More great and detailed info Doug, thanks again. Obviously there is a lot of information out there and it isn't always in sync. I have a good friend who is highly studied and experienced in "para-vetrinary" practice, reptiles, birds and mammals and he is offering some conflictory information regarding what Flagyl and probiotics actually do. I'm posting this below not to debate his or your information but to extend the discussion. I believe it should be helpful to us all regardless of the utimate correctness of any of this. You're both obviously well studied on this issue but I believe you've had much more practical experience in application. Whatever the truth is, your highly positive results pretty much tell me that, however, whatever, the prescription works ...and that is by far most important to me 
Selected excerpts from a train of email correspondence... I know, tons of information and lots to digest (pun intended).
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Part of the confusion lies in single dosing vs dosing over 7 - 14 days. A single large dose targeted on a known pathogen will not lead to organ failure and death. Smaller doses over a longer period may do a number on kidneys and/or liver. When we are treating anorectic snakes, we seldom do kidney/liver function tests before treatment and thus will not know if primary kidney/liver disfunction is in fact at the heart of the problem. In human medicine, this would be malpractice.
Still not clear whether DM is discussing a single treatment or treatment repeated every day over 7 to 14 days. Funk and Klingenberg are very reliable practitioners, Markel is a hobbyist. But, hey! I believe in Magic! Bring it! (Even when the anecdotal information addresses treatment of symptoms and not specific pathogens or pathology. If it works, don't knock it.) - PT
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The only microorganisms flagyl affects in the gut are Protozoa and such anaerobes as the Clostridia. The latter include C. botulinum, tetani, schottmuelleri (gas gangrene), and the increasingly deadly difficile. These do not contribute to the health of the gut. And they can flat kill their hosts. There a few dozen more genera of anaerobes, none of which you can't live without in your gut.
Flagyl belongs to a group of drugs known as imidazoles that as a group are somewhat more deadly to commensals than to their hosts. They are not drugs about which anyone with a high regard for the truth would say, "Well, it can't do any harm." Why they work only on anaerobes is interesting: in a reducing environment inside the organism, metronidazole yields hundreds of daughter products such as sulfanilamides that do a job on on the organism. Another compound in this group. fenbendazole, has been found somewhat more effective against Giardia, even though the labeled use is as an antihelminithic drug (Panacur). - PT
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Here is what DVM Doug Mader says about Flagyl -
Thought of as anti-protozoal agent but is also excellent anti-bacterial agent (anaerobes)
Metabolized by the liver, excreted by kidneys
Compromised liver necessitates lowering dose
Excellent penetration of tissues to target anaerobic bacteria
Best used with an antibiotic such as Amikacin to extend its spectrum
Flagyl [in reptiles] is dosed at 50 mg/kg PO SID for 7 to 14 days; Amikacin at 5. mg/kg loading dose, dropped to 2.5 mg/kg every third day
Refs in reptilian literature suggest dosages up to 275 mg/kg
Higher doses have been reported to cause such problems as star gazing, head tilt, locomotion problems; this has not been reported for 50 mg/kg even over a 14 day period. Problems have been reversible over a period of months
Deaths have occurred in Calif and Ariz Mtn King Snakes and Indigo Snakes at doses above 100/mg/kg, and in Uracoan Rattlesnakes at doses of 40 mg/kg with 14 day dosing. "A lower dosage might be prudent."
To summarize, 50 mg/kg is a safe dosage for your snake. Mader et al. suggest a regime of this dose for 7 days minimum. From my experience with birds I am concerned about such long term use in an already compromised snake. Furthermore, Amikacin belongs to a group of drugs, the aminoglycosides, with known toxic effects on birds and reptiles. I would rather combine it with a safer group of drugs, Lincomycin/Clindomycin. I have forgotten the length of treatment your correspondent suggested, but I suggest we try dosing on alternate days for a week at the scaled dosage of 60 mg Flagyl and 5 mg Lincomycin SID. I can load some syringes for you to give the snake PO. After a week, we can consider extending the treatment for another week, either consecutively or with a two week break. - PT
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Flagyl (el Metronidazolo) BeneBac© . Flagyl is selective in gut sterilization. It controls obligate and facultative anaerobes and protozoans in the gut and deep wounds/surgical fields. It does not control the plethora of gram neg/pos bugs in the gut. Frequent small meals of low residue food are the way to go. That would be rat pups before they become furry and/or grown mice with their bodies degloved. That means, leave the fur on the head and present that to the snake, but pull the fur back via a circumsizing incision just caudal to the head. As the snake's digestion improves you can progress to larger unclipped fare. My colleague, Bob, can identify fecal Coccidia, and might see some other stuff like Balantidia. [Balantidium coli is a parasitic species of ciliate protozoan that causes the disease Balantidiasis.[1][2] It is the only member of the ciliate phylum known to be pathogenic to humans.] This organism is not confined to mammals, but is seen in Chelonians. It is treatable with Flagyl. - PT
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