qiita_sid_10823
Comparison of oral collection methods for studies of microbiota
Background: A number of cohort studies have collected Scope mouthwash samples by mail which are being used for microbiota measurements. We evaluated the stability of Scope mouthwash samples at ambient temperature and determined the comparability of Scope mouthwash with saliva collection using the OMNIgene ORAL kit.  Methods: Fifty-three healthy volunteers from Mayo Clinic and fifty cohort members from Bangladesh provided oral samples. One aliquot of the OMNIgene ORAL and Scope mouthwash were frozen immediately and one aliquot of the Scope mouthwash remained at ambient temperature for four days and then was frozen. DNA was extracted and the V4 region of the 16S rRNA gene was PCR amplified and sequenced using the HiSeq. Intraclass correlation coefficients (ICC) were calculated.  Results: The overall stability of the Scope mouthwash samples was relatively high for alpha and beta diversity. For example, the meta-analyzed ICC for the Shannon Index was 0.86 (95% CI: 0.76, 0.96). Similarly, the ICCs for the relative abundance of the top 25 genera were generally high. The comparability of the two sample types was relatively low when measured using ICCs, but were increased by using a Spearman correlation coefficient (SCC) to compare the rank order of individuals.  Conclusions: Overall, the Scope mouthwash samples appear to be stable at ambient temperature which suggests that oral rinse samples received by the mail can be used for microbial analyses. However, Scope mouthwash samples were distinct compared to OMNIgene ORAL samples.  Impact: Studies should try to compare oral microbial metrics within one sample collection type.
Background: A number of cohort studies have collected Scope mouthwash samples by mail which are being used for microbiota measurements. We evaluated the stability of Scope mouthwash samples at ambient temperature and determined the comparability of Scope mouthwash with saliva collection using the OMNIgene ORAL kit.  Methods: Fifty-three healthy volunteers from Mayo Clinic and fifty cohort members from Bangladesh provided oral samples. One aliquot of the OMNIgene ORAL and Scope mouthwash were frozen immediately and one aliquot of the Scope mouthwash remained at ambient temperature for four days and then was frozen. DNA was extracted and the V4 region of the 16S rRNA gene was PCR amplified and sequenced using the HiSeq. Intraclass correlation coefficients (ICC) were calculated.  Results: The overall stability of the Scope mouthwash samples was relatively high for alpha and beta diversity. For example, the meta-analyzed ICC for the Shannon Index was 0.86 (95% CI: 0.76, 0.96). Similarly, the ICCs for the relative abundance of the top 25 genera were generally high. The comparability of the two sample types was relatively low when measured using ICCs, but were increased by using a Spearman correlation coefficient (SCC) to compare the rank order of individuals.  Conclusions: Overall, the Scope mouthwash samples appear to be stable at ambient temperature which suggests that oral rinse samples received by the mail can be used for microbial analyses. However, Scope mouthwash samples were distinct compared to OMNIgene ORAL samples.  Impact: Studies should try to compare oral microbial metrics within one sample collection type.