mmvec metagenomic full abundance table or sub-selected table

Hi :)

I have a little question related to the input.
I have a full species table from MetaPhlAn. And I also have a sub-table after selecting some species that I am interested in.
Same in metabolites table. My data is targeted metabolites data from LC/GC-MS. I have a full table also a selective table with only the ones I am interested in.

So my question is: the two types of input will have different results. May I use the full table or the selective table? Do you have any suggestions?

Best,
Lu