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Open Access Highly Accessed Open Badges Methodology article

Comparison of methods for fecal microbiome biospecimen collection

Christine Dominianni1, Jing Wu1, Richard B Hayes12 and Jiyoung Ahn12*

Author Affiliations

1 Division of Epidemiology, Department of Population Health, New York University School of Medicine, 650 First Avenue, New York, NY 10016, USA

2 NYU Cancer Institute, 522 First Avenue, New York, NY 10016, USA

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BMC Microbiology 2014, 14:103  doi:10.1186/1471-2180-14-103

Published: 23 April 2014



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.


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.


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.

Comparison; Methods; Fecal; Microbiome; Collection