Vacuuming the gravel will not get rid of beneficial bacteria. The bacteria will adhere to the gravel. The rotting food is creating ammonia to feed the bacteria, but it can also create a lot of things in your tank that you do not want such as fungus and algae. It's like having a dead fish in your tank because the food has fish in it.
Originally Posted by FishFreak2012
If this were my tank, which it is not, I'd vacuum the gravel thoroughly and switch to using pure ammonia. It is a more precise method because you don't overfeed the tank. You just put in enough ammonia to create and feed the cycle in your filter.
When in doubt, do a water change.
"This ain't rocket science!"