Sample size estimations based on human microbiome temporal stability over six months: a shallow shotgun metagenome sequencing analysis

We evaluated the temporal stability of fecal microbial diversity, species level composition, and genes and functional pathways based on shallow shotgun metagenome sequencing from a population-based study in Costa Rica with two fecal samples separated by an interval of six months. We quantified the biological variability over six months with intraclass correlation coefficients (ICC). We then estimated the numbers of cases, assuming 1:1 or 1:3 matched case-control study, required to detect an association at significance levels of 0.05 and 0.001 with 80% power, based on the number of fecal specimens collected per participant.To detect modest disease associations, our calculations indicate a need for a large number of cases. Using repeated prediagnostic samples and matching cases to a greater number of controls could reduce the required number of cases for detecting these associations.