I think it is just becoz of diet. if you eat something unwashed that is having dust particles (except some veggies like raw tomatoes) they will be filtered by the kidneys but deposited in the body itself.
you will then have the problem of stone.
I don’t think that there’s any bacteria that might produce dust in your body internally.

To avoid Stone problem,
1. Wash the veggies, Fruits & other washable eatables prior to eat.
2. Avoid eating Raw Tomatoes (but you can eat the cooked ones or anything with a tomato flavour).
3. Drink Plenty of water, it will pass more & more water from the kidneys & in result the stones will be sent out of the body via Urine.

Hope it works for you.

Regards