I need some help to interpret the beta diversity results better. I am especially confused by Bray-Curtis results when compared with weighted, unweighted and taxonomic analysis.
In Bray-Curtis, I observe a clear clustering pattern by library preparation plate: samples from plate 1 cluster together in cluster 1, whereas those from plate 2 and 3 cluster together in another cluster. Once I look at the taxonomy, I am not detecting any specific taxonomic profile driving this divergence. Moreover, I am not able to see the pattern in beta diversity UniFrac metrics (weighted or unweighted).
Bray-Curtis PCoA colored by library plate:
Weighted UniFrac PCoA colored by library plate:
I feel that same bacterial species are classified to different ASVs, maybe driving this divergence in Bray-Curtis, which is lost when using phylogeny-aware metrics.
How should I interpret these results? Do we have a technical bias in this dataset? Why is this pattern not observed in UniFrac metrics? How can we identify the specificities of this issue?
Thanks a lot for your time.