At the present time, use of the 16S rRNA
gene is thought to be a 'paragon' for identification and phylogenetic analysis of bacteria (Ludwig and Schleifer, 1999).
All the 16S rRNA
gene sequences obtained using cloning and Sanger sequencing have been archived in GenBank, which stores all the sequences including sequences of poor quality and chimeric sequences from any sample.
gene-based identification of Elizabethkingia meningoseptica (Flavobacteriales: Flavobacteriaceae) as a dominant midgut bacterium of the Asian malaria vector Anopheles stephensi (Dipteria: Culicidae) with antimicrobial activities.
2 ul water free nuclease for full length 16S rRNA
gene amplification and initially was denatured at 94degC for 2 min followed by 30 cycles consisting of denaturation at 94degC for 60 s, primer annealing at 55degC for 60s and primer extension at 72degC for 3 min and a final extension at 72degC for 10 min using multigene thermal cycler.
The average sizes of PCR products of COII and 16S rRNA
genes for the 2 species examined were 763 and 432 base pairs (bp), respectively.
It is proposed that the identified strain Trichoderma longibrachiatum 28CP be assigned as the type strain of a species of the genus Trichoderma based on phylogenetic tree analysis together with the 28S rRNA
gene sequence search in Ribosomal Database Project, small subunit rRNA
and large subunit rRNA
Although it has been validated that 16S rRNA
gene sequencing with a less than 97% of similarity with the closest strain represents a new species, it is not as definitive as DNA-DNA hybridization, however, Bavykin et al.
Caption: FIGURE 1: Neighbor-joining phylogenetic tree based on comparison of 16S rRNA
Prevalence of Streptococcus mutans and its genotypes in children with and without caries: Overall, prevalence of S mutans based on 16S rRNA
species Identification was 14.
Our research goal was to identify the seven isolates of endophytic actinomycetes from Indonesian rice plant based on their morphological characteristics and 16S rRNA
These species had 16S rRNA
gene sequence similarity more than 97% with strain NCCP-54T, which made it mandatory to provide further evidence to establish the novelty of strain NCCP-54T by DNA-DNA hybridization (Stackebrandt and Goebel, 1994) and to describe strain NCCP-54T as Lysinibacillus pakistanensis sp.
Sequences of mitochondrial cytochrome c oxidase 1 (CO1), 16S rRNA
and 18S rRNA
genes have been used to assess genetic divergence within many taxa.