.2, 39.7 and 46.1 %, respectively. These results, together with differences in several phenotypic features, support the classification of a novel species, for which the name Pseudomonas yamanorum sp. nov. is proposed. The type strain is 8H1T ( = DSM 26522T = CCUG 63249T = LMG 27247T).

Acinetobacter kookii sp. nov., isolated from soil

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4402-4406 ◽  
Author(s):  
Ji Young Choi ◽  
Gwangpyo Ko ◽  
Weonghwa Jheong ◽  
Geert Huys ◽  
Harald Seifert ◽  
...  
Keyword(s):  
16S Rrna ◽  
Related Species ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
Content Type ◽  
Link Type

Two Gram-stain-negative, non-fermentative bacterial strains, designated 11-0202T and 11-0607, were isolated from soil in South Korea, and four others, LUH 13522, LUH 8638, LUH 10268 and LUH 10288, were isolated from a beet field in Germany, soil in the Netherlands, and sediment of integrated fish farms in Malaysia and Thailand, respectively. Based on 16S rRNA, rpoB and gyrB gene sequences, they are considered to represent a novel species of the genus Acinetobacter . Their 16S rRNA gene sequences showed greatest pairwise similarity to Acinetobacter beijerinckii NIPH 838T (97.9–98.4 %). They shared highest rpoB and gyrB gene sequence similarity with Acinetobacter johnsonii DSM 6963T and Acinetobacter bouvetii 4B02T (85.4–87.6 and 78.1–82.7 %, respectively). Strain 11-0202T displayed low DNA–DNA reassociation values (<40 %) with the most closely related species of the genus Acinetobacter . The six strains utilized azelate, 2,3-butanediol, ethanol and dl-lactate as sole carbon sources. Cellular fatty acid analyses showed similarities to profiles of related species of the genus Acinetobacter : summed feature 3 (C16 : 1ω7c, C16 : 1ω6c; 24.3–27.2 %), C18 : 1ω9c (19.9–22.1 %), C16 : 0 (15.2–22.0 %) and C12 : 0 (9.2–14.2 %). On the basis of the current findings, it is concluded that the six strains represent a novel species, for which the name Acinetobacter kookii sp. nov. is proposed. The type strain is 11-0202T ( = KCTC 32033T = JCM 18512T).

scholarly journals Alkalibacillus almallahensis sp. nov., a halophilic bacterium isolated from an inland solar saltern

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 2066-2071 ◽  
Author(s):  
Azahara Pérez-Davó ◽  
Margarita Aguilera ◽  
Alberto Ramos-Cormenzana ◽  
Mercedes Monteoliva-Sánchez
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Related Species ◽  
Type Species ◽  
Halophilic Bacterium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Solar Saltern ◽  
Content Type ◽  
Link Type

A halophilic, Gram-staining-positive, non-motile, endospore forming rod-shaped bacterial strain, S1LM8T, was isolated from a sediment sample collected from an inland solar saltern located in La Malahá, Granada (Spain). Growth was observed in media containing 7.5–30 % total salts (optimum 15 % total salts), at pH 7–10 (optimum pH 8) and at 15–50 °C (optimum 35–38 °C). The predominant isoprenoid quinone was MK-7. It contained A1γ-type peptidoglycan with meso-diaminopimelic acid as the diagnostic diamino acid. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The G+C content of its genomic DNA was 38.2 mol%. The affiliation of strain S1LM8T with the species of the genus Alkalibacillus was determined by 16S rRNA gene sequence comparison. The most closely related species were Alkalibacillus halophilus YIM 012T with 99.8 % similarity, Alkalibacillus salilacus BH163T with 99.8 % similarity and Alkalibacillus flavidus ISL-17T with 98.1 % similarity between their 16S rRNA gene sequences. However, DNA–DNA relatedness between the novel isolate and the related species of the genus Alkalibacillus was less than 34 %. Based on the phylogenetic, phenotypic and chemotaxonomic features, a novel species, Alkalibacillus almallahensis sp. nov. is proposed. The type strain is S1LM8T ( = CECT 8373T = DSM 27545T).

scholarly journals Bacillus invictae sp. nov., isolated from a health product

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3867-3876 ◽  
Author(s):  
Raquel Branquinho ◽  
Clara Sousa ◽  
Hugo Osório ◽  
Luís Meirinhos-Soares ◽  
João Lopes ◽  
...  
Keyword(s):  
Related Species ◽  
Acid Production ◽  
Type Species ◽  
Rrna Gene ◽  
Spectroscopic Techniques ◽  
Health Product ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-positive, rod-shaped, endospore-forming Bacillus isolate, Bi.FFUP1 T, recovered in Portugal from a health product was subjected to a polyphasic study and compared with the type strains of Bacillus pumilus , Bacillus safensis , Bacillus altitudinis and Bacillus xiamenensis , the phenotypically and genotypically most closely related species. Acid production from cellobiose, d-glucose and d-mannose and absence of acid production from d-arabinose, erythritol, inositol, maltose, mannitol, raffinose, rhamnose, sorbitol, starch and l-tryptophan discriminated this new isolate from the type strains of the most closely related species. Additionally, a significant different protein and carbohydrate signature was evidenced by spectroscopic techniques, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and Fourier transform IR spectroscopy with attenuated total reflectance. Using a chemometric approach, the score plot generated by principal component analysis clearly delineated the isolate as a separate cluster. The quinone system for strain Bi.FFUP1 T comprised predominantly menaquinone MK-7 and major polar lipids were diphosphatidylglycerol, an unidentified phospholipid and an unidentified glycolipid. Strain Bi.FFUP1 T showed ≥99 % 16S rRNA gene sequence similarity to B. safensis FO-036bT, B. pumilus (7061T and SAFR-032), B. altitudinis 41KF2bT and B. xiamenensis HYC-10T. Differences in strain Bi.FFUP1 T gyrB and rpoB sequences in comparison with the most closely related species and DNA–DNA hybridization experiments with Bi.FFUP1 T and B. pumilus ATCC 7061T, B. safensis FO-036bT, B. altitudinis 41KF2bT and B. xiamenensis HYC-10T gave relatedness values of 39.6 % (reciprocal 38.0 %), 49.9 % (reciprocal 42.9 %), 61.9 % (reciprocal 52.2 %) and 61.7 % (reciprocal 49.2 %), respectively, supported the delineation of strain Bi.FFUP1 T as a representative of a novel species of the genus Bacillus , for which the name Bacillus invictae sp. nov. is proposed, with strain Bi.FFUP1 T ( = DSM 26896T = CCUG 64113T) as the type strain.

scholarly journals Exiguobacterium enclense sp. nov., isolated from sediment

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1611-1616 ◽  
Author(s):  
Syed G. Dastager ◽  
Rahul Mawlankar ◽  
Vidya V. Sonalkar ◽  
Meghana N. Thorat ◽  
Poonam Mual ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phenotypic Traits ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Marine Sediment Sample

A Gram-stain-positive bacterium, designated strain NIO-1109T, was isolated from a marine sediment sample from Chorao Island, Goa, India. Phenotypic and chemotaxonomic characteristics and data from phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NIO-1109T was related to the genus Exiguobacterium . Strain NIO-1109T exhibited >98.0 % 16S rRNA gene sequence similarity with respect to Exiguobacterium indicum HHS 31T (99.5 %) and Exiguobacterium acetylicum NCIMB 9889T (99.1 %); the type strains of other species showed <98 % similarity. Levels of DNA–DNA relatedness between strain NIO-1109T and E. acetylicum DSM 20416T and E. indicum LMG 23471T were less than 70 % (33.0±2.0 and 37±3.2 %, respectively). Strain NIO-1109T also differed from these two closely related species in a number of phenotypic traits. Based on phenotypic, chemotaxonomic and phylogenetic data, strain NIO-1109T is considered to represent a novel species of the genus Exiguobacterium , for which the name Exiguobacterium enclense sp. nov. is proposed. The type strain is NIO-1109T ( = NCIM 5457T = DSM 25128T = CCTCC AB 2011124T).

scholarly journals Bacillus aciditolerans sp. nov., isolated from paddy soil

2019 ◽  
Vol 69 (4) ◽  
pp. 1155-1161 ◽  
Author(s):  
Meng-Jiao Ding ◽  
Nian-Jie Shang ◽  
Zhi-xin Xiao ◽  
Fei Shao ◽  
Li Liu ◽  
...  
Keyword(s):  
Related Species ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Test Results ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
The Town

A Gram-stain-positive, motile, rod-shaped bacterial strain, YN-1T, was isolated from a rice field in the town of Jietou, Yunnan Province, PR China. Colonies were circular, 1–2 mm in diameter, creamy white, with slightly irregular margins. The isolate grew optimally at 37 °C, pH 7.0 and with 1.0 % (w/v) NaCl. On the basis of the results of 16S rRNA gene sequence similarity comparisons, YN-1T clustered together with other species of the genus Bacillus and showed highest similarities with Bacillus onubensis 0911MAR22V3T (98.0 %), Bacillus humi LMG22167T (97.5 %), ' Bacillus timonensis ' 10403023 (97.4 %) and ' Bacillus sinesaloumensis' P3516 (97.1 %). However, the DNA–DNA hybridization values between YN-1T and closely related strains of species of the genus Bacillus were well below 47 %, indicating that they represent different taxa. The average nucleotide identity and the Genome-to-Genome Distance Calculator also revealed low relatedness (below 95 and 70 %, respectively) between YN-1T and type strains of closely related species of the genus Bacillus . The DNA G+C content of the strain was 40 mol%. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, and C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, three unidentified aminophospholipids and two other unidentified lipids. Physiological and biochemical test results were also different from those of the most closely related species. On the basis of the phenotypic, genetic and chemotaxonomic data, strain YN-1T is considered to represent a novel species of the genus Bacillus , for which the name Bacillus aciditolerans sp. nov. is proposed, with strain YN-1T (=CCTCC AB 2017280T=JCM 32973T) as the type strain.

scholarly journals Veillonella nakazawae sp. nov., an anaerobic Gram-negative coccus isolated from the oral cavity of Japanese children

2020 ◽  
Author(s):  
Izumi Mashima ◽  
Citra F. Theodorea ◽  
Ariadna A. Djais ◽  
Tadao Kunihiro ◽  
Yoshiaki Kawamura ◽  
...  
Keyword(s):  
16S Rrna ◽  
Oral Cavity ◽  
Related Species ◽  
Type Strain ◽  
Type Species ◽  
Japanese Children ◽  
Closely Related Species ◽  
Gram Negative ◽  
Content Type ◽  
Link Type

Two strains of previously unknown Gram-negative cocci, T1-7T and S6-16, were isolated from the oral cavity of healthy Japanese children. The two strains showed atypical phenotypic characteristics of members of the genus Veillonella , including catalase production. Sequencing of their 16S rRNA genes confirmed that they belong to genus Veillonella . Under anaerobic conditions, the two strains produced acetic acid and propionic acid as metabolic end-products in a trypticase–yeast extract–haemin medium containing 1 % (w/v) glucose, 1 % (w/v) fructose and 1 % (v/v) sodium lactate. Comparative analysis of the 16S rRNA, dnaK, rpoB and gltA gene sequences revealed that the two strains are phylogenetically homogeneous and comprise a distinct, novel lineage within the genus Veillonella . The sequences from the two strains shared the highest similarity, at 99.9, 95.8, 96.9 and 96.7 %, using the partial 16S rRNA, dnaK, rpoB and gltA gene sequences, respectively, with the type strains of the two most closely related species, Veillonella dispar ATCC 17748T and Veillonella infantium JCM 31738T. Furthermore, strain T1-7T shared the highest average nucleotide identity (ANI) value (94.06 %) with type strain of the most closely related species, V. infantium . At the same time, strain T1-7T showed the highest digital DNA–DNA hybridization (dDDH) value (55.5 %) with the type strain of V. infantium . The two strains reported in this study were distinguished from the previously reported species from the genus Veillonella based on catalase production, partial dnaK, rpoB and gltA sequences, average ANI and dDDH values. Based on these observations, the two strains represent a novel species, for which the name Veillonella nakazawae sp. nov. is proposed. The type strain is T1-7T (JCM 33966T=CCUG 74597T).

scholarly journals Vagococcus silagei sp. nov., isolated from brewer’s grain used to make silage in Taiwan

2020 ◽  
Vol 70 (3) ◽  
pp. 1953-1960 ◽  
Author(s):  
Yen-Chi Wu ◽  
Shih-Ting Lin ◽  
Jia-Rong Guu ◽  
Tomohiko Tamura ◽  
Koji Mori ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Sequence Similarity ◽  
Housekeeping Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-positive, coccus- or oval-shaped, non-motile, haemolytic, asporogenous, catalase- and oxidase-negative, and facultatively anaerobic strain, 2B-2T, was isolated from a brewer’s grain used to make silage in Taiwan. Comparative analyses of 16S rRNA, hsp60 and pheS gene sequences demonstrated that strain 2B-2T was a member of the genus Vagococcus . On the basis of 16S rRNA gene sequence similarity, the type strains of Vagococcus teuberi (98.4 % similarity), Vagococcus carniphilus (98.4 %), Vagococcus martis (98.2 %), Vagococcus penaei (98.2 %) and Vagococcus fluvialis (98.0 %) were the closest neighbours to this novel strain. The similarity levels of concatenated housekeeping gene sequences (hsp60 and pheS) between strain 2B-2T and these closely related species ranged from 84.5 to 88.0 %. The average nucleotide identity and in silico DNA–DNA hybridization values between strain 2B-2T and its closest relatives were lower than 72.9 and 21.6 %, respectively. The DNA G+C content was 34.7 mol%. Phenotypic and genotypic features demonstrated that strain 2B-2T represents a novel species of the genus Vagococcus , for which the name Vagococcus silagei sp. nov. is proposed. The type strain is 2B-2T (=BCRC 81132T=NBRC 113536T).

Massilia lurida sp. nov., isolated from soil

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2118-2123 ◽  
Author(s):  
Xiaonan Luo ◽  
Qiong Xie ◽  
Jiewei Wang ◽  
Huancheng Pang ◽  
Jinping Fan ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Inner Mongolia Autonomous Region

A bacterial isolate, designated strain D5T, was isolated from a soil sample collected from the Inner Mongolia Autonomous Region, China, and subjected to a taxonomic investigation using a polyphasic approach. Strain D5T was aerobic, Gram-stain-negative, rod-shaped and motile. Strain D5T fell within the evolutionary radius of the genus Massilia in the phylogenetic tree based on 16S rRNA gene sequences and was most closely related to Massilia plicata 76T with 97.3 % 16S rRNA gene sequence similarity. The predominant quinone of strain D5T was Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. These chemotaxonomic data supported the affiliation of strain D5T to the genus Massilia . The genomic DNA G+C content was 65.9 mol%. Mean DNA–DNA relatedness values between strain D5T and the phylogenetically most closely related species of the genus Massilia , Massilia plicata KCTC 12344T and Massilia dura KCTC 12342T, were 26 and 21 %, respectively. Strain D5T could be differentiated from recognized species of the genus Massilia by several phenotypic characteristics. It is clear from the data presented that strain D5T represents a novel species of the genus Massilia , for which the name Massilia lurida sp. nov. is proposed. The type strain is D5T ( = CGMCC 1.10822T = KCTC 23880T).

Flavobacterium tructae sp. nov. and Flavobacterium piscis sp. nov., isolated from farmed rainbow trout (Oncorhynchus mykiss)

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 392-399 ◽  
Author(s):  
L. Zamora ◽  
A. I. Vela ◽  
C. Sánchez-Porro ◽  
M. A. Palacios ◽  
E. R. B. Moore ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
16S Rrna ◽  
Related Species ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type

Four Gram-staining-negative, catalase- and oxidase-positive, pale-orange pigmented bacterial strains (435-08T, 47B-3-09, 412R-09T and 60B-3-09) were isolated from diseased rainbow trout. Analysis of their 16S rRNA gene sequences suggested their adscription to the genus Flavobacterium . Strains formed two phylogenetic groups represented by strains 435-08T and 47B-3-09 (group A), and strains 412R-09T and 60B-3-09 (group B) displaying 16S rRNA sequence similarities greater than 99.8–99.9 % within their respective groups. Strain 435-08T exhibited the highest levels of similarity with Flavobacterium aquidurense WB-1.1.56T (98.6 % sequence similarity) and strain 412R-09T with Flavobacterium frigidimaris KUC-1T and Flavobacterium aquidurense WB-1.1.56T (98.9 % and 98.6 % sequence similarity, respectively). DNA–DNA hybridization studies showed low levels of relatedness between strain 435-08T and strain 412R-09T and between both strains and the most closely related species of the genus Flavobacterium . The genomic DNA G+C contents of strains 435-08T and 412R-09T were 36.2 and 34.3 mol%, respectively. The predominant respiratory quinone of both strains was MK-6 and the major fatty acids were iso-C15 : 0, C16 : 1ω7c and C15 : 0. The two groups of strains could be distinguished from each other and from related species of the genus Flavobacterium by a number of phenotypic properties. Phylogenetic, genotypic and phenotypic evidence indicated that strains of groups A and B represent two novel species of the genus Flavobacterium , for which the names Flavobacterium tructae sp. nov. (type strain 435-08T = CECT 7791T = CCUG 60100T) and Flavobacterium piscis sp. nov. (type strain 412R-09T = CECT 7911T = CCUG 60099T) are proposed.

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