Quantitative Insights into Microbial Ecology software allows the dissection of oral microbial diversity
Keywords:
Metagenomic Analysis, open-reference Operational taxonomic units (OTU), Quantitative insights into microbial ecology (QIIME), taxonomyAbstract
Objective: Recent approach based on the 16S rRNA gene sequence, which bypasses the need for culturing was being used to assess the diversity and relative abundance of bacteria in the carious patients. Here, we report the use of 16S rRNA V3-V4 marker gene approach to dissect the oral microbial diversity in patients’ caries. Methods: A total of 8 subjects with caries aged between 20-30 years old from Dental Clinic, Hospital Universiti Sains Malaysia, Kelantan were recruited. The DNA from collected plaque samples were examined by high-throughput sequencing of the V3-V4 hypervariable region of the 16S rRNA gene using MiSeq sequencing platform. For 16S rRNA amplicon analysis, the Quantitative Insights into Microbial Ecology (QIIME) programme was utilised and the Greengenes database was used for taxonomy classification. Results: By using this platform, we identified six top communities of microbial in the caries samples. Protobacteria OTUs were most dominant in all samples with abundance value of (47.4%), followed by Firmicutes (21%), Bacteroidetes (15.6%), Actinobacteria (7.5%) and Fusobacteria (5.2%) and TM7 (3.2%). Conclusion: The QIIME is a robust platform that is able to support a wide range of microbial community analyses and to classify the oral microbial taxa in the taxonomic hierarchy i.e. from kingdom, phylum, class, order, family, genus to species level.
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