Comparison of oral collection methods for studies of microbiota

Emily Vogtmann, Jun Chen, Muhammad G. Kibriya, Amnon Amir, Jianxin Shi, Yu Chen, Tariqul Islam, Mahbubul Eunes, Alauddin Ahmed, Jabun Naher, Anisur Rahman, Bhaswati Barmon, Rob Knight, Nicholas D Chia, Habibul Ahsan, Christian C. Abnet, Rashmi Sinha

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Pages (from-to)137-143
Number of pages7
JournalCancer Epidemiology Biomarkers and Prevention
Volume28
Issue number1
DOIs
StatePublished - Jan 1 2019

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Microbiota
Postal Service
Temperature
Bangladesh
Scope mouthwash
rRNA Genes
Saliva
Healthy Volunteers
Cohort Studies
Confidence Intervals
Polymerase Chain Reaction
DNA

ASJC Scopus subject areas

  • Epidemiology
  • Oncology

Cite this

Comparison of oral collection methods for studies of microbiota. / Vogtmann, Emily; Chen, Jun; Kibriya, Muhammad G.; Amir, Amnon; Shi, Jianxin; Chen, Yu; Islam, Tariqul; Eunes, Mahbubul; Ahmed, Alauddin; Naher, Jabun; Rahman, Anisur; Barmon, Bhaswati; Knight, Rob; Chia, Nicholas D; Ahsan, Habibul; Abnet, Christian C.; Sinha, Rashmi.

In: Cancer Epidemiology Biomarkers and Prevention, Vol. 28, No. 1, 01.01.2019, p. 137-143.

Research output: Contribution to journalArticle

Vogtmann, E, Chen, J, Kibriya, MG, Amir, A, Shi, J, Chen, Y, Islam, T, Eunes, M, Ahmed, A, Naher, J, Rahman, A, Barmon, B, Knight, R, Chia, ND, Ahsan, H, Abnet, CC & Sinha, R 2019, 'Comparison of oral collection methods for studies of microbiota', Cancer Epidemiology Biomarkers and Prevention, vol. 28, no. 1, pp. 137-143. https://doi.org/10.1158/1055-9965.EPI-18-0312
Vogtmann, Emily ; Chen, Jun ; Kibriya, Muhammad G. ; Amir, Amnon ; Shi, Jianxin ; Chen, Yu ; Islam, Tariqul ; Eunes, Mahbubul ; Ahmed, Alauddin ; Naher, Jabun ; Rahman, Anisur ; Barmon, Bhaswati ; Knight, Rob ; Chia, Nicholas D ; Ahsan, Habibul ; Abnet, Christian C. ; Sinha, Rashmi. / Comparison of oral collection methods for studies of microbiota. In: Cancer Epidemiology Biomarkers and Prevention. 2019 ; Vol. 28, No. 1. pp. 137-143.
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abstract = "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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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 D

AU - Ahsan, Habibul

AU - Abnet, Christian C.

AU - Sinha, Rashmi

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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.

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