If your guinea pig has maggots on its bottom, the best thing to do is to take them to the vet. The vet will use a special microscope to determine what type of maggot infestation your pet has and may need antibiotic treatment. If you can’t come into town or if you live in an area with Fly Season, close to a body of water where flies are common, then you can try taking steps to keep the flies away from your guinea pig by covering their food and water dishes with a fly screen or by placing them in aia sprayed withapple cider vinegar.