Comparative pilot study of three commercial kits for bacterial DNA extraction from human subgingival biofilm samples collected with a single paper point.

Objective: In periodontal research, subgingival biofilm samples are typically collected using sterile paper points and pooled for molecular analyses. Streamlining this process by using a single paper point for molecular analysis could simplify sample collection and allow additional paper points to be used for other investigations. This pilot study evaluated the performance of three commercial DNA extraction kits for analysing small sample volumes (<10 µL). Methods: Samples were collected from six participants, each contributing 18 paper points from both healthy and periodontitis-affected sites. Bacterial and human DNA yields were quantified using fluorometric measurements combined with qPCR, employing universal 16S primers for bacterial DNA and human-specific GAPDH primers. Results: Among the tested kits, the DNeasy Blood and Tissue Kit demonstrated the highest efficiency, yielding significantly more total dsDNA in samples from healthy sites compared to both other kits and in samples from periodontitis-affected sites compared to one kit. Bacterial DNA yields were also significantly higher with the DNeasy Kit compared to one of the other kits in both health conditions. Conclusion: These results suggest that one paper point is sufficient to extract DNA for subsequent bacterial analyses and that the DNeasy Blood and Tissue Kit appears to be the most efficient among the three tested kits.