If it is antibiotic, then it won't kill fungi. Antifungals kill fungi, antibiotics kill bacteria in terms of prescription drugs. Pretty straightforward. Are you sure your issues are caused by fungi (that should be the first to start I guess).
Antibiotics that are not absorbed by the intestines, means drug will remain in the digestive tract and kill all the bacteria that the drug is effective to, that is on the digective tract (stomach, small intestine, colon). Good bacteria is "on" your intestines as well, and it will kill them if that drug is effective on that type of strain.
It might be prescription called xifaxan (also called rifaximin or normix). Most "in" antibiotic for SIBO / IDS-D, since it only kills bacteria in intestines and does not effect organs outside digestive tract.