How Proper Fecal Sample Collection Matters in Outcomes
Having robust and reliable fecal samples is the cornerstone of any gut microbiome study. However, fecal material is not homogeneous and requires careful handling to obtain accurate and replicable results. A recent study published in Scientific Reports systematically compared different fecal sample collection and storage methods to provide recommendations for reducing variability in microbiome and metabolite profiling.
The researchers found that subsampling small aliquots from unhomogenized stool resulted in sporadic detection of some microbial taxa and inconsistent metabolite levels between samples. This heterogeneity was detected both within a single bowel movement and between consecutive stools collected less than a day apart. To minimize sampling bias, the study recommends homogenizing the entire stool sample prior to aliquotting for different analyses.
Additionally, immediate freezing of samples was found to best preserve the native bacterial and fungal composition compared to collection tubes with stabilizing liquid, which significantly altered the abundance of certain taxa. The study also detected differences in microbial diversity, metabolite levels, and community structure between two consecutive stools from the same individual, highlighting the importance of consistent collection timing.
Based on these results, the researchers advise participants in microbiome studies to collect their first bowel movement of the day, homogenize the entire sample, and freeze it immediately. For situations where immediate freezing is not possible, commercial stabilization tubes may be used but should be kept consistent across the study. Precise collection protocols can maximize sample quality and study reproducibility in the dynamic landscape of gut microbiome research.
Here are some interesting viewpoints from the study:
With growing interest in the links between gut microbes to health, high-quality fecal samples are invaluable. By adopting evidence-based protocols for proper fecal sample collection, researchers can optimize their microbiome study outcomes.
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Jones, J., Reinke, S.N., Ali, A. et al. Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations. Sci Rep 11, 13964 (2021). https://doi.org/10.1038/s41598-021-93031-z
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