the more specialised filter material is porous so even more bacteria can grow.
You do not need to throw out your filter media.. a good rinse to get rid of the large stuff and you will be right as rain.
I have got media in some of my filters that are 7 years old. and still going.
I would recommend the Eheim Substrate, bit expensive but works really well IMO
Aqua One do some cheaper media which I guess is ok.. only just started to use it so no feed back from me yet.