TY - JOUR
T1 - Comparison of oral collection methods for studies of microbiota
AU - Vogtmann, Emily
AU - Chen, Jun
AU - Kibriya, Muhammad G.
AU - Amir, Amnon
AU - Shi, Jianxin
AU - Chen, Yu
AU - Islam, Tariqul
AU - Eunes, Mahbubul
AU - Ahmed, Alauddin
AU - Naher, Jabun
AU - Rahman, Anisur
AU - Barmon, Bhaswati
AU - Knight, Rob
AU - Chia, Nicholas
AU - Ahsan, Habibul
AU - Abnet, Christian C.
AU - Sinha, Rashmi
N1 - Funding Information:
This work was supported by the Intramural Research Program of the NCI at the NIH; the Gerstner Family Career Development Awards, and Mayo Clinic Center for Individualized Medicine (to J. Chen); grants from the NIH (1R01CA179243 to N. Chia and P42ES10349 and R01CA107431 to H. Ahsan); and the Howard Hughes Medical Institute and the Sloan Foundation awards (to R. Knight).
Publisher Copyright:
©2018 American Association for Cancer Research.
PY - 2019/1
Y1 - 2019/1
N2 - 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 50 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 4 days and was then 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% confidence interval, 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 with OMNIgene ORAL samples. Impact: Studies should try to compare oral microbial metrics within one sample collection type.
AB - 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 50 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 4 days and was then 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% confidence interval, 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 with OMNIgene ORAL samples. Impact: Studies should try to compare oral microbial metrics within one sample collection type.
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U2 - 10.1158/1055-9965.EPI-18-0312
DO - 10.1158/1055-9965.EPI-18-0312
M3 - Article
C2 - 30262598
AN - SCOPUS:85060826300
SN - 1055-9965
VL - 28
SP - 137
EP - 143
JO - Cancer Epidemiology Biomarkers and Prevention
JF - Cancer Epidemiology Biomarkers and Prevention
IS - 1
ER -