Hi @jng,
If you have run Dada2 or Deblur, there is no ASV in your original table which contains less than 10 counts. If you've since filtered your data (for example, to split experiments, discard samples, etc) then this may no longer be true.
I was involved in writing the PD mice tutorial and, to be honest, I can't remember the exact logic behind that specific depth. (I double checked my notes from that period, and... its not recorded :/. Sometimes that's the way it goes in this field: you pick a something and work with it). The mean/total abundance and prevalence co-vary pretty closely so most of the low abundance features will be picked up in your first filtering.
Best,
Justine