Abstract
BackgroundEffective means are needed to efficiently collect fecal samples for microbiome analysis in large-scale epidemiological studies. Using twenty-four fecal aliquots prepared from three healthy individuals, we compared the following four fecal sample collection methods for assessment of human gut microbiome: 1) fecal occult blood test cards, held at room temperature for three days, 2) Eppendorf tubes, at room temperature for three days, 3) Eppendorf tubes with RNAlater, at room temperature, and 4) as controls, samples immediately frozen at −80°C. The 24 samples were assayed by 16S rRNA gene sequencing to compare overall microbiome structure and taxon distributions according to collection method.ResultsStoring fecal occult blood test card samples at room temperature for three days did not affect total DNA purity and relative 16S rRNA bacterial gene contents, compared with fresh frozen collection. Overall microbiome structure, based on phylogenetic UniFrac index, differed significantly by subject (p = 0.001), but microbiome structure (p = 0.497) and relative abundance of major microbial taxa (phyla) (p > 0.05) did not differ significantly by collection method.ConclusionsOur findings suggest that low-cost fecal occult blood test card collection may be a feasible means of sample collection for fecal microbiome assessment in large-scale population-based studies.
Highlights
Effective means are needed to efficiently collect fecal samples for microbiome analysis in large-scale epidemiological studies
Case–control investigation points to a potential role of the gut microbiome in colorectal cancer [2], large-scale prospective study of this association has been impeded by the lack of validated fecal sample collection methods suitable for large-scale studies
The OD 260/280 ratio, a measure of DNA purity, was greater than 1.8 in samples collected from card, room temperature, and frozen methods; DNA purity from these methods were higher than DNA purity from RNAlater (Table 1, p < 0.05)
Summary
Effective means are needed to efficiently collect fecal samples for microbiome analysis in large-scale epidemiological studies. Because fecal collections may take place outside of research clinics, we wished to develop a fecal collection approach which would not require immediate sample processing To address this need, we evaluated the utility of the Beckman Coulter Hemoccult Sensa® card (Beckman Coulter, CA) for gut microbiome characterization because it offers a practical way to collect fecal samples for largescale study. As freezing at ultralow temperatures stabilizes bacterial samples [3], we compared results for samples collected by the card method to results for samples immediately stored in Eppendorf tubes at −80°C [4]; we included storage in Eppendorf tubes at room temperature as part of our evaluation. Our main goal was to assess the effect the different storage conditions have on gut microbiome diversity parameters including overall diversity and specific taxon abundances because different methods might differentially impact bacterial overgrowth or DNA degradation that could lead to biased assessment of these microbial parameters
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
