Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts

Abstract Background To initiate fecal and oral collections in prospective cohort studies for microbial analyses, it is essential to understand how field conditions and geographic differences may impact microbial communities. This study aimed to investigate the impact of fecal and oral sample collect...

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Autores principales:	Zeni Wu, Autumn G. Hullings, Reza Ghanbari, Arash Etemadi, Yunhu Wan, Bin Zhu, Hossein Poustchi, Behnam Bagheri Fahraji, Mohammad Javad Zare Sakhvidi, Jianxin Shi, Rob Knight, Reza Malekzadeh, Rashmi Sinha, Emily Vogtmann
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Comparability Feces Iran Microbiome Saliva Stability Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/9326821ea2b84489b01a4948d8e68bc4
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spelling	oai:doaj.org-article:9326821ea2b84489b01a4948d8e68bc42021-11-28T12:07:08ZComparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts10.1186/s12866-021-02387-91471-2180https://doaj.org/article/9326821ea2b84489b01a4948d8e68bc42021-11-01T00:00:00Zhttps://doi.org/10.1186/s12866-021-02387-9https://doaj.org/toc/1471-2180Abstract Background To initiate fecal and oral collections in prospective cohort studies for microbial analyses, it is essential to understand how field conditions and geographic differences may impact microbial communities. This study aimed to investigate the impact of fecal and oral sample collection methods and room temperature storage on collection samples for studies of the human microbiota. Results We collected fecal and oral samples from participants in two Iranian cohorts located in rural Yazd (n = 46) and urban Gonbad (n = 38) and investigated room temperature stability over 4 days of fecal (RNAlater and fecal occult blood test [FOBT] cards) and comparability of fecal and oral (OMNIgene ORAL kits and Scope mouthwash) collection methods. We calculated interclass correlation coefficients (ICCs) based on 3 alpha and 4 beta diversity metrics and the relative abundance of 3 phyla. After 4 days at room temperature, fecal stability ICCs and ICCs for Scope mouthwash were generally high for all microbial metrics. Similarly, the fecal comparability ICCs for RNAlater and FOBT cards were high, ranging from 0.63 (95% CI: 0.46, 0.75) for the relative abundance of Firmicutes to 0.93 (95% CI: 0.89, 0.96) for unweighted Unifrac. Comparability ICCs for OMNIgene ORAL and Scope mouthwash were lower than fecal ICCs, ranging from 0.55 (95% CI: 0.36, 0.70) for the Shannon index to 0.79 (95% CI: 0.69, 0.86) for Bray-Curtis. Overall, RNAlater, FOBT cards and Scope mouthwash were stable up to 4 days at room temperature. Samples collected using FOBT cards were generally comparable to RNAlater while the OMNIgene ORAL were less similar to Scope mouthwash. Conclusions As microbiome measures for feces samples collected using RNAlater, FOBT cards and oral samples collected using Scope mouthwash were stable over four days at room temperature, these would be most appropriate for microbial analyses in these populations. However, one collection method should be consistently since each method may induce some differences.Zeni WuAutumn G. HullingsReza GhanbariArash EtemadiYunhu WanBin ZhuHossein PoustchiBehnam Bagheri FahrajiMohammad Javad Zare SakhvidiJianxin ShiRob KnightReza MalekzadehRashmi SinhaEmily VogtmannBMCarticleComparabilityFecesIranMicrobiomeSalivaStabilityMicrobiologyQR1-502ENBMC Microbiology, Vol 21, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Comparability Feces Iran Microbiome Saliva Stability Microbiology QR1-502
spellingShingle	Comparability Feces Iran Microbiome Saliva Stability Microbiology QR1-502 Zeni Wu Autumn G. Hullings Reza Ghanbari Arash Etemadi Yunhu Wan Bin Zhu Hossein Poustchi Behnam Bagheri Fahraji Mohammad Javad Zare Sakhvidi Jianxin Shi Rob Knight Reza Malekzadeh Rashmi Sinha Emily Vogtmann Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts
description	Abstract Background To initiate fecal and oral collections in prospective cohort studies for microbial analyses, it is essential to understand how field conditions and geographic differences may impact microbial communities. This study aimed to investigate the impact of fecal and oral sample collection methods and room temperature storage on collection samples for studies of the human microbiota. Results We collected fecal and oral samples from participants in two Iranian cohorts located in rural Yazd (n = 46) and urban Gonbad (n = 38) and investigated room temperature stability over 4 days of fecal (RNAlater and fecal occult blood test [FOBT] cards) and comparability of fecal and oral (OMNIgene ORAL kits and Scope mouthwash) collection methods. We calculated interclass correlation coefficients (ICCs) based on 3 alpha and 4 beta diversity metrics and the relative abundance of 3 phyla. After 4 days at room temperature, fecal stability ICCs and ICCs for Scope mouthwash were generally high for all microbial metrics. Similarly, the fecal comparability ICCs for RNAlater and FOBT cards were high, ranging from 0.63 (95% CI: 0.46, 0.75) for the relative abundance of Firmicutes to 0.93 (95% CI: 0.89, 0.96) for unweighted Unifrac. Comparability ICCs for OMNIgene ORAL and Scope mouthwash were lower than fecal ICCs, ranging from 0.55 (95% CI: 0.36, 0.70) for the Shannon index to 0.79 (95% CI: 0.69, 0.86) for Bray-Curtis. Overall, RNAlater, FOBT cards and Scope mouthwash were stable up to 4 days at room temperature. Samples collected using FOBT cards were generally comparable to RNAlater while the OMNIgene ORAL were less similar to Scope mouthwash. Conclusions As microbiome measures for feces samples collected using RNAlater, FOBT cards and oral samples collected using Scope mouthwash were stable over four days at room temperature, these would be most appropriate for microbial analyses in these populations. However, one collection method should be consistently since each method may induce some differences.
format	article
author	Zeni Wu Autumn G. Hullings Reza Ghanbari Arash Etemadi Yunhu Wan Bin Zhu Hossein Poustchi Behnam Bagheri Fahraji Mohammad Javad Zare Sakhvidi Jianxin Shi Rob Knight Reza Malekzadeh Rashmi Sinha Emily Vogtmann
author_facet	Zeni Wu Autumn G. Hullings Reza Ghanbari Arash Etemadi Yunhu Wan Bin Zhu Hossein Poustchi Behnam Bagheri Fahraji Mohammad Javad Zare Sakhvidi Jianxin Shi Rob Knight Reza Malekzadeh Rashmi Sinha Emily Vogtmann
author_sort	Zeni Wu
title	Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts
title_short	Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts
title_full	Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts
title_fullStr	Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts
title_full_unstemmed	Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts
title_sort	comparison of fecal and oral collection methods for studies of the human microbiota in two iranian cohorts
publisher	BMC
publishDate	2021
url	https://doaj.org/article/9326821ea2b84489b01a4948d8e68bc4
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Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts

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