I think the important thing is that your 'store bought' yoghurt must be live, not pasturised. That way the right bacteria will be used.

I've been living in a country where paople eat tons of 'gone off' milk products, yoghurt, kefir, smetana and loads of cheeses. I've never heard of anyone getting ill on them. If you are into fermented milk products you might like to try kefir. It's even better for you than yoghurt.