Stability of the fecal and oral microbiome for multiple collection methods

In prospective cohorts, biological samples are generally stored over long periods before an adequate number of cases have accrued. At present, we have limited knowledge regarding the stability of the fecal and oral microbiome in frozen samples stored for long periods. Among 51 healthy volunteers, we investigated microbiome stability in fecal and oral samples stored for two years at minus 80 degrees, collected via seven different collection methods using 16S rRNA gene amplicon sequencing data. Intraclass correlation coefficients (ICCs) were calculated for the relative abundance of the top three phyla, the 20 most abundant genera, three alpha diversity metrics, and the first principal coordinates of three beta diversity matrices (Bray-Curtis and weighted and unweighted UniFrac distances) to estimate stability of fecal and oral microbial profiles. Our findings suggest that freezing fecal and oral samples for two years in commonly used sample collection methods is, in general, acceptable for fecal and oral microbiome analyses except for fecal samples stored with no additive.