Comparison of oral microbiota collected using multiple methods: Recommendations for new epidemiological studies

Epidemiologic studies use various biosample collection methods to study associations between human oral microbiota and health outcomes. However, the agreement between the different methods is unclear. We compared a commercially available OMNIgene ORAL kit to three alternative collection methods: Saccomanno's fixative, Scope mouthwash, and non-ethanol mouthwash. Oral samples were collected from 40 individuals over 4 visits. Two samples were collected from each subject per visit: OMNIgene and one alternative method. DNA was extracted using the DSP DNA Virus Pathogen kit, and the V4 region of the 16S rRNA gene was PCR amplified and sequenced using the MiSeq. Oral collection methods were compared based on alpha and beta diversity metrics, and phylum and genus level relative abundances. There were clear differences in oral microbial communities between the four oral collection methods.