Dealing with skewed diversity in low abundance ASVs?

hi all,

question for the "die-hard" ecologists/statisticians:

How does one "correctly" deals with this situation. Say one has some microbial data where there are 10 ASVs (or OTUs, whatever), with a relatively normal distribution. Then there are some other samples that have the same OTUs making 95% of the data. But in the 5% additional diversity there are 1000 other OTUs at very low relative abundance. How does one deal with such situation? It will throw off the alpha and beta diversity significance comparisons. That diversity tail is not biologically informative, these are engineered environment communities. Assuming they are, how does compare such communities skewed in rare components. I dont even know how to filter them out from the datasets, is there an option for that in Q2?

Thanks !


It is a very complex question.
Yes, you can filter them out. Please, read the docs:

For alpha-diversity, Shannon index is less sensitive to counts, and for beta-diversity weighted Unifrac penalizes low-abundance species.