I am trying to calculate the core microbiome in my samples using the get.coremicrobiome command but am unclear as to which shared file I am to be using for this command. If I use the ‘’ file I get results that make some sense but if I use ‘’ there are no OTUs shared among all samples which doesn’t make sense. What is the difference between these files and which one am I supposed to use?
Thanks for any insight you can provide

an.shared = OTUs
tx.shared = phylotypes

Are you using 0.03 as your cutoff with the OTUs? What environment?

I did the calculation using 0.03, 0.07 and 0.10 levels to define OTU.
They are samples from the rumen.
If I use the OTU file regardless of level I was looking at there are none that are found in all of the samples. If I use the phylotype files I am able to find some that are present in all and these are common inhabitants of the rumen so it makes some sense

Can you send your an.shared file to us to look at?


Thanks for sending the files. So at the 0.03 level, there are no OTUs that are observed in every sample. So it appears that while there are genera that are ubiquitous, there are no “species” that are ubiquitous. You do have 6 OTUs that are seen in 30 or 31 of the 38 samples. This is similar to the case of the human microbiome (i.e. there is no core microbiome).