Air carrier First Officer reported a fume event during gate preflight. Maintenance determined the APU bleed system had malfunctioned; APU was deferred and flight departed safely.

Narrative

When I stepped onto the airplane I immediately noticed a odor similar to being on a farm. Like manure and livestock. I mentioned this to the F1 who was near the door. I believe the rest of the Flight Attendant's were on the air stairs getting fresh air. The Captain noticed as well and determined that this was a fume event. The odor was strong enough that the rear Flight Attendant's asked to open the exits to air out the plane. It was my leg to fly so I began to set up the airplane while the captain referenced the appropriate literature and spoke with Maintenance. With Maintenance on board we decided to do an engine run test at the hard stand without the APU to isolate packs and engines to determine where the odor originated. The odor seemed to dissipate as we ran through the tests so we assumed the APU bleed was causing the odor. The APU was deferred and we continued on. Approximately 30 minutes into the flight I noticed that I had stomach ache and scratchy throat even though I hadn't consumed anything other than what I normally eat and drink. This lasted to approximately 2hrs then went away. I didn't notice any other odors throughout the flight.