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

Author(s):  
Izumi Mashima ◽  
Citra F. Theodorea ◽  
Ariadna A. Djais ◽  
Tadao Kunihiro ◽  
Yoshiaki Kawamura ◽  
...  

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).

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 424-431 ◽  
Author(s):  
Víctor Gonzalo Arnau ◽  
Leandro Arturo Sánchez ◽  
Osvaldo Daniel Delgado

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).


2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 418-422 ◽  
Author(s):  
Masaaki Okamoto ◽  
Susumu Imai ◽  
Mayu Miyanohara ◽  
Wataru Saito ◽  
Yasuko Momoi ◽  
...  

Six strains, TKU 25, TKU 28, TKU 30, TKU 31T, TKU 33 and TKU 34, were isolated from the oral cavity of a chimpanzee (Pan troglodytes). Colonies of strains grown on Mitis–Salivarius agar were similar in morphology to that of Streptococcus mutans . The novel strains were Gram-stain-positive, facultatively anaerobic cocci that lacked catalase activity. Analysis of the partial 16S rRNA gene sequences of these isolates showed that the most closely related strain was the type strain of S. mutans (96.4 %). The next closely related strains to the isolates were the type strains of Streptococcus devriesei (94.5 %) and Streptococcus downei (93.9 %). These isolates could be distinguished from S. mutans by inulin fermentation and alkaline phosphatase activity (API ZYM system). The peptidoglycan type of the novel isolates was Glu–Lys–Ala3. Strains were not susceptible to bacitracin. On the basis of phenotypic characterization, partial 16S rRNA gene and two housekeeping gene (groEL and sodA) sequence data, we propose a novel taxon, Streptococcus troglodytae sp. nov.; the type strain is TKU 31T ( = JCM 18038T = DSM 25324T).


2020 ◽  
Vol 70 (5) ◽  
pp. 3037-3048 ◽  
Author(s):  
Dmitriy V. Volokhov ◽  
Jochen Blom ◽  
Megan Amselle ◽  
Pierluigi Delmonte ◽  
Yamei Gao ◽  
...  

Two independent strains of a Leptotrichia species (ES3154-GLUT and ES2714_GLU) were isolated from the oral cavity of northern elephant seals (Mirounga angustirostris) that were admitted to The Marine Mammal Centre facilities in California, USA. The strains were isolated from oral swabs by cultivation in PPLO broth supplemented with serum, penicillin and colistin in anaerobic conditions. The strains were Gram-negative, pleomorphic, indole-, oxidase- and catalase-negative, non-spore-forming, non-motile rods/coccobacilli in short chains. The 16S rRNA gene sequence of these strains shared 94.42 % nucleotide similarity with Oceanivirga salmonicida AVG 2115T but demonstrated ≤86.00–92.50 % nucleotide similarity to the 16S rRNA genes of other species of the family Leptotrichiaceae . The genome was sequenced for strain ES3154-GLUT. Average nucleotide identity values between strain ES3154-GLUT and 15 type strain genomes from the family Leptotrichiaceae ranged from 66.74 % vs. Sebaldella termitidis to 73.35 % vs. O. salmonicida . The whole genome phylogeny revealed that the novel species was most closely related to O. salmonicida AVG 2115T. This relationship was also confirmed by nucleotide similarity and multilocus phylogenetic analyses employing various housekeeping genes (partial 23S rRNA, rpoB, rpoC, rpoD, polC, adh, gyrA and gyrB genes). Chemotaxonomic and phenotypical features of strain ES3154-GLUT were in congruence with closely related members of the family Leptotrichiaceae , represented by similar enzyme profiles and fatty acid patterns. MALDI-TOF MS analysis was capable to clearly discriminate strain ES3154-GLUT from all currently described taxa of the family Leptotrichiaceae . Based on these data, we propose a novel species of the genus Oceanivirga , for which the name Oceanivirga miroungae sp. nov. is proposed with the type strain ES3154-GLUT (=DSM 109740T=CCUG 73653T=ATCC TSD-189T=NCTC 14411T) and one representative strain ES2714_GLU. The G+C content is 26.82 %, genome size is 1 356 983 bp.


2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1913-1919 ◽  
Author(s):  
Luis Collado ◽  
Ronald Jara ◽  
Susana González

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).


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 ◽  
...  

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.


2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2572-2578 ◽  
Author(s):  
Mie Johanne Hansen ◽  
Mads Frost Bertelsen ◽  
Henrik Christensen ◽  
Anders Miki Bojesen ◽  
Magne Bisgaard

A total of 27 bacterial isolates from California sea lions and a walrus tentatively classified within the family Pasteurellaceae was further characterized by genotypic and phenotypic tests. Phylogenetic analysis of partial 16S rRNA and rpoB gene sequences showed that the isolates investigated formed a monophyletic group, tentatively designated Bisgaard taxon 57. According to 16S rRNA gene sequences, the most closely related species with a validly published name was Bisgaardia hudsonensis and the most closely related species based on rpoB sequence comparison was Pasteurella multocida subsp. multocida; highest similarities between the isolates and the type strains of B. hudsonensis and P. multocida subsp. multocida were 95.0 and 88.2%. respectively. All isolates of Bisgaard taxon 57 exhibit the phenotypic characters of the family Pasteurellaceae . Members of Bisgaard taxon 57 can be separated from existing genera of the Pasteurellaceae by the following tests: positive reactions for catalase, oxidase, Voges–Proskauer and indole; no X- or V-factor dependency; and acid production from l-arabinose (slow), l-fucose, maltose and trehalose, but not from dulcitol, d-mannitol, d-mannose or sucrose. The main fatty acids of Bisgaard taxon 57 (CCUG 59994T) are C14 : 0, C16 : 0, C16 : 1ω7c and the summed feature C14 : 0 3-OH/iso-C16 : 1 I. This fatty acid profile is characteristic of members of the Pasteurellaceae . The quinone profile of Bisgaard taxon 57 (DSM 23800T) was similar to that of other genera in the Pasteurellaceae . The DNA G+C content of strain Baika1T is 36.2 mol%, which is at the lower end of the range for members of the family Pasteurellaceae . On the basis of both phylogenetic and phenotypic evidence, it is proposed that members of Bisgaard taxon 57 should be classified as representatives of a novel species in a new genus, Otariodibacter oris gen. nov., sp. nov. The type strain of Otariodibacter oris is Baika1T ( = CCUG 59994T = DSM 23800T), which was isolated from the oral cavity of a healthy California sea lion in Copenhagen Zoo, Denmark, in 2007.


2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3571-3577 ◽  
Author(s):  
Atsuko Ueki ◽  
Misa Watanabe ◽  
Yoshimi Ohtaki ◽  
Nobuo Kaku ◽  
Katsuji Ueki

A strictly anaerobic bacterial strain, WK011T, was isolated from a methanogenic reactor treating waste from cattle farms. The cells stained Gram-negative and were curved rods with a polar or subpolar flagellum. Spore formation was not observed. The optimum temperature for growth was 35 °C and the optimum pH was 6.7. Tests for oxidase, catalase and nitrate-reduction activities were negative. Hydrogen sulfide was produced. The strain fermented carbohydrates and produced acetate and propionate as major fermentation products. The genomic DNA G+C content was 41.7 mol%. The major cellular fatty acids were C15 : 0, C16 : 1ω9c and C18 : 1 dimethylacetal. The diagnostic diamino acid of the cell-wall peptidoglycan was meso-diaminopimelic acid. The most closely related species to strain WK011T on the basis of 16S rRNA gene sequences were Propionispira arboris and Zymophilus raffinosivorans (95.6 % sequence similarity to the type strains of both species). It was shown by phylogenetic and phenotypic examination of the type strains of related species, including the second species of the genus Zymophilus , Zymophilus paucivorans , that the two genera should be combined and that the two species of the genus Zymophilus should be transferred to the genus Propionispira, as Propionispira raffinosivorans comb. nov. (type strain SH2T = ATCC 49691T = DSM 20765T) and Propionispira paucivorans comb. nov. (type strain AA1T = ATCC 49689T = DSM 20756T), with an emended description of the genus Propionispira . Based on differences in the phylogenetic and phenotypic characteristics of strain WK011T from those of closely related species, the novel species Propionispira arcuata sp. nov. is proposed to accommodate the strain. The type strain is WK011T ( = JCM 16475T = DSM 22929T).


2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1819-1824 ◽  
Author(s):  
Sooyeon Park ◽  
Ji-Min Park ◽  
Chul-Hyung Kang ◽  
Song-Gun Kim ◽  
Jung-Hoon Yoon

A Gram-stain-negative, non-motile, aerobic and pleomorphic bacterium, designated BS-W13T, was isolated from a tidal flat on the South Sea, South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain BS-W13T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Neighbour-joining and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain BS-W13T clustered with the type strain of Seohaeicola saemankumensis , showing the highest sequence similarity (95.96 %) to this strain. Strain BS-W13T exhibited 16S rRNA gene sequence similarity values of 95.95, 95.91, 95.72 and 95.68 % to the type strains of Sulfitobacter donghicola , Sulfitobacter porphyrae , Sulfitobacter mediterraneus and Roseobacter litoralis , respectively. Strain BS-W13T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The polar lipid profile of strain BS-W13T, containing phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid as major components, was distinguishable from those of some phylogenetically related taxa. The DNA G+C content of strain BS-W13T was 58.1 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain BS-W13T constitutes a novel genus and species within family Rhodobacteraceae of the class Alphaproteobacteria , for which the name Pseudoseohaeicola caenipelagi gen. nov., sp. nov. is proposed. The type strain is BS-W13T ( = KCTC 42349T = CECT 8724T).


2020 ◽  
Vol 70 (10) ◽  
pp. 5287-5295 ◽  
Author(s):  
Yajun Ge ◽  
Yuanmeihui Tao ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Dong Jin ◽  
...  

Four unknown strains belonging to the genus Arthrobacter were isolated from plateau wildlife on the Qinghai–Tibet Plateau of PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four isolates were separated into two clusters. Cluster I (strains 785T and 208) had the greatest 16S rRNA gene sequence similarity to Arthrobacter citreus (98.6 and 98.7 %, respectively), Arthrobacter luteolus (98.0 and 98.1%, respectively), Arthrobacter gandavensis (97.9 and 98.0 %, respectively) and Arthrobacter koreensis (97.6 and 97.7 %, respectively). Likewise, cluster II (strains J391T and J915) had the highest sequence similarity to Arthrobacter ruber (98.6 and 98.3 %, respectively) and Arthrobacter agilis (98.1 and 97.9  %, respectively). Average nucleotide identity and the digital DNA–DNA hybridization values illustrated that the two type strains, 785T and J391T, represented two separate novel species that are distinct from all currently recognized species in the genus Arthrobacter . These strains had DNA G+C contents of 66.0–66.1 mol% (cluster I) and 68.0 mol% (cluster II). The chemotaxonomic properties of strains 785T and J391T were in line with those of the genus Arthrobacter : anteiso-C15:0 (79.3 and 40.8 %, respectively) as the major cellular fatty acid, MK-8(H2) (65.8 %) or MK-9(H2) (75.6 %) as the predominant respiratory quinone, a polar lipid profile comprising diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, glycolipids and phospholipid, and A3α or A4α as the cell wall peptidoglycan type. On the basis of our results, two novel species in the genus Arthrobacter are proposed, namely Arthrobacter yangruifuii sp. nov. (type strain, 785T=CGMCC 1.16725T=GDMCC 1.1592T=JCM 33491T) and Arthrobacter zhaoguopingii sp. nov. (type strain, J391T=CGMCC 1.17382T=GDMCC 1.1667T=JCM 33841T).


2020 ◽  
Vol 70 (12) ◽  
pp. 6301-6306
Author(s):  
Sooyeon Park ◽  
Seo Yeon Lee ◽  
Wonyong Kim ◽  
Jung-Hoon Yoon

A Gram-stain-negative, aerobic, non-spore-forming, motile by single polar flagellum and ovoid or rod-shaped bacterial strain, designated JBTF-M23T, was isolated from tidal flat sediment collected from the Yellow Sea, Republic of Korea. Neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain JBTF-M23T fell within the clade comprising the type strains of Pseudoalteromonas species, clustering with the type strains of P. byunsanensis and P. amylolytica . Strain JBTF-M23T exhibited the highest 16S rRNA gene sequence similarity value (98.6 %) to the type strain of P. rubra and sequence similarities of 98.3 and 97.7 % to the type strains of P. byunsanensis and P. amylolytica, respectively. The DNA G+C content of strain JBTF-M23T from genomic sequence data was 41.98 %. The ANI and dDDH values between strain JBTF-M23T and the type strains of P. rubra , P. byunsanensis and P. amylolytica were 71.3–76.6 and 19.4–19.9 %, respectively. Strain JBTF-M23T contained Q-8 as the predominant ubiquinone and C16 : 1  ω7c and/or C16 : 1  ω6c, C16 : 0 and C18 : 1  ω7c as the major fatty acids. The major polar lipids of strain JBTF-M23T were phosphatidylethanolamine and one unidentified aminolipid. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain JBTF-M23T is separated from recognized Pseudoalteromonas species. On the basis of the data presented, strain JBTF-M23Tis considered to represent a novel species of the genus Pseudoalteromonas , for which the name Pseudoalteromonas caenipelagi sp. nov. is proposed. The type strain is JBTF-M23T(=KACC 19900T=NBRC 113647T).


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