Ribosomes are essential intracellular machines composed of proteins and RNA molecules. The DNA sequences (rDNA) encoding ribosomal RNAs (rRNAs) are tandemly repeated and give origin to the nucleolus. Here we develop a computational method for estimating rDNA dosage (copy number) and mitochondrial DNA abundance using whole-genome short-read DNA sequencing. We estimate these attributes across hun...

For many years the taxonomy of the genus Pasteuria has been marred with confusion because the bacterium could not be cultured in vitro and, therefore, descriptions were based solely on morphological, developmental, and pathological characteristics. The current study sought to devise a simple method for PCR-amplification, cloning, and sequencing of Pasteuria 16S rDNA from small numbers of endosp...

Miseq sequencing and data analysis for the actin gene and v9 region of 18S rDNA of 7 simulated samples consisting of different mixture of dinoflagellates and diatoms were carried out. Not all the species were detectable in all the 18S v9 samples, and sequence percent in all the v9 samples were not consistent with the corresponding cell percent which may suggest that 18S rDNA copy number in diff...

Gene amplification using 16S rDNA primers has been proposed as a strategy for the diagnosis of bacterial meningitis. The aim of this study was to evaluate the performance of the MicroSeq 500 16S ribosomal DNA test (Applied Biosystems) from patients with suspected bacterial meningitis and CSF negative-culture in comparison to traditional methods. Twelve purulent culture-negative CSF samples were...

In prokaryotes, the ribosomal gene locus contains three rRNA species: 16S, 23S and 5S. The potential of sequencing 16S rDNA of bacteria and archaea for establishing phylogenetic relationships and for use in molecular diagnostics is well-documented. Currently, over 3000 16S rRNA sequences are available in the databases. However, the potential of the 23S rRNA gene as a diagnostic tool has not bee...

Background: Traditional dairy products are the main sources for probiotic bacteria. This study aimed to isolate and characterize the potentially probiotic Lactobacillus strains isolated from traditional dairy products in Iran. Methods: Microbial population of each dairy product was enriched and screened for acid- and bile- resistant strains. The isolates were ...

Although 16S rRNA gene (rDNA) sequencing is the gold standard for categorizing bacteria or characterizing microbial communities its clinical utility is limited by bias in metagenomic studies, in either the experiments or the data analyses. To evaluate the efficiency of current metagenomic methods, we sequenced seven simulated samples of ten bacterial species mixed at different concentrations. T...

Although most Myxozoa species of the genera Ceratomyxa and Ellipsomyxa have been described in marine hosts worldwide, an increasing diversity has reported infecting South American freshwater fish, mainly Amazonian waters. The present study deals with two myxozoan ceratomyxids parasitizing gallbladder ornamental cichlids fish: amazonensis is identified from a new host—Geophagus altifrons; while ...

This study aimed to characterize and identify the genotypes of Fasciola spp. isolated from sheep, goats, cattle in Duhok province based on ITS1 region rDNA. About 54 adult flukes were individually livers naturally infected ruminants. After morphological identification, genomic DNA was successfully extracted, ITS1segment (518 bp) rDNA amplified. The amplicons confirmed by gel electrophoresis yie...