Hello Ruben,
You have probably already found the qiime feature-table core-features plugin.
I’m not sure I understand what you are trying to test. I think you can report “The following microbes appear in 90% of samples in my cohort” and “but only these these microbes appear in 100% of the samples in my cohort,” without needing to report a p value.
Mehrbod discusses it more in this thread. Let’s see what he has to say!
Colin