Hi @Alxdu,
I think your high abundance/low prevelance is addressed in the filter-features function I linked above; most low prevalence taxa are also low abundance. Depending on your sequencing depth, etc you could easily select for features that are abundant in a single sample as long as they have enough reads.
If you're looking for contaminat filtering specifically, I recommend looking into decontam and the forum discussion on decontamination. It's a more complex topic than what you're describing and I think that's a good area to start.
Best,
Justine