A healthy gut has the correct pH, food for the bacteria to eat, minimal adrenaline stress, and the goat is not in fight/flight mode. pH has been addressed in a separate thread. Food for bacteria is the "soup" of plant matter making it's way through the gut. Adrenaline stress and fight/flight mode is something we don't hear discussed as much, so I'll expand on that a bit.
When the gut becomes stressed and gut conditions become less than ideal, the healthy bacteria go into dormancy and the harmful bacteria come out to play. Of the three tactics I see used when the harmful bacteria become dominant, two are not very effective.
The three approaches to a harmful bacteria overgrowth are antibiotics to kill the harmful bacteria, probiotics to repopulate the gut, and prebiotics to change the gut conditions.
Research has proven that bacteria can go dormant when gut conditions are not favorable. Antibiotics are unable to kill bacteria in a dormant state. Research has also proven that when an antibiotic is used, some of the harmful bacteria go dormant and evade the antibiotic. So antibiotics will drive the harmful bacteria into dormancy, but will not prevent them from coming back, and will do nothing for new harmful bacteria introduced from outside the body.
Probiotics also have a drawback. Most probiotics work on the theory that the bacteria in the gut need to be repopulated. However, the bacteria are always there, both the healthy bacteria and the nasty ones. So using probiotics on an unhealthy gut will not rebalance the bacterial population of the gut. The healthy bacteria from the probiotic will just go dormant right along with the bacteria already in dormancy.
The third approach is using a prebiotic. A good prebiotic is designed to provide the ideal "soup" the healthy bacteria live in. A good prebiotic also balances the gut pH, and contains ingredients that reduce mental and emotional stress, calm the animal, and relax the muscles. When the gut is restored to ideal conditions, the good bacteria will leave dormancy and begin the repopulate and the harmful bacteria will enter dormancy or die off. Using a good probiotic to boost the healthy gut bacteria along with the prebiotic can be useful, although it is not necessary.
How and when you use your prebiotic is just as important as your choice of prebiotic. Remember, the stress hormones from fight flight response must be burned off or used up from the bloodstream after they are released. The best time to use a prebiotic is BEFORE the stress occurs and before the hormones are released, shutting down digestion. If you know you will be rounding up goats, trimming hooves, hauling to a show, have a goat about to kid, or any other stress you can control the timing of, give the prebiotic in the feed before the stress occurs. For stresses you cannot control, the frequency of the dose is as important as the amount. Give small amounts of prebiotic every few minutes, and continue for a couple hours after the stress occurred.