One of the major questions in microbial ecology is "who is there?" This question can be answered using various tools, but one of the long-lasting gold standards is to sequence 16S ribosomal RNA (rRNA) gene amplicons generated by domain-level PCR reactions amplifying from genomic DNA. Traditionally, this was performed by cloning and Sanger (capillary electrophoresis) sequencing of PCR amplicons....

We describe the characterization of Salmonella enterica serovar Typhi, isolated from the blood of patients with perforation and non-perforation typhoid fever, by a combination of conventional microbiological tests, 16S rRNA gene sequencing, and flagellin gene and CDP-tyvelose epimerase (rfbE) gene sequencing. The 16S rRNA gene sequencing showed that there were four base mutations from perforati...

pasteurella multocida is known as an important heterogenic bacterial agent causes some severe diseases such as fowl cholera in poultry and haemorrhagic septicaemia in cattle and buffalo. a polymerase chain reaction (pcr) assay was developed using primers derived from conserved part of 16s-23s rrna gene. the pcr amplified a fragment size of 0.7 kb using dna from nine avian p. multocida  isolates...

The complete nucleotide sequence of the 16S RNA gene from the rrnB cistron of Escherichia coli has been determined by using three rapid DNA sequencing methods. Nearly all of the structure has been confirmed by two to six independent sequence determinations on both DNA strands. The length of the 16S rRNA chain inferred from the DNA sequence is 1541 nucleotides, in close agreement with previous e...

BACKGROUND High-throughput bacterial 16S rRNA gene sequencing followed by clustering of short sequences into operational taxonomic units (OTUs) is widely used for microbiome profiling. However, clustering of short 16S rRNA gene reads into biologically meaningful OTUs is challenging, in part because nucleotide variation along the 16S rRNA gene is only partially captured by short reads. The recen...

Culture-independent studies to characterize skin microbiota are increasingly common, due in part to affordable and accessible sequencing and analysis platforms. Compared to culture-based techniques, DNA sequencing of the bacterial 16S ribosomal RNA (rRNA) gene or whole metagenome shotgun (WMS) sequencing provides more precise microbial community characterizations. Most widely used protocols wer...

Rapid advances in sequencing technology have changed the experimental landscape of microbial ecology. In the last 10 years, the field has moved from sequencing hundreds of 16S rRNA gene fragments per study using clone libraries to the sequencing of millions of fragments per study using next-generation sequencing technologies from 454 and Illumina. As these technologies advance, it is critical t...