scholarly journals A Phylogenetic Analysis of the Family Pseudonocardiaceae and the Genera Actinokineospora and Saccharothrix with 16S rRNA Sequences and a Proposal To Combine the Genera Amycolata and Pseudonocardia in an Emended Genus Pseudonocardia

1994 ◽  
Vol 44 (2) ◽  
pp. 293-299 ◽  
Author(s):  
S. WARWICK ◽  
T. BOWEN ◽  
H. McVEIGH ◽  
T. M. EMBLEY
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
The Family ◽  
Rrna Sequences ◽  
16S Rrna Sequences

scholarly journals Evidence and molecular characterization ofBartonellaspp. and hemoplasmas in neotropical bats in Brazil

2017 ◽  
Vol 145 (10) ◽  
pp. 2038-2052 ◽  
Author(s):  
P. IKEDA ◽  
M. C. SEKI ◽  
A. O. T. CARRASCO ◽  
L. V. RUDIAK ◽  
J. M. D. MIRANDA ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Clinical Manifestations ◽  
Rrna Gene ◽  
Zoonotic Virus ◽  
The World ◽  
Neotropical Bats ◽  
Latin America Countries ◽  
Rrna Sequences ◽  
16S Rrna Sequences

SUMMARYThe order Chiroptera is considered the second largest group of mammals in the world, hosting important zoonotic virus and bacteria.Bartonellaand hemotropic mycoplasmas are bacteria that parasite different mammals’ species, including humans, causing different clinical manifestations. The present work aimed investigating the occurrence and assessing the phylogenetic positioning ofBartonellaspp. andMycoplasmaspp. in neotropical bats sampled from Brazil. Between December 2015 and April 2016, 325 blood and/or tissues samples were collected from 162 bats comprising 19 different species sampled in five states of Brazil. Out of 322 bat samples collected, while 17 (5·28%) were positive to quantitative PCR forBartonellaspp. based onnuoGgene, 45 samples (13·97%) were positive to cPCR assays for hemoplasmas based on 16S rRNA gene. While seven sequences were obtained forBartonella(nuoG) (n= 3),gltA(n= 2),rpoB(n= 1),ftsZ(n= 1), five 16S rRNA sequences were obtained for hemoplasmas. In the phylogenetic analysis, theBartonellasequences clustered withBartonellagenotypes detected in bats sampled in Latin America countries. All five hemoplasmas sequences clustered together as a monophyletic group by Maximum Likelihood and Bayesian Inference analyses. The present work showed the first evidence of circulation ofBartonellaspp. and hemoplasmas among bats in Brazil.

scholarly journals Molecular Phylogenetic Analysis of 16S rRNA Sequences Identified Two Lineages of Helicobacter pylori Strains Detected from Different Regions in Sudan Suggestive of Differential Evolution

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Abeer Babiker Idris ◽  
Hadeel Gassim Hassan ◽  
Maryam Atif Salaheldin Ali ◽  
Sulafa Mohamed Eltaher ◽  
Leena Babiker Idris ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Helicobacter Pylori ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Human Migration ◽  
Rrna Gene ◽  
Migration Patterns ◽  
H Pylori ◽  
Rrna Sequences ◽  
16S Rrna Sequences

Background. Helicobacter pylori (H. pylori) is ubiquitous among humans and one of the best-studied examples of an intimate association between bacteria and humans. Phylogeny and Phylogeography of H. pylori strains are known to mirror human migration patterns and reflect significant demographic events in human prehistory. In this study, we analyzed the molecular evolution of H. pylori strains detected from different tribes and regions of Sudan using 16S rRNA gene and the phylogenetic approach. Materials and methods. A total of 75 gastric biopsies were taken from patients who had been referred for endoscopy from different regions of Sudan. The DNA extraction was performed by using the guanidine chloride method. Two sets of primers (universal and specific for H. pylori) were used to amplify the 16S ribosomal gene. Sanger sequencing was applied, and the resulted sequences were matched with the sequences of the National Center for Biotechnology Information (NCBI) nucleotide database. The evolutionary aspects were analyzed using MEGA7 software. Results. Molecular detection of H. pylori has shown that 28 (37.33%) of the patients were positive for H. pylori and no significant differences were found in sociodemographic characteristics, endoscopy series, and H. pylori infection. Nucleotide variations were observed at five nucleotide positions (positions 219, 305, 578, 741, and 763–764), and one insertion mutation (750_InsC_751) was present in sixty-seven percent (7/12) of our strains. These six mutations were detected in regions of the 16S rRNA not closely associated with either tetracycline or tRNA binding sites; 66.67% of them were located in the central domain of 16S rRNA. The phylogenetic analysis of 16S rRNA sequences identified two lineages of H. pylori strains detected from different regions in Sudan. The presence of Sudanese H. pylori strains resembling Hungarian H. pylori strains could reflect the migration of Hungarian people to Sudan or vice versa. Conclusion. This finding emphasizes the significance of studying the phylogeny of H. pylori strains as a discriminatory tool to mirror human migration patterns. In addition, the 16S rRNA gene amplification method was found useful for bacterial identification and phylogeny.

scholarly journals cumA Multicopper Oxidase Genes from Diverse Mn(II)-Oxidizing and Non-Mn(II)-OxidizingPseudomonas Strains

2001 ◽  
Vol 67 (9) ◽  
pp. 4272-4278 ◽  
Author(s):  
Chris A. Francis ◽  
Bradley M. Tebo
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Multicopper Oxidase ◽  
Copper Binding ◽  
Gene Sequences ◽  
Degenerate Primers ◽  
Oxidase Gene ◽  
Alternative Function ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT A multicopper oxidase gene, cumA, required for Mn(II) oxidation was recently identified in Pseudomonas putida strain GB-1. In the present study, degenerate primers based on the putative copper-binding regions of the cumAgene product were used to PCR amplify cumA gene sequences from a variety of Pseudomonas strains, including both Mn(II)-oxidizing and non-Mn(II)-oxidizing strains. The presence of highly conserved cumA gene sequences in several apparently non-Mn(II)-oxidizing Pseudomonasstrains suggests that this gene may not be expressed, may not be sufficient alone to confer the ability to oxidize Mn(II), or may have an alternative function in these organisms. Phylogenetic analysis of both CumA and 16S rRNA sequences revealed similar topologies between the respective trees, including the presence of several distinct phylogenetic clusters. Overall, our results indicate that both thecumA gene and the capacity to oxidize Mn(II) occur in phylogenetically diverse Pseudomonas strains.

Scytolyngbya timoleontis, gen. et sp. nov. (Leptolyngbyaceae, Cyanobacteria): a novel false branching Cyanobacteria from China

Phytotaxa ◽  
2015 ◽  
Vol 224 (1) ◽  
pp. 72 ◽  
Author(s):  
Gaofei Song ◽  
Yongguang Jiang ◽  
Renhui Li
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Type Species ◽  
Intergenic Spacer ◽  
Secondary Structures ◽  
Sensu Stricto ◽  
Polyphasic Approach ◽  
23S Rrna ◽  
Rrna Sequences ◽  
16S Rrna Sequences

A novel genus within Leptolyngbyaceae related to Leptolyngbya morphotypes, Scytolyngbya, gen. nov., is described based on a polyphasic approach in the present study. From a freshwater sample with filaments of oscillatorean cyanobacteria from a well in Hubei Province, China, Scytolyngbya (type species: Scytolyngbya timoleontis, sp. nov.) was found to possess richly and repeatedly false branches and thick sheaths, which distinguishs this genus from Leptolyngbya sensu stricto. Phylogenetic analysis based on 16S rRNA sequences showed that this species was clustered into the Leptolyngbyaceae and separated from the type species Leptolyngbya boryana. The secondary structures of 16S-23S rRNA intergenic spacer of Scytolyngbya timoleontis did not correspond to any previously described species in cyanobacteria.

scholarly journals Unusually High Archaeal Diversity in a Crystallizer Pond, Pomorie Salterns, Bulgaria, Revealed by Phylogenetic Analysis

Archaea ◽  
2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Margarita Kambourova ◽  
Iva Tomova ◽  
Ivanka Boyadzhieva ◽  
Nadja Radchenkova ◽  
Evgenia Vasileva-Tonkova
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Community Composition ◽  
Archaeal Community ◽  
Hypersaline Environment ◽  
Archaeal Diversity ◽  
Operational Taxonomic Units ◽  
Crystallizer Pond ◽  
Rrna Sequences ◽  
16S Rrna Sequences

Recent studies on archaeal diversity in few salterns have revealed heterogeneity between sites and unique structures of separate places that hinder drawing of generalized conclusions. Investigations on the archaeal community composition in P18, the biggest crystallizer pond in Pomorie salterns (PS) (34% salinity), demonstrated unusually high number of presented taxa in hypersaline environment. Archaeal clones were grouped in 26 different operational taxonomic units (OTUs) assigned to 15 different genera from two orders, Halobacteriales and Haloferacales. All retrieved sequences were related to culturable halophiles or unculturable clones from saline (mostly hypersaline) niches. New sequences represented 53.9% of archaeal OTUs. Some of them formed separate branches with 90% similarity to the closest neighbor. Present results significantly differed from the previous investigations in regard to the number of presented genera, the domination of some genera not reported before in such extreme niche, and the identification of previously undiscovered 16S rRNA sequences.

scholarly journals Comparison of 16S rRNA Sequences from the Family Pasteurellaceae: Phylogenetic Relatedness by Cluster Analysis

Microbiology ◽  
1988 ◽  
Vol 134 (7) ◽  
pp. 1923-1930
Author(s):  
P. J. Chuba ◽  
R. Bock ◽  
G. Graf ◽  
T. Adam ◽  
U. gobel
Keyword(s):  
Cluster Analysis ◽  
16S Rrna ◽  
Phylogenetic Relatedness ◽  
The Family ◽  
Rrna Sequences ◽  
16S Rrna Sequences
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