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KMID : 0365220160530020001
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Korean Journal of Public Health
2016 Volume.53 No. 2 p.1 ~ p.7
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Comparison of nucleic acid extraction efficiency for vaginal microbiome analyses between a routine commercial kit and the bead beating method
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Lee Jung-Eun
Kim Ji-Young
Sung Joo-Hon
Song Yun-Mi
Ko Gwang-Pyo
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Abstract
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To compare the efficiency of nucleic acid extraction for identifying microbiomes in cervicovaginal samples between a commercial kit (chemagic viral DNA/RNA kit,Chemagen,Germany), conventionally applied method for diagnosing human papilloma virus infection, and the standard bead beating method. Cervicovaginal samples collected from 10 participants in the Healthy Twin Study were simultaneously subjected to the two different DNA extraction methods. Extracted DNA was amplified by nested-PCR and analyzed by denaturing gradient gel electrophoresis (DGGE), DGGE profiling, and phylogenetic sequencing based on the Greengenes database. Although chemagic kit method produced slightly more diverse bands compared to bead beating method, DGGE band patterns were very similar between the two methods for 60% of samples. Multi-dimensional scaling analysis of the DGGE fingerprints revealed randomly distributed bacterial community compositions with both methods. An unweighted pair group analysis using arithmetic average clustering showed that the clustering of DGGE fingerprints was not related to the DNA extraction method. With the bead beating method, Lactobacillus sp. and Enterobacteriaceae were found most often; Lactobacillus sp. and Pseudomonas spp. were more common with the chemagic kit method. According to UniFrac distance analysis, the microbial communities by phylogenetic analysis did not differ significantly between the two methods. DNA extraction using a commercial chemagic kit did not cause significant difference in an analysis of the vaginal microbiome, compared with the bead beating method. These findings suggest that commercial nucleic acid extraction kits would be useful for analyzing the cervicovaginal microbiome, with comparable efficiency and greater convenience than the bead beating extraction method. This study will help to investigate the effect of vaginal microbiota on women’ health.
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KEYWORD
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DNA, metagenome, human, vaginal smears
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