I've noticed tiny bubbles accumulating in two toilets (bowl not tank) placed directly above each other on the first and second floor. There has been a musty smell coming from the upstairs bathroom (full), no smell downstairs (half bath). These bubbles accumulate on the upper lip of the hole in the bowl. There is no smell coming from either tank.

Strangely, when I turn on the upstair shower/bath on full, the musty smell is increasingly noticeable just for a short while.

My concern is that my whole family is sick - currently on week 3. Don't know if I have a mold/fungi problem or a simple vent/sewer clog?

Bubbles are caused by back pressure in the drain line which is usually caused by a partial blockage. The smaller the bubble the less backpressure. Did this come on all of a sudden or gradually?
It's just possible that you may have two separate problems but address the sewer gas one first. Have the main drain snaked out and see if that doesn't stop your bubbles. Keep us informed. Tom

Smell came on suddenly. But what perplexed me is that it smells like a wet gym towel, not so much like sewer gas. As far as the shower in the upstairs bath, I don't know if the water coming out smells initially, or if it is the water draining, that forces the musty smell out of the tub drain tube.