Hi @Lisa_Crummett,
I won't necessarily jump the gun saying that the ANCOM results are invalid. But it does require a little bit of investigation - it is possible that some of the assumptions about few changing species were violated (ANCOM requires at most 50% of the species are changing).
Do you have specific qzvs for us to help diagnose? May also be worthwhile to contact Siddhartha or Shyamal (the first and last authors on the ANCOM paper. They'll likely have a better idea about the underlying statistical assumptions.