Comparison of methods for fecal microbiome biospecimen collection - PubMed (original) (raw)

Comparison of methods for fecal microbiome biospecimen collection

Christine Dominianni et al. BMC Microbiol. 2014.

Abstract

Background: Effective 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.

Results: Storing 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.

Conclusions: Our 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.

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Figures

Figure 1

Alpha rarefaction plot of Shannon indices (±Standard Error) according to collection method. Card (green), Room Temperature (blue), RNAlater (orange), Frozen (red). Statistical significance was tested by using non-parametric Monte Carlo permutations (QIIME).

Figure 2

Unweighted PCoA plots of the first two principal coordinates. A), B) The first two principal coordinates were grouped by subject (1 [red], 2 [blue], 3 [orange]) A) or collection method (card [green], room temperature [blue], RNAlater [orange], frozen [red]) B). Adonis was used to test for significant differences in the variation in distances across subjects or collection methods using QIIME. C) UPGMA clustering on unweighted UniFrac distances (subject 1 [red], 2 [blue], 3 [orange]). D) Mean (±Std) unweighted UniFrac distances within and between sample collection methods or subjects.

Figure 3

Relative abundances of phyla by subject and by collection method. Card (1A-3A), Room Temperature (1B-3B), RNAlater (1C-3C), Frozen (1D-3D). Kruskal-Wallis or Mann-Whitney-Wilcoxon tests were used to test for overall differences using SAS software (version 9.3).

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Comparison of methods for fecal microbiome biospecimen collection - PubMed (original) (raw)