The human oral microbiome is the most studied human microflora, but 53% of the species have not yet been validly named and 35% remain uncultivated. The uncultivated taxa are known primarily from 16S rRNA sequence information. Sequence information tied solely to obscure isolate or clone numbers, and usually lacking accurate phylogenetic placement, is a major impediment to working with human oral...

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...

Phylogenetic analysis of the class 'Alphaproteobacteria', including physiologically diverse species, was conducted by using small-subunit rRNA gene sequences. The 16S rRNA gene sequences of 261 species in the class 'Alphaproteobacteria' were obtained from GenBank/EMBL/DDBJ for constructing a phylogenetic tree by using maximum-likelihood analysis. In the resulting tree, members of the class 'Alp...

Bacillus represents microbes of high economic, medical and biodefense importance. Bacillus strain identification based on 16S rRNA sequence analyses is invariably limited to species level. Secondly, certain discrepancies exist in the segregation of Bacillus subtilis strains. In the RDP/NCBI databases, out of a total of 2611 individual 16S rDNA sequences belonging to the 175 different species of...

Chronic idiopathic colitis is a common clinical entity in young captive rhesus monkeys. Eight isolates, cultured from five monkeys in colony 1 with endemic diarrhea and three from colony 2 without diarrhea, were grown under microaerobic conditions on selective agar and were classified by full 16S rRNA sequence, biochemical, and phenotypic analysis as a novel helicobacter, "Helicobacter macacae"...

The traditional identification of bacteria on the basis of phenotypic characteristics is generally not as accurate as identification based on genotypic methods. Comparison of the bacterial 16S rRNA gene sequence has emerged as a preferred genetic technique. 16S rRNA gene sequence analysis can better identify poorly described, rarely isolated, or phenotypically aberrant strains, can be routinely...

Eukaryotic 18S ribosomal RNA (rRNA) gene primers that feature a wide coverage are critical in detecting the composition of eukaryotic microscopic organisms in ecosystems. Here, we predicted 18S rRNA primers based on consecutive conserved sites and evaluated their coverage efficiency and scope of application to different eukaryotic groups. After evaluation, eight of them were considered as quali...

We have analyzed the 16S rDNA sequence and the phylogenetic position of an uncultivated spirochete from the hindgut contents of the Australian termite Mastotermes darwiniensis Froggatt. The 16S rRNA genes of bacteria from the hindgut contents of Mastotermes darwiniensis were amplified by polymerase chain reaction. The amplification products were cloned and sequenced. The sequences were compared...

Sequence analysis of the cloned 16S rRNA genes of Clostridium paradoxum DSM 7308T revealed the presence of 15 different sequences in variable region I (Escherichia coli position 73-97) of the 16S rRNA. The majority of the cloned genes contained intervening sequences (IVSs), which varied in length from 120-131 nt, and were present in the DNA obtained from single colonies of C. paradoxum. The abs...

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...