We've already run this over almost all individuals- I don't think we'd want to have some SMP personalized results using Bonferroni, while others use FDR. Do you think this is an issue? If so, I guess we'd need to rerun the analysis.

I also thought using Bonferroni in this case was a bit overkill because it is highly conservative, and we're just trying to paint a broad picture of what OTU abundances differed (though we're not reporting p-values).