Comparison of Oral Microbiota Collected Using Multiple Methods and Recommendations for New Epidemiologic Studies
ABSTRACT 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 met...
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American Society for Microbiology
2020
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oai:doaj.org-article:3fbaac9f709e4519b5d082b6b3531be92021-12-02T19:47:35ZComparison of Oral Microbiota Collected Using Multiple Methods and Recommendations for New Epidemiologic Studies10.1128/mSystems.00156-202379-5077https://doaj.org/article/3fbaac9f709e4519b5d082b6b3531be92020-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00156-20https://doaj.org/toc/2379-5077ABSTRACT 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 nonethanol mouthwash. Oral samples were collected from 40 individuals over 4 visits. Two samples were collected from each subject per visit: one with OMNIgene and one with an 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 MiSeq. Oral collection methods were compared based on alpha and beta diversity metrics and phylum- and genus-level relative abundances. All alpha diversity metrics were significantly lower for Saccomanno’s fixative than for OMNIgene (P < 0.001), whereas the two mouthwashes were more similar to OMNIgene. Principal-coordinate analysis (PCoA) using the Bray-Curtis and weighted UniFrac beta diversity matrices showed large differences in the microbial compositions of samples collected with Saccomanno’s compared to those with OMNIgene and the mouthwashes. Clustering by collection method was not observed in unweighted UniFrac PCoA plots, suggesting differences in relative abundances but not specific taxa detected by the collection methods. Relative abundances of most taxa were significantly different between OMNIgene and the other methods at each taxonomic level, with Saccomanno’s showing the least agreement with OMNIgene. There were clear differences in oral microbial communities between the four oral collection methods, particularly for Saccomanno’s fixative. IMPORTANCE We compared four different oral collection methods for studying the human oral microbiome: an OMNIgene ORAL kit, Scope mouthwash, nonethanol mouthwash, and Saccomanno’s fixative. Our study shows that the type of the collection method can have a large impact on the results of an oral microbiome analysis. We recommend that one consistent oral collection method should be used for all oral microbiome comparisons. While Scope and nonethanol mouthwashes are less expensive and provide results similar to those with OMNIgene, Saccomanno’s fixative may be unfavorable due to the microbial differences detected in this study. Our results will help guide the design of future oral microbiome studies.Yukiko YanoXing HuaYunhu WanShalabh SumanBin ZhuCasey L. DagnallAmy HutchinsonKristine JonesBelynda D. HicksJianxin ShiChristian C. AbnetEmily VogtmannAmerican Society for Microbiologyarticleoral microbiomecollection methodepidemiologyMicrobiologyQR1-502ENmSystems, Vol 5, Iss 4 (2020) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
oral microbiome collection method epidemiology Microbiology QR1-502 |
| spellingShingle |
oral microbiome collection method epidemiology Microbiology QR1-502 Yukiko Yano Xing Hua Yunhu Wan Shalabh Suman Bin Zhu Casey L. Dagnall Amy Hutchinson Kristine Jones Belynda D. Hicks Jianxin Shi Christian C. Abnet Emily Vogtmann Comparison of Oral Microbiota Collected Using Multiple Methods and Recommendations for New Epidemiologic Studies |
| description |
ABSTRACT 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 nonethanol mouthwash. Oral samples were collected from 40 individuals over 4 visits. Two samples were collected from each subject per visit: one with OMNIgene and one with an 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 MiSeq. Oral collection methods were compared based on alpha and beta diversity metrics and phylum- and genus-level relative abundances. All alpha diversity metrics were significantly lower for Saccomanno’s fixative than for OMNIgene (P < 0.001), whereas the two mouthwashes were more similar to OMNIgene. Principal-coordinate analysis (PCoA) using the Bray-Curtis and weighted UniFrac beta diversity matrices showed large differences in the microbial compositions of samples collected with Saccomanno’s compared to those with OMNIgene and the mouthwashes. Clustering by collection method was not observed in unweighted UniFrac PCoA plots, suggesting differences in relative abundances but not specific taxa detected by the collection methods. Relative abundances of most taxa were significantly different between OMNIgene and the other methods at each taxonomic level, with Saccomanno’s showing the least agreement with OMNIgene. There were clear differences in oral microbial communities between the four oral collection methods, particularly for Saccomanno’s fixative. IMPORTANCE We compared four different oral collection methods for studying the human oral microbiome: an OMNIgene ORAL kit, Scope mouthwash, nonethanol mouthwash, and Saccomanno’s fixative. Our study shows that the type of the collection method can have a large impact on the results of an oral microbiome analysis. We recommend that one consistent oral collection method should be used for all oral microbiome comparisons. While Scope and nonethanol mouthwashes are less expensive and provide results similar to those with OMNIgene, Saccomanno’s fixative may be unfavorable due to the microbial differences detected in this study. Our results will help guide the design of future oral microbiome studies. |
| format |
article |
| author |
Yukiko Yano Xing Hua Yunhu Wan Shalabh Suman Bin Zhu Casey L. Dagnall Amy Hutchinson Kristine Jones Belynda D. Hicks Jianxin Shi Christian C. Abnet Emily Vogtmann |
| author_facet |
Yukiko Yano Xing Hua Yunhu Wan Shalabh Suman Bin Zhu Casey L. Dagnall Amy Hutchinson Kristine Jones Belynda D. Hicks Jianxin Shi Christian C. Abnet Emily Vogtmann |
| author_sort |
Yukiko Yano |
| title |
Comparison of Oral Microbiota Collected Using Multiple Methods and Recommendations for New Epidemiologic Studies |
| title_short |
Comparison of Oral Microbiota Collected Using Multiple Methods and Recommendations for New Epidemiologic Studies |
| title_full |
Comparison of Oral Microbiota Collected Using Multiple Methods and Recommendations for New Epidemiologic Studies |
| title_fullStr |
Comparison of Oral Microbiota Collected Using Multiple Methods and Recommendations for New Epidemiologic Studies |
| title_full_unstemmed |
Comparison of Oral Microbiota Collected Using Multiple Methods and Recommendations for New Epidemiologic Studies |
| title_sort |
comparison of oral microbiota collected using multiple methods and recommendations for new epidemiologic studies |
| publisher |
American Society for Microbiology |
| publishDate |
2020 |
| url |
https://doaj.org/article/3fbaac9f709e4519b5d082b6b3531be9 |
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