Skip to content


Archives of Public Health

Volume 73 Supplement 1

Methods in Epidemiology Symposium

Open Access

Perspectives and pitfalls of microbiome research through home based fecal sampling: the Flemish Gut Flora Project experience

  • Doris Vandeputte1,
  • Rianne Vanleeuwen1,
  • Gwen Falony1,
  • Marie Joossens1 and
  • Jeroen Raes1
Archives of Public HealthThe official journal of the Belgian Public Health Association201573(Suppl 1):P33

Published: 17 September 2015

The set up of large-scale, longitudinally sampled cohorts for microbiome research is logistically challenging as sample quality highly depends on the applied storage conditions. Ideally, fecal material intended for microbiome monitoring needs to be frozen immediately after sampling in order to stop the growth of residing bacteria and to conserve baseline microbial abundances. Effective fecal sampling protocols should not only combine comprehensive collection and storage instructions, but also excel in simplicity and hygiene of sample handling to avoid creating a potential population selection. To meet these criteria, the Flemish Gut Flora Project (FGFP), a large-scale (n>5000) microbiome research project based in Flanders (Belgium), developed a home sampling, aliquotting, and freezing protocol that, in combination with a cold chain collection network, would generate high-quality samples for microbiome research, while at the same time reducing logistic and post-collection analysis expenses.

Here we evaluate the FGFP sampling procedure in order to share the lessons learned from this project and improve future fecal sampling methods. We investigate selection bias imposed by the recruitment and check drop out values of the different steps of the sampling procedure. Based on questionnaires and temperature-time data of a subset of the samples we evaluate the cold chain and identify pitfalls of this crucial step in fecal sample collection for microbiome research. Furthermore recommendations to improve fecal sampling user experience are deduced from the responses to a user experience questionnaire and options for better fecal sampling procedures that combine these insights with methods to reduce laboratory efforts are proposed.

Authors’ Affiliations

Katholieke Universiteit Leuven, Leuven, Belgium


© Vandeputte et al. 2015

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.