Is this pattern stronger based on unweighted UniFrac or Bray-Curtis distance? Based on how you know about these metrics, what does this suggest to you about what is changing in the microbiome with fecal microbiota transplant?
I found a stronger pattern for the Bray-Curtis distance compared to unweighted UniFrac. Unlike unweighted UniFrac, I am aware that Bray-Curtis does not take phylogeny into account. But I am struggling to understand what this suggests about the change in microbiome with the FMT treatment. Any help please? Thank you!
Like Justine suggested, Bray-Curtis is a waited metric (uses abundance values) and Unweighted UniFrac is a unwaited metric (uses only presence-absence values).
Because the main difference is weighted vs unweighted, this is driving the finding. In the weighted metric, the most abundant microbes will contribute more to the differance. In the unweighted metric, all microbes contribute equally, i.e. less abundant microbes will be measured more by the differance.
So there is not a strong phylogenetic pattern (unweighted UniFrac), but the composition of more abundant microbes does change between groups (Bray-Curtis).
P.S. Weighted UniFrac is more comparable to Bray-Curtis as it’s also waited. So when you compare them, Bray-Curtis vs Weighted UniFrac, the main question is composition vs phylogenetic composition. Now that’s interesting!