we just stumbled over the calculation of the observed core microbiome and predicted core microbiome (see MiSeq SOP -> beta diversity -> venn and shared.summary commands).
So, in the provided example the observed (?) core microbiome comprised 67 OTUs while the predicted core microbiome consisted 86 OTUs. Unfortunatly, the SOP does not further evaluate the predicted number or the range of acceptable difference between observed (?) and predicted. Is this just a gut-feeling thing?
Thanks for comments and hints as always!