scholarly journals Bradyrhizobium neotropicale sp. nov., isolated from effective nodules of Centrolobium paraense

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 3950-3957 ◽  
Author(s):  
Jerri E. Zilli ◽  
Alexandre C. Baraúna ◽  
Krisle da Silva ◽  
Sofie E. De Meyer ◽  
Eliane N. C. Farias ◽  
...  

Root nodule bacteria were isolated from Centrolobium paraense Tul. grown in soils from the Amazon region, State of Roraima (Brazil). 16S rRNA gene sequence analysis of seven strains (BR 10247T, BR 10296, BR 10297, BR 10298, BR 10299, BR 10300 and BR 10301) placed them in the genus Bradyrhizobium with the closest neighbours being the type strains of Bradyrhizobium paxllaeri (98.8 % similarity), Bradyrhizobium icense (98.8 %), Bradyrhizobium lablabi (98.7 %), Bradyrhizobium jicamae (98.6 %), Bradyrhizobium elkanii (98.6 %), Bradyrhizobium pachyrhizi (98.6 %) and Bradyrhizobium retamae (98.3 %). This high similarity, however, was not confirmed by the intergenic transcribed spacer (ITS) 16S–23S rRNA region sequence analysis nor by multi-locus sequence analysis. Phylogenetic analyses of five housekeeping genes (dnaK, glnII, gyrB, recA and rpoB) revealed Bradyrhizobium iriomotense EK05T ( = LMG 24129T) to be the most closely related type strain (95.7 % sequence similarity or less). Chemotaxonomic data, including fatty acid profiles [major components being C16 : 0 and summed feature 8 (18 : 1ω6c/18 : 1ω7c)], DNA G+C content, slow growth rate and carbon compound utilization patterns, supported the placement of the novel strains in the genus Bradyrhizobium . Results of DNA–DNA relatedness studies and physiological data (especially carbon source utilization) differentiated the strains from the closest recognized species of the genus Bradyrhizobium . Symbiosis-related genes for nodulation (nodC) and nitrogen fixation (nifH) placed the novel species in a new branch within the genus Bradyrhizobium . Based on the current data, these seven strains represent a novel species for which the name Bradyrhizobium neotropicale sp. nov. is proposed. The type strain is BR 10247T ( = HAMBI 3599T).

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1323-1328 ◽  
Author(s):  
William J. Wolfgang ◽  
Teresa V. Passaretti ◽  
Reashma Jose ◽  
Jocelyn Cole ◽  
An Coorevits ◽  
...  

A polyphasic analysis was undertaken of seven independent isolates of Gram-negative cocci collected from pathological clinical samples from New York, Louisiana, Florida and Illinois and healthy subgingival plaque from a patient in Virginia, USA. The 16S rRNA gene sequence similarity among these isolates was 99.7–100 %, and the closest species with a validly published name was Neisseria lactamica (96.9 % similarity to the type strain). DNA–DNA hybridization confirmed that these isolates are of the same species and are distinct from their nearest phylogenetic neighbour, N. lactamica . Phylogenetic analysis of 16S and 23S rRNA gene sequences indicated that the novel species belongs in the genus Neisseria . The predominant cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C18 : 1ω7c. The cellular fatty acid profile, together with other phenotypic characters, further supports the inclusion of the novel species in the genus Neisseria . The name Neisseria oralis sp. nov. (type strain 6332T  = DSM 25276T  = LMG 26725T) is proposed.


2020 ◽  
Vol 70 (4) ◽  
pp. 2369-2381 ◽  
Author(s):  
Dmitriy V. Volokhov ◽  
Dénes Grózner ◽  
Miklós Gyuranecz ◽  
Naola Ferguson-Noel ◽  
Yamei Gao ◽  
...  

In 1983, Mycoplasma sp. strain 1220 was isolated in Hungary from the phallus lymph of a gander with phallus inflammation. Between 1983 and 2017, Mycoplasma sp. 1220 was also identified and isolated from the respiratory tract, liver, ovary, testis, peritoneum and cloaca of diseased geese in several countries. Seventeen studied strains produced acid from glucose and fructose but did not hydrolyse arginine or urea, and all grew under aerobic, microaerophilic and anaerobic conditions at 35 to 37 ˚C in either SP4 or pleuropneumonia-like organism medium supplemented with glucose and serum. Colonies on agar showed a typical fried-egg appearance and transmission electron microscopy revealed a typical mycoplasma cellular morphology. Molecular characterization included analysis of the following genetic loci: 16S rRNA, 23S rRNA, 16S–23S rRNA ITS, rpoB, rpoC, rpoD, uvrA, parC, topA, dnaE, fusA and pyk. The genome was sequenced for type strain 1220T. The 16S rRNA gene sequences of studied strains of Mycoplasma sp. 1220 shared 99.02–99.19 % nucleotide similarity with M. anatis strains but demonstrated ≤95.00–96.70 % nucleotide similarity to the 16S rRNA genes of other species of the genus Mycoplasma . Phylogenetic, average nucleotide and amino acid identity analyses revealed that the novel species was most closely related to Mycoplasma anatis . Based on the genetic data, we propose a novel species of the genus Mycoplasma , for which the name Mycoplasma anserisalpingitidis sp. nov. is proposed with the type strain 1220T (=ATCC BAA-2147T=NCTC 13513T=DSM 23982T). The G+C content is 26.70 mol%, genome size is 959110 bp.


Author(s):  
Tobias Eisenberg ◽  
Sabine Gronow ◽  
Jane Falgenhauer ◽  
Can Imirzalioglu ◽  
Kristin Mühldorfer ◽  
...  

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.


2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1831-1837 ◽  
Author(s):  
Yao Yao ◽  
Xin Hua Sui ◽  
Xiao Xia Zhang ◽  
En Tao Wang ◽  
Wen Xn Chen

Six slow-growing rhizobial strains isolated from effective nodules of Erythrophleum fordii were classified into the genus Bradyrhizobium based on their 16S rRNA gene sequences. The results of multilocus sequence analysis of recA, glnII and gyrB genes and 16S–23S rRNA intergenic spacer (IGS) sequence phylogeny indicated that the six strains belonged to two novel species, represented by CCBAU 53325T and CCBAU 51502T, which were consistent with the results of DNA–DNA hybridization; CCBAU 53325T had 17.65–25.59 % relatedness and CCBAU 51502T had 22.69–44.58 % relatedness with five closely related type strains, Bradyrhizobium elkanii USDA 76T, B. pachyrhizi LMG 24246T, B. lablabi CCBAU 23086T, B. jicamae LMG 24556T and B. japonicum USDA 6T. In addition, analysis of phenotypic characteristics and fatty acid profiles also distinguished the test strains from defined species of Bradyrhizobium . Two novel species, Bradyrhizobium erythrophlei sp. nov., represented by the type strain CCBAU 53325T ( = HAMBI 3614T = CGMCC 1.13002T = LMG 28425T), and Bradyrhizobium ferriligni sp. nov., represented by the type strain CCBAU 51502T ( = HAMBI 3613T = CGMCC 1.13001T), are proposed to accommodate the strains.


2020 ◽  
Vol 70 (12) ◽  
pp. 6458-6467 ◽  
Author(s):  
Ping Mo ◽  
Jun Liu ◽  
Yunlin Zhao ◽  
Zhenggang Xu

Two novel actinobacteria, designated strains GY16T and T44T, were isolated from the leaves and rhizosphere soil of Broussonetia papyrifera, respectively. A polyphasic approach was used for determining their taxonomic position. Results of 16S rRNA gene sequence analysis indicated that strain GY16T exhibited highest similarities to Streptomyces cinereoruber subsp. fructofermentans CGMCC 4.1593T (98.82 %), Streptomyces deccanensis KCTC 19241T (98.76 %), Streptomyces scabiei NRRL B-16523T (98.69 %), Streptomyces europaeiscabiei KACC 20186T (98.69 %) and Streptomyces rishiriensis NBRC 13407T (98.69 %), and strain T44T showed 99.2, 99.1, 99.1 and <98.7 % sequence similarities to Streptomyces filipinensis CGMCC 4.1452T, Streptomyces achromogenes subsp. achromogenes DSM 40028T, Streptomyces durhamensis DSM 40539T and other Streptomyces species, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain GY16T formed an independent subclade, which indicated that strain GY16T should belong to a potential novel species; and strain T44T was closely related to S. filipinensis CGMCC 4.1452T, S. achromogenes subsp. achromogenes DSM 40028T, S. durhamensis DSM 40539T and S. yokosukanensis DSM 40224T. However, the multilocus sequence analysis evolutionary distance, average nucleotide identity and DNA–DNA hybridization values between closely related relatives were far from the species-level thresholds. In addition, phenotypic and chemotaxonomic characteristics further confirmed that strains GY16T and T44T belonged to two distinct species. Based on these results, it is concluded that the isolated strains represent novel species within the genus Streptomyces , for which the names Streptomyces phaeolivaceus sp. nov. (type strain GY16T=CICC 24807T=KCTC 49326T) and Streptomyces broussonetiae sp. nov. (type strain T44T=CICC 24819T=JCM 33918T) are proposed.


Author(s):  
Juan Zhou ◽  
Sihui Zhang ◽  
Gui Zhang ◽  
Jing Yang ◽  
Xin-He Lai ◽  
...  

Six novel strains (ZJ34T, ZJ561, ZJ750T, ZJ1629, zg-993T and zg-987) isolated from faeces and respiratory tracts of Marmota himalayana from the Qinghai–Tibet Plateau of PR China were characterized comprehensively. The results of analyses of the 16S rRNA gene and genome sequences indicated that the six strains represent three novel species of the genus Actinomyces , and are closely related to Actinomyces urogenitalis DSM 15434T (16S rRNA gene sequences similarities, 94.9–98.7 %), Actinomyces weissii CCUG 61299T (95.6–96.6 %), Actinomyces bovis CCTCC AB2010168T (95.7 %) and Actinomyces bowdenii DSM 15435T (95.2–96.4 %), with values of digital DNA–DNA hybridization less than 30.1 % when compared with their closest relatives but higher than 70 % within each pair of novel strains (ZJ34T/ZJ561, ZJ750T/ZJ1629 and zg-993T/zg-987). All the novel strains had C18 : 1 ω9c and C16 : 0 as the two most abundant major fatty acids. MK-9(H4) or MK-8(H4) was the sole or predominant respiratory quinone of strains ZJ34T, ZJ750T and zg-993T and their polar lipid profiles differed, but all had diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and phosphatidyl inositol mannoside as major components. ZJ750T shared identical peptidoglycan amino acid profile with ZJ34T (alanine, glutamic acid, lysine and ornithine) and the same whole-cell sugar composition with zg-993T (glucose, rhamnose and ribose). Strain zg-993T contained alanine, aspartic acid, glutamic acid, glycine and lysine in the peptidoglycan, and the only sugar in ZJ34T was ribose. The DNA G+C contents of the novel strains were within the range of 65.8–70.1 mol%. On the basis of the results from the aforementioned analyses, the six novel strains were classified as representing three novel species of genus Actinomyces , for which the names Actinomyces faecalis sp. nov. [type strain ZJ34T (=GDMCC 1.1952T=JCM 34355T)], Actinomyces respiraculi sp. nov. [type strain ZJ750T (=GDMCC 1.1950T=JCM 34356T)] and Actinomyces trachealis sp. nov. [type strain zg-993T (=GDMCC 1.1956T=JCM 34357T)] were proposed, respectively.


2020 ◽  
Vol 70 (9) ◽  
pp. 5131-5140 ◽  
Author(s):  
Pavel Švec ◽  
Marcel Kosina ◽  
Michal Zeman ◽  
Pavla Holochová ◽  
Stanislava Králová ◽  
...  

A taxonomic study of two fluorescent Pseudomonas strains (HJ/4T and SJ/9/1T) isolated from calcite moonmilk samples obtained from two caves in the Moravian Karst in the Czech Republic was carried out. Results of initial 16S rRNA gene sequence analysis assigned both strains into the genus Pseudomonas and showed Pseudomonas yamanorum 8H1T as their closest neighbour with 99.8 and 99.7 % 16S rRNA gene similarities to strains HJ/4T and SJ/9/1T, respectively. Subsequent sequence analysis of rpoD, rpoB and gyrB housekeeping genes confirmed the highest similarity of both isolates to P. yamanorum 8H1T, but phylogeny and sequences similarities implied that they are representatives of two novel species within the genus Pseudomonas . Further study comprising whole-genome sequencing followed by average nucleotide identity and digital DNA–DNA hybridization calculations, repetitive sequence-based PCR fingerprinting with the REP and ERIC primers, automated ribotyping with the EcoRI restriction endonuclease, cellular fatty acid analysis, quinone and polar lipid characterization, and extensive biotyping confirmed clear separation of both analysed strains from the remaining Pseudomonas species and showed that they represent two novel species within the genus Pseudomonas for which the names Pseudomonas karstica sp. nov. (type strain HJ/4T=CCM 7891T=LMG 27930T) and Pseudomonas spelaei sp. nov. (type strain SJ/9/1T=CCM 7893T=LMG 27931T) are suggested.


2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1277-1283 ◽  
Author(s):  
Susan Joseph ◽  
Esin Cetinkaya ◽  
Hana Drahovska ◽  
Arturo Levican ◽  
Maria J. Figueras ◽  
...  

A re-evaluation of the taxonomic position of five strains, one assigned to Cronobacter sakazakii (strain 1330T, isolated from spiced meat purchased in Slovakia), two previously assigned to Cronobacter genomospecies 1 (strains NCTC 9529T and 731, isolated from water and a leg infection, respectively) and two previously assigned to Cronobacter turicensis (strains 96 and 1435, isolated from onion powder and rye flour, respectively) was carried out. The analysis included phenotypic characterization, 16S rRNA gene sequencing and multilocus sequence analysis (MLSA) of seven housekeeping genes (atpD, fusA, glnS, gltB, gyrB, infB, ppsA; 3036 bp). 16S rRNA gene sequence analysis and MLSA showed that strain 1330T formed an independent phylogenetic lineage in the MLSA, with Cronobacter dublinensis LMG 23823T as the closest neighbour. DNA–DNA reassociation and phenotypic analysis revealed that strain 1330T represented a novel species, for which the name Cronobacter condimenti sp. nov. is proposed (type strain 1330T = CECT 7863T = LMG 26250T). Strains NCTC 9529T, 731, 96 and 1435 clustered together within an independent phylogenetic lineage, with C. turicensis LMG 23827T as the closest neighbour in the MLSA. DNA–DNA reassociation and phenotypic analysis confirmed that these strains represent a novel species, for which the name Cronobacter universalis sp. nov. is proposed (type strain NCTC 9529T = CECT 7864T = LMG 26249T).


2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 874-882 ◽  
Author(s):  
Jose R. López ◽  
Ana L. Diéguez ◽  
Alejandra Doce ◽  
Elena De la Roca ◽  
Roberto De la Herran ◽  
...  

Five Gram-negative bacterial isolates, recovered from an outbreak that occurred in March 2006 in Huelva, Spain, affecting adult diseased cultured wedge sole [Dicologlossa cuneata (Moreau)], were characterized phenotypically and genotypically in order to clarify their taxonomic position. On the basis of 16S rRNA gene sequence analysis, the isolates were included in the genus Pseudomonas , within the Pseudomonas fluorescens -related species group, their closest relatives being the Pseudomonas jessenii and Pseudomonas koreensis subgroups. The highest sequence similarities were recorded with the type strains of Pseudomonas reinekei , P. moorei , P. umsongensis , P. jessenii and P. mohnii (99.4–99.3 % similarity). Sequence analysis of the housekeeping genes gyrB and rpoD clearly differentiated the isolates from currently described Pseudomonas species, the highest sequence similarities recorded to type strains being below 95 % for both genes. Phylogenetic analysis using concatenated sequences of the three genes showed Pseudomonas moraviensis DSM 16007T and P. koreensis DSM 16610T as the closest reference strains. DNA–DNA hybridization assays with related strains confirmed that these isolates belong to a novel species of the genus Pseudomonas , for which the name Pseudomonas baetica sp. nov. is proposed. The type strain is strain a390T ( = CECT 7720T  = LMG 25716T). The novel species could be easily distinguished from phylogenetically related species by several phenotypic characteristics, including gelatin hydrolysis, acid production from glucose and growth at 6 % NaCl. Virulence assays revealed that the novel species is pathogenic for wedge sole.


2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 53-59 ◽  
Author(s):  
Sylvie Cousin ◽  
Laurence Motreff ◽  
Marie-Laure Gulat-Okalla ◽  
Catherine Gouyette ◽  
Cathrin Spröer ◽  
...  

Strains 1517T and 61DT were characterized by phenotypic and molecular taxonomic methods. These Gram-positive lactic acid bacteria were homo-fermentative, facultatively anaerobic short rods. They were phylogenetically related to the genus Lactobacillus according to 16S rRNA gene sequence analysis, with 99 % similarity between strain 1517T and the type strain of Lactobacillus gigeriorum , and 98.6, 98.5 and 98.4 % between strain 61DT and Lactobacillus gasseri , Lactobacillus taiwanensis and Lactobacillus johnsonii , respectively. Multilocus sequence analysis and metabolic analysis of both strains showed variation between the two strains and their close relatives, with variation in the position of the pheS and rpoA genes. The DNA–DNA relatedness of 43.5 % between strain 1517T and L. gigeriorum , and 38.6, 29.9 and 39.7 % between strain 61DT and L. johnsonii , L. taiwanensis and L. gasseri , respectively, confirmed their status as novel species. Based on phenotypic and genotypic characteristics, two novel species of Lactobacillus are proposed: Lactobacillus pasteurii sp. nov., with 1517T ( = CRBIP 24.76T = DSM 23907T) as the type strain, and Lactobacillus hominis sp. nov., with 61DT ( = CRBIP 24.179T = DSM 23910T) as the type strain.


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