Regarding a fecal test for gut flora.. I can say that I am unaware of how to quantify "good" bacteria. What we are typically looking for on a direct smear is either a protozoal infestation, coccidia, crypto, giardia, or an overgrowth of "bad" bacteria. In essence, we then can conclude that they are overloading the gut and inhibiting the good bugs. Bad bacteria include an overgrowth of spirochetes, clostridium, etc.
Elliot, you certainly have the gear to check your own direct smears. To prep, a tiny amount of feces is mixed in a drop of saline and smeared on a microscope slide. Some folks stain them, I choose not to since stains can harbor bacteria over time and give a false result. Reading them unstained takes some practice. There are great reference texts with photos to learn to identify everything. Red or white cells should definitely be noted if present, as well. Oh, and the smear should be examined under 40x magnification.
The other (common) test for intestinal parasites is a floatation. We use centrifugation and Sheather's sugar solution to "float" ova to the surface of a test tube of feces. This is MUCH more accurate than using Fecasol or other non-centrifuge techniques. This test can sometimes (if you have a good tech, and they use centrifugation) diagnose coccidia. Those cysts are hard to float. Otherwise a direct smear is needed.
Does that help?
-Tami*