Self-collected oral swab comparison for supragingival microbiome characterization
The oral microbiome is a microbially dense and complex environment with links to local and systemic health outcomes such as periodontitis and cardiovascular disease respectively. Multiple factors may influence microbiome composition, where pre-analytical influence, such as the sample collection method should be minimized. Our aim was to compare three different commercial oral swabs to assess ease-of-use, bacterial DNA yield, and microbiome composition. The Isohelix buccal swab with Dri-Capsules (I), the Omnigene oral swab (O), and the Zymo Research DNA/RNA Shield SafeCollect swab (Z) were evaluated in parallel. Fifteen anonymized participants collected supragingival samples for 30 seconds per swab. Questionnaires regarding ease-of-use and comfort were completed. Swabs were subject to DNA extraction with the Maxwell RSC Buccal Swab DNA kit and 16S rRNA qPCR was performed to measure bacterial DNA density. DNA was subject to 16S rRNA and ITS sequencing using the QIAseq 16S/ITS Screening Panel on the Illumina MiSeq platform. The 16S V3 and V4 hypervariable regions were analyzed for genus-level alpha- and beta-diversity and were performed using QIIME2 v.2024.10. Participants preferred O and Z for ease-of-use and comfort. Both O and Z swabs resulted in positive ease-of-use assessments while the I swab had generally negative assessments. The O swab resulted in the highest 16s rRNA density followed by the the Z and I swabs. There were no differences in Shannon's diversity, richness as well as Bray-Curtis dissimilarity at the genus level between swabs. Considering pre-analytical quality is key for oral microbiome studies.
The oral microbiome is a microbially dense and complex environment with links to local and systemic health outcomes such as periodontitis and cardiovascular disease respectively. Multiple factors may influence microbiome composition, where pre-analytical influence, such as the sample collection method should be minimized. Our aim was to compare three different commercial oral swabs to assess ease-of-use, bacterial DNA yield, and microbiome composition. The Isohelix buccal swab with Dri-Capsules (I), the Omnigene oral swab (O), and the Zymo Research DNA/RNA Shield SafeCollect swab (Z) were evaluated in parallel. Fifteen anonymized participants collected supragingival samples for 30 seconds per swab. Questionnaires regarding ease-of-use and comfort were completed. Swabs were subject to DNA extraction with the Maxwell RSC Buccal Swab DNA kit and 16S rRNA qPCR was performed to measure bacterial DNA density. DNA was subject to 16S rRNA and ITS sequencing using the QIAseq 16S/ITS Screening Panel on the Illumina MiSeq platform. The 16S V3 and V4 hypervariable regions were analyzed for genus-level alpha- and beta-diversity and were performed using QIIME2 v.2024.10. Participants preferred O and Z for ease-of-use and comfort. Both O and Z swabs resulted in positive ease-of-use assessments while the I swab had generally negative assessments. The O swab resulted in the highest 16s rRNA density followed by the the Z and I swabs. There were no differences in Shannon's diversity, richness as well as Bray-Curtis dissimilarity at the genus level between swabs. Considering pre-analytical quality is key for oral microbiome studies.
Institute of Medical Microbiology