Rifaximin safe? Be the side effects?

So i was being treated for stomach discomfort(mostly nauseous feeling and hunger type pain). This was started after i was prescribed amoxyclav for 5 days, since then i have been facing such symptoms also light yellowish mushy stool as well. So initially I consulted a practo doctor, he prescribed me with esomac, esomac d and econorm for 1 week, it reduced the pain but still sometimes i feel nauseous and weird type feeing. So today i went to a local doctor, he prescribed me with rifaximin 550, but i read that it creates a irreversible change in gut bacteria, is that true? Sorry i read another patient's post here on practo hence i got the query.. Please help me, rifaximin has been prescribed for 5 days, twice a day.. so what should i do? Should I go ahead with that or not... and what will be the side effects?