Abstract
BackgroundTo 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.ResultsWe 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.ConclusionsAs 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.
Highlights
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
Oral samples were collected at a clinic visit using the OMNIgene oral collection kit and Scope mouthwash
Looking comprehensively at metrics of alpha diversity, beta diversity, and the relative abundance of three specific phyla, we found that RNAlater, fecal occult blood test (FOBT) card, and Scope mouthwash were stable at room temperature for up to 4 days
Summary
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. Large-scale, prospective cohort studies with sample collections for microbiota analysis prior to disease development are needed to better understand. Other studies have investigated the impact of sample collection method and duration of sample storage on microbial community measures [13,14,15]. Few studies have investigated the impact of these logistical challenges in low- and middle-income countries and in rural versus urban settings where the gold standard collection method may not be feasible (i.e., fresh, immediately frozen for fecal samples). Since there is no community gold standard method for oral microbiota due to oral community differences by site in the oral cavity, [16] other collection methods such as the OMNIgene oral collection kit and Scope mouthwash must be compared to each other
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