The RDP Classifier is a widely used bioinformatic program that performs taxonomic classification of 16S rRNA gene sequences. However, the accuracy of the program is not clear when it is applied to common PCR products of the 16S rRNA variable regions, which are heavily used in microbiome projects. In this study, fulllength 16S rRNA gene alignments from the SILVA database were used to simulate th...

BACKGROUND: The extensive consumption of milk anddairy products makes these foodstuffs targets for potentialadulteration with financial gains for unscrupulous producers.OBJECTIVES: The aim of this study was using PCR assay todetect cow milk in labeled sheep milk, sheep yoghurt, andLighvan cheese (a traditional ripened cheese produced fromsheep's milk). METHODS: The assay utilized primers target...

Even though the 16S rRNA gene is the most commonly used taxonomic marker in microbial ecology, its poor resolution is still not fully understood at the intra-genus level. In this work, the number of rRNA gene operons, intra-genomic heterogeneities and lateral transfers were investigated at a fine-scale resolution, throughout the Pseudomonas genus. In addition to nineteen sequenced Pseudomonas s...

      Uricase or Urate oxidase (urate:oxygen oxidoreductase, EC 1.7.3.3), a peroxisomal enzyme which is found in many bacteria, catalyzes the oxidative opening of the purine ring of urate to yield allantoin, carbon dioxide, and hydrogen peroxide. In this study, the phylogeny of urate oxidase (uricase) producing bacteria was studied based on gene sequences of 16S rRNA and uricase protein. Repres...

S. coelicolor A3(2) contains six ribosomal RNA operons. Here we describe the cloning of rrnA, rrnC and rrnE, thereby completing the cloning of all operons. Southern hybridisation of genomic DNA with a heterologous probe from the E.coli rrnB 16S rRNA gene showed differences in hybridisation among the six rRNA operon-containing bands. The nucleotide sequence of the 16S rRNA gene and the upstream ...

Ribosomal (r) RNA interoperon sequence heterogeneity in the 'Fragaria multicipita' phytoplasma, a member of group 16SrVI, was initially observed in RFLP patterns of rDNA amplified in the polymerase chain reaction (PCR), and was confirmed through sequence analysis of cloned rDNA. Sequences from operons rrnA and rrnB were amplified in PCR primed by primer pair P1/P7 but from only rrnA in PCR prim...

Deep-subsurface samples obtained by deep drilling are likely to be contaminated with mesophilic microorganisms in the drilling fluid, and this could affect determination of the community structure of the geothermal microflora using 16S rRNA gene clone library analysis. To eliminate possible contamination by PCR-amplified 16S rRNA genes from mesophiles, a combined thermal denaturation and enzyme...

The availability of a large number of completely sequenced bacterial genomes allows the rapid and reliable determination of intragenomic sequence heterogeneity of 16S rRNA genes. In the present study we assessed the intragenomic sequence heterogeneity of 16S rRNA genes in 55 bacterial genomes, representing various phylogenetic groups. The total number of rRNA operons in genomes included ranged ...

The complete mitochondrial genome of a widely distributed pelagic ray, the Spinetail Devilray (Mobula japanica), consists of 18,880 bp with high A+T and low G content. Gene configuration and length is similar to other vertebrates and comprises 13 protein-coding genes, 2 rRNAs genes (12S and 16S rRNA), 22 tRNAs genes, and 1 major non-coding sequence, the control region. A remarkable feature in t...