Core microbiome - observed and predicted

Commands in mothur
1

Dear mothur-community,

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!

Regards

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To be honest, I’m not sure how useful the estimated overlap value is since it really only represents a minimum value - the true value is likely larger. So, yeah, this makes it kind of difficult to interpret.

Pat

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Thanks for your answer, Pat. It still leaves us a bit unsure. But maybe it will make more sense when we advance in the SOP.