Should I calculate beta diversity with or without rarefaction?

Question

[dpc]

Hi there!!! I am doing metagenomic analysis with metaphlan output data that show relative abundance s of the species. I am going to calculate the beta diversity (Bray-Curtis method) between case and control samples. In the case of alpha diversity, I have done rarefaction (without replacement) and then calculate dthe Shannon diversity index. Now, what should I do for Beta diversity index among the two following options?

1. Is it better to multiply the relative abundance file (metaphlan output) with read counts of the samples and then do the rarefaction and then calculate the beta diversity?

2. Or, is it better to just find the pseudo counts (by multiplying all samples with 10E6) and find the beta diversity without rarefaction?

Thanks