Patel A, et al. Arch Dis Child Educ Pract Ed 2017;0:1–4. doi:10.1136/archdischild-2016-312049 INTRODUCTION PCRs have revolutionised the detection of bacteria in clinical samples since their widespread introduction in the 1990s. Quantitative PCR (qPCR), also known as specific PCR, involves the targeting of particular bacterial species. The technique uses specific primers (short strands of nuclei...

the intestinal bacterial diversity of stichopus japonicus was investigated using 16s ribosomal rna gene (rdna) clone library and polymerase chain reaction/denaturing gradient gel electrophoresis (pcr-dgge). the clone library yielded a total of 188 clones, and these were sequenced and classified into 106 operational taxonomic units (otus) with sequence similarity ranging from 88 to 100%. the cov...

Studies were conducted on the improvement of A. culicicola identification. This species is phenotypically very similar to A. veronii biotype sobria, A. sobria, and A. allosaccharophila. The sequences of 16S rDNA of A. culicicola isolates show the highest similarity with A. jandaei, A. veronii, and A. caviae. Digestion of 16S rDNA PCR product with AluI and MboI restriction endonucleases allowed ...

MOTIVATION Many current studies of complex microbial communities rely on the isolation of community genomic DNA, amplification of 16S ribosomal RNA genes (rDNA) and subsequent examination of community structure through interrogation of the amplified 16S rDNA pool by high-throughput sequencing, phylogenetic microarrays or quantitative PCR. RESULTS Here we describe the development of a mathemat...

A rapid approach to the 16S rRNA gene (16S rDNA)-based bacterial identification has been developed that combines uracil-DNA-glycosylase (UDG)-mediated base-specific fragmentation of PCR products with matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). 16S rDNA signature sequences were PCR-amplified from both cultured and as-yet-uncultured bacteria in the...

OBJECTIVE To evaluate broad-range 16S ribosomal DNA (rDNA) polymerase chain reaction (PCR) as a rapid screening tool to detect bacterial contamination of stem-cell products. METHODS We performed the evaluation using whole blood spiked with serially diluted bacterial-type strains. Detection sensitivity was defined as the bacterial concentration for which all replicates were positive at each co...

16S ribosomal DNA (rDNA) and 16S-23S internal transcribed spacer rDNA sequence analyses were performed on Mycobacterium farcinogenes and M. senegalense strains and 26 strains of other rapidly growing mycobacteria to investigate the phylogenetic structure of bovine farcy mycobacteria within the M. fortuitum complex. M. farcinogenes and M. senegalense were indistinguishable in their 5"-end 16S rD...

We amplified bacterial 16S rRNA encoding DNA (rDNA) with the polymerase chain reaction (PCR) to detect amniotic fluid infection in 69 women in premature labor whose membranes were intact. Bacterial rDNA was detected by PCR in samples from 15 (94%) of 16 patients with positive amniotic fluid cultures. Bacteria were detected by PCR in samples from 5 (36%) of 14 patients with negative cultures and...

Microbial translocation (MT) from the gut is implicated in driving immune activation, increasing morbidity and mortality in HIV. We used bacterial 16S rDNA PCR, Sanger sequencing, and high-throughput sequencing to identify microbial DNA in the bloodstream of HIV-infected children in London, United Kingdom. Blood samples were collected from sequential children attending the HIV clinic at Great O...

The diversity and dynamics of the microbial communities during the manufacturing of Ragusano cheese, an artisanal cheese produced in Sicily (Italy), were investigated by a combination of classical and culture-independent approaches. The latter included PCR, reverse transcriptase-PCR (RT-PCR), and denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes (rDNA). Bacterial and Lactobacillu...