scholarly journals Detection of novel strains genetically related to Anaplasma platys in Tunisian one-humped camels (Camelus dromedarius)

2015 ◽  
Vol 9 (10) ◽  
pp. 1117-1125 ◽  
Author(s):  
Hanène Belkahia ◽  
Mourad Ben Said ◽  
Lotfi Sayahi ◽  
Alberto Alberti ◽  
Lilia Messadi
Keyword(s):  
Polymerase Chain Reaction ◽  
16S Rrna ◽  
Quantitative Polymerase Chain Reaction ◽  
Bacterial Species ◽  
Chain Reaction ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Nested Polymerase Chain Reaction ◽  
16S Rrna Sequence Analysis ◽  
Polymerase Chain

Introduction: Little information is currently available regarding the presence of Anaplasma species in North African dromedaries. To fill this gap in knowledge, the prevalence, risk factors, and genetic diversity of Anaplasma species were investigated in Tunisian dromedary camels. Methodology: A total of 226 camels from three different bioclimatic areas were sampled and tested for the presence of Anaplasma species by quantitative polymerase chain reaction (qPCR) and nested polymerase chain reaction (nPCR) assays. Detected Anaplasma strains were characterized by 16S rRNA sequence analysis. Results: Overall infection rate of Anaplasma spp. was 17.7%, and was significantly higher in females. Notably, A. marginale, A. centrale, A. bovis, and A. phagocytophilum were not detected. Animals were severely infested by three tick species belonging to the genus Hyalomma (H. dromedarii, H. impeltatum, and H. excavatum). Alignment, similarity comparison, and phylogenetic analysis of the 16S rRNA sequence variants obtained in this study suggest that Tunisian dromedaries are infected by more than one novel Anaplasma strain genetically related to A. platys. Conclusions: This study reports the presence of novel Anaplasma sp. strains genetically related to A. platys in dromedaries from various bioclimatic areas of Tunisia. Findings raise new concerns about the specificity of the direct and indirect diagnostic tests routinely used to detect different Anaplasma species in ruminants and provide useful molecular information to elucidate the evolutionary history of bacterial species related to A. platys.

scholarly journals Airway Bacteria Quantification Using Polymerase Chain Reaction Combined with Neutrophil and Eosinophil Counts Identifies Distinct COPD Endotypes

Biomedicines ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 1337
Author(s):  
Augusta Beech ◽  
Simon Lea ◽  
Jian Li ◽  
Natalie Jackson ◽  
Alex Mulvanny ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Quantitative Polymerase Chain Reaction ◽  
Bacterial Species ◽  
Bacterial Load ◽  
Bacterial Colonisation ◽  
Chain Reaction ◽  
Cell Counts ◽  
Copd Patients ◽  
Polymerase Chain ◽  
Eosinophil Counts

Background: Chronic obstructive pulmonary disease (COPD) inflammatory endotypes are associated with different airway microbiomes. We used quantitative polymerase chain reaction (qPCR) analysis of sputum samples to establish the bacterial load upper limit in healthy controls; these values determined the bacterial colonisation prevalence in a longitudinal COPD cohort. Bacteriology combined with sputum inflammatory cells counts were used to investigate COPD endotypes. Methods: Sixty COPD patients and 15 healthy non-smoking controls were recruited. Sputum was analysed by qPCR (for Haemophilus influenzae, Moraxella catarrhalis, Streptococcus pneumoniae and Psuedomonas aeruginosa) and sputum differential cell counts at baseline and 6 months. Results: At baseline and 6 months, 23.1% and 25.6% of COPD patients were colonised with H. influenzae, while colonisation with other bacterial species was less common, e.g., S. pneumoniae—1.9% and 5.1%, respectively. H. influenzae + ve patients had higher neutrophil counts at baseline (90.1% vs. 67.3%, p < 0.01), with similar results at 6 months. COPD patients with sputum eosinophil counts ≥3% at ≥1 visit rarely showed bacterial colonisation. Conclusions: The prevalence of H. influenzae colonisation was approximately 25%, with low colonisation for other bacterial species. H. influenzae colonisation was associated with sputum neutrophilia, while eosinophilic inflammation and H. influenzae colonisation rarely coexisted.

scholarly journals Detection and genetic characterization of "Candidatus Mycoplasma haemomacaque" infection among long-tailed macaques (Macaca fascicularis) in Thailand using broad-range nested polymerase chain reaction assay

2021 ◽  
Vol 14 (4) ◽  
pp. 943-948
Author(s):  
Wanat Sricharern ◽  
Supakarn Kaewchot ◽  
Sarawan Kaewmongkol ◽  
Natnaree Inthong ◽  
Thitichai Jarudecha ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Genetic Characterization ◽  
Rrna Gene ◽  
Chain Reaction ◽  
Nested Polymerase Chain Reaction ◽  
Blood Samples ◽  
Polymerase Chain ◽  
The 16S Rrna Gene

Background and Aim: Hemoplasmas are defined as small, epicellular parasitic bacteria that can infect the red blood cells of several mammalian species. Diseases caused by these bacteria range from asymptomatic infections to acute hemolytic anemia. However, data on hemoplasmas in non-human primates in Thailand remain to be limited. Therefore, this study aims to determine the occurrence and genetic diversity of hemoplasmas among long-tailed macaques in Thailand. Materials and Methods: Blood samples were collected from 339 long-tailed macaques in three provinces of Thailand. DNA was then extracted from the blood samples and tested for hemoplasma using broad-range nested polymerase chain reaction (PCR) based on the 16S rRNA gene. PCR-positive samples were sequenced, and phylogenetic analysis for species identification was conducted. Results: In total, 38 (11.2%) out of the 339 samples were found to be positive for hemoplasmas, based on the broad-range nested PCR assay of the 16S rRNA gene. The 16S rRNA sequences of Mycoplasma spp. were highly similar (98-99% identity) to "Candidatus Mycoplasma haemomacaque." Furthermore, phylogenetic analysis using maximum likelihood demonstrated that the sequences were located in the same cluster of "Ca. M. haemomacaque." Conclusion: The detection of hemoplasmas among long-tailed macaques in Thailand is reported. Genetic characterization confirmed that these hemoplasmas are closely related to "Ca. M. haemomacaque." These results indicate that long-tailed macaques in several locations in Thailand may be infected and serve as reservoirs for this parasite.

scholarly journals Analysis of bacterial genetic diversity in biofloc by using ARDRA 16S-rRNA gene

2015 ◽  
Vol 12 (2) ◽  
pp. 128
Author(s):  
, Widanarni ◽  
Dewi Nurhayati ◽  
Dinamella Wahjuningrum
Keyword(s):  
Genetic Diversity ◽  
Polymerase Chain Reaction ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Pseudomonas Putida ◽  
Restriction Enzyme ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Chain Reaction ◽  
Polymerase Chain

<p class="NoParagraphStyle" align="center"><strong>ABSTRACT</strong></p><p class="NoParagraphStyle" align="center"> </p><p class="NoParagraphStyle">This study aimed to analyze the genetic diversity of bacteria associated in bioflocs using 16S-rRNA polymerase chain reaction (PCR) with ARDRA technique. A total of 38 dominant bacterial isolates was obtained from bioflocs samples and of these isolates, 16S-rRNA gene was then isolated and amplified using PCR. The 16S-rRNA gene of the isolates was then cut using <em>Hae</em>III (5’-GG↓CC) and <em>Hha</em>I (5’-GCG↓C) restriction enzymes resulting an ARDRA pattern which was further used as the binary data for the construction of phylogenetics tree that was used to estimate the group of bacteria. The result with <em>Hae</em>III cut restriction enzyme from biofloc-associated bacteria gave 11 ARDRA patterns, while with the restriction enzyme <em>Hha</em>I gave eight ARDRA patterns. Phylogenetics of bacterial populations from biofloc-based cultivation system water consisted of at least 13 different bacterial species. Result of sequencing from two gene sample 16S-rRNA were identified as <em>Microbacterium foliorumand</em> and <em>Pseudomonas putida</em>.</p><p class="NoParagraphStyle"> </p><p class="NoParagraphStyle">Keywords: bacterial diversity, ARDRA, biofloc, phylogeny</p><p class="NoParagraphStyle" align="center"> </p><p class="NoParagraphStyle" align="center"> </p><p class="NoParagraphStyle" align="center"><strong>ABSTRAK</strong></p><p class="NoParagraphStyle" align="center"> </p><p class="NoParagraphStyle">Penelitian ini bertujuan untuk menganalisis keragaman genetika bakteri bioflok menggunakan metode <em>polymerase chain reaction</em> (PCR) 16S-rRNA dengan teknik ARDRA. Sebanyak 38 isolat bakteri dominan yang diperoleh diamplifikasi gen 16S-rRNAnya dengan PCR, kemudian dipotong dengan enzim restriksi <em>Hae</em>III (5’-GG↓CC) dan <em>Hha</em>I (5’-GCG↓C). Pola ARDRA ini dijadikan data biner sebagai input untuk konstruksi pohon filogenetika yang dapat digunakan untuk memerkirakan jenis bakteri yang ada. Gen 16S-rRNA hasil PCR setelah dipotong dengan enzim restriksi <em>Hae</em>III didapatkan 11 pola ARDRA, sedangkan dengan enzim restriksi <em>Hha</em>I menghasilkan delapan pola ARDRA. Berdasarkan pohon filogenetika, diketahui populasi bakteri pada air sistem budidaya bioflok sedikitnya terdiri atas 13 jenis bakteri. Berdasarkan sekuensing dari dua sampel gen 16S-rRNA teridentifikasi jenis bakteri <em>Microbacterium foliorum</em> dan <em>Pseudomonas putida</em>.</p><p class="NoParagraphStyle"> </p><p>Kata kunci: keragaman bakteri, ARDRA, bioflok, filogenetika</p>

scholarly journals The Genus Caedibacter Comprises Endosymbionts of Paramecium spp. Related to the Rickettsiales (Alphaproteobacteria) and to Francisella tularensis (Gammaproteobacteria)

2002 ◽  
Vol 68 (12) ◽  
pp. 6043-6050 ◽  
Author(s):  
Cora L. Beier ◽  
Matthias Horn ◽  
Rolf Michel ◽  
Michael Schweikert ◽  
Hans-Dieter Görtz ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Sister Group ◽  
Rrna Gene ◽  
Paramecium Tetraurelia ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
16S Rrna Sequence Analysis ◽  
Bacterial Endosymbionts

ABSTRACT Obligate bacterial endosymbionts of paramecia able to form refractile inclusion bodies (R bodies), thereby conferring a killer trait upon their ciliate hosts, have traditionally been grouped into the genus Caedibacter. Of the six species described to date, only the Paramecium caudatum symbiont Caedibacter caryophilus has been phylogenetically characterized by its 16S rRNA gene sequence, and it was found to be a member of the Alphaproteobacteria related to the Rickettsiales. In this study, the Caedibacter taeniospiralis type strain, an R-body-producing cytoplasmatic symbiont of Paramecium tetraurelia strain 51k, was investigated by comparative 16S rRNA sequence analysis and fluorescence in situ hybridization with specific oligonucleotide probes. C. taeniospiralis is not closely related to C. caryophilus (80% 16S rRNA sequence similarity) but forms a novel evolutionary lineage within the Gammaproteobacteria with the family Francisellaceae as a sister group (87% 16S rRNA sequence similarity). These findings demonstrate that the genus Caedibacter is polyphyletic and comprises at least two phylogenetically different bacterial species belonging to two different classes of the Proteobacteria. Comparative phylogenetic analysis of C. caryophilus, five closely related Acanthamoeba endosymbionts (including one previously uncharacterized amoebal symbiont identified in this study), and their hosts suggests that the progenitor of the alphaproteobacterial C. caryophilus lived within acanthamoebae prior to the infection of paramecia.

AN IMPROVED METHOD FOR INHIBITOR FREE NUCLEIC ACIDS FROM POLYPHENOL RICH LEAVES OF MUSA SPP

2017 ◽  
Vol 23 (1) ◽  
Author(s):  
N.NANDHA KUMAR ◽  
K. SOURIANATHA SUNDARAM ◽  
D. SUDHAKAR ◽  
K.K. KUMAR
Keyword(s):  
Polymerase Chain Reaction ◽  
Quantitative Polymerase Chain Reaction ◽  
Proteinase K ◽  
Chain Reaction ◽  
Banana Plant ◽  
High Molecular Weight Dna ◽  
Musa Spp ◽  
Leaf Tissues ◽  
Polymerase Chain

Excessive presence of polysaccharides, polyphenol and secondary metabolites in banana plant affects the quality of DNA and it leads to difficult in isolating good quality of DNA. An optimized modified CTAB protocol for the isolation of high quality and quantity of DNA obtained from banana leaf tissues has been developed. In this protocol a slight increased salt (NaCl) concentration (2.0M) was used in the extraction buffer. Polyvinylpyrrolidone (PVP) and Octanol were used for the removal of polyphenols and polymerase chain reaction (PCR) inhibitors. Proteins like various enzymes were degraded by Proteinase K and removed by centrifugation from plant extract during the isolation process resulting in pure genomic DNA, ready to use in downstream applications including PCR, quantitative polymerase chain reaction (qPCR), ligation, restriction and sequencing. This protocol yielded a high molecular weight DNA isolated from polyphenols rich leaves of Musa spp which was free from contamination and colour. The average yields of total DNA from leaf ranged from 917.4 to 1860.9 ng/ìL. This modified CTAB protocol reported here is less time consuming 4-5h, reproducible and can be used for a broad spectrum of plant species which have polyphenol and polysaccharide compounds.

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