We have examined the microbiota in the airways at two time points. A referee wants us to identify which of the ASVs that are stable/don’t change. His/her suggestion was to “compare the microbiome of those subjects that have little variability vs. the microbiome of those that have high variability (for example defined as below vs. above the median value of beta diversity distance of the within individual pairs). The authors could use LEfSe, DESeq or other form of comparison to explore this.” However, these methods (as I understand it) don’t take the compositionality of the data into account, and are also not very good at handling paired data.
Does anyone have a suggestion on how to look for stable ASVs? And how to test for it statistically?
Grateful for any suggestions!