Metronidazole/ Flagyl is a narrow-spectrum antibiotic that targets anaerobic bacteria. Clostridium are a genus of anaerobic bacteria that colonize GI tracts and don't cause problems when everything is going well. However, these bacteria produce many deadly toxins and have the potential to quickly kill an animal if they overgrow or get out of the GI tract and into the blood. They also produce gas as bi-product of their metabolism, and as we all know excessive gas in the GI tract is painful. Have you ever seen a dead animal that's been on the side of a road for a couple days and is all bloated? That's the work of the Clostridium in the GI tract producing gas. So metronidazole is a good antibiotic for GI tract infections that are suspected to be caused by Clostridium, and is also good to use when there is compromise of the mucosal barrier of the GI tract, evidenced by blood in the feces.
Metronidazole is also used to treat giardia in dogs, cats, and people and, because it has GI anti-inflammatory properties, also has a role in the treatment of acute diarrhea.