Treating Clostridia

By Leah Hochbaum
Posted May 6, 2012

My 18 year old son with ASD suffers from reocurring bouts of Clostridia. At best, this causes him pain and bloating in his abdomen - and at worst, starts to affect his behavior and he can become self-abusive. We have been doing biomedical interventions and diets since he was four. In the past, the SCD diet, combined with HBOT and bioresonance therapy were our most effective treatments for this. Now, keeping to SCD strictly is really challenging (we do our best!), HBOT is currently not available to us and bioresonance is not sufficient on its own. Would you suggest antibiotics like Flagyl or Vancomycin or do we have any other options? We are using strong probiotics daily -VSL3 and Sach. Boulardii too. What else could we try?


Answered:  May 8, 2012 by Dr. Sidney Baker

Genta/Vanco is my short cut name for the combined simultaneous use of two different antibiotics: Gentamycin and Vancomycin.  Each is an antibacterial (as opposed to, say, antifungal or antiparasitic) medication.  Gentamycin is used almost exclusively as an intravenous treatment for serious infections in hospitalized patients.  By the intravenous route is has significant toxicity: if you look it up you will find cautions that would alarm you if you fail to understand that when taken by mouth it is not absorbed into the blood stream. It has none of that toxicity when given in the way described below.  Its action is limited to the gastrointestinal tract where, combined with vancomycin, it nearly always results in odorless poops within three days.  No other combination of antibacterial medications (such as metronidazole, neomycin, ciprofloxacin, Xifaxan, and Alina) has the same effect on fecal odor.  That effect signifies that a very substantial part of the gut flora has been eliminated.  By “eliminated” I mean not only pooped out but also killed so that it is not longer part of the resident flora of the gut.  Vancomycin, also used intravenously for severe infections, is similarly free of systemic toxicity when taken by mouth. Its oral preparation is very expensive.  Gentamycin for oral use must be obtained from a compounding pharmacy.

The germs that account for the strong odor of stools are so-called anaerobic (without air) germs.  The clostridia that you mention is one such an consists of many normal species in the human gut.  They thrive in environments where there is little or no oxygen (such as deep penetrating wound or a jar of certain foods (beans) that has been “canned” after imperfect heat-sterilization).  As we know, the germs that multiply in such circumstances produce lethal neurotoxins (tetanus and botulism, respectively) which are devastating in very tiny quantities.  They are not always stinky as individual species of germs but anyone who has worked in a microbiology lab where pure cultures of both aerobe and anaerobe germs are grown knows that collectively most such germs are have a very unpleasant odor as do the poops of many children in the autism spectrum.

A hundred years ago the medical profession was still gripped by the idea that toxins from the gut accounted for many diseases.  An era of aggressive “bowel hygiene” ensued with its emphasis on bowel regularity and enemas.  The pendulum of enthusiasm swung back the other way by the time of my training in the 1960’s and little mention was made of the gut flora, its toxins, its beneficial role, and the extreme ease with which it is damaged by antibiotics, and the variety of negative consequences that could result from that damage.  New research has validated the old view and the pendulum is returning toward an appreciation of those consequences and their remedies.

Dysbiosis – the wrong balance of germs in the wrong part of the intestinal tract – is a feature of many chronic illnesses.  It may be present in the absence of significant bowel symptoms, among which bloating and gas (both burps and farts) are the signature symptoms of dysbiosis: the gas is produced by germs not by you.  (The only gas you produce is the carbon dioxide in you exhaled breath.  It is the “smoke” from your metabolic fire.)  Inflammatory bowel disease is found in most children with autism and abnormal bowel flora is a feature of such inflammation.  I say “feature” to avoid presenting a linear cause and effect picture.  The chemistry of chronic illness involves nested vicious cycles, so our standard medical way of speaking about “the cause” fails to give a good basis for thinking about how to restore the self-perpetuating healthy cycles from which the vicious cycles descended.  In the case of abnormal flora the smart thing would be to restore the milieu that favors balance among the 500 to 1000 or so different germs that inhabit the digestive tract with a normally healthy interaction with the immune system, detoxification chemistry, and nutrition.  Sometimes restoration of that milieu is easy with probiotics or a change in diet that favors plant-based food sources and high fiber intake with, say, supplements of psillium seed husk powder.  Saccharomyces boulardii is generally one of the best probiotics.  It produces substances that improve the milieu and inhibit yeasts.  For some people with chronic illness it can result in a quick and sustained cure.  If one is not so lucky and a yeast problem is suspected then a diagnostic trail of antifungal medications is the only decisive way to include or exclude the possibility that such treatment would be helpful.  No lab test can establish with certainty that a person is not a candidate for antifungal medication.  Neither can a lab test establish that the unhealthy dominance of certain bacteria is an issue that is safely accessible to treatment and restoration of balance.  Again, a diagnostic trial is the best measure of potential success.

A diagnostic trial with antibiotics is a much trickier deal than a diagnostic trial with probiotics or antifungal medications or diet because all antibiotics produce collateral damage beyond the germs that are their intended target.  Some antibiotics such as plain penicillin have a narrow spectrum of susceptible germs and tend to produce less risk of damaging good flora.  Were it not for a high level of suspicion and motivation concerning an already damaged flora we would not contemplate marching down the gut with broad spectrum antibiotics that indiscriminately kill both friendly and unfriendly germs.  Were it not that such treatment – with Genta/Vanco – has a track record solving very complex problems in some patients I would not be very impressed by the theory that wiping out a lot of normal flora to try to get to the “bad guys” would be a good thing.  In fact, when I first heard about this protocol at an immunology conference in England in the 1990’s I thought I would never do such a thing especially in patients who might have a yeast problem (from taking antibiotics) to begin with.

Experience, at first with adult patients with diverse problems involving multiple sensitivities, has taught me differently particularly as regards the risk of stirring up trouble.

Three days of Genta/Vanco will produce odorless stools in just about everyone but it does not produce profuse watery diarrhea as I would have expected.  With antifungal coverage - using a maintenance dose of which ever antifungal seems to have provided the best results previously – the Genta/Vanco treatment does not result in yeast problems. What it does produce is:

Information.  That is, the answer to the question, “Will eliminating most of the gut flora and its toxins result in a major shift in systemic, immune and/or central nervous system symptoms.”

Results.  That is, a platform for introducing a normal gut flora by the administration of a mixture of antifungal medication, probiotics such as VSL3, Culturelle or Klaire Labs Vital 10  – sometimes including S. boularii, and fiber, usually in the form of psillium seed husk powder in doses of less than a teaspoonful per day.

The main problem is getting the results to stick.  If three days is sufficient time to prove the first point, then sometimes it is worth trying to extend it to 9 days before introducing the probiotics and fiber.  (An antifungal medication should be concurrent with the Genta/Vanco.)  The downside of this whole idea is not much on the risk side, but on the difficulty of getting the results to stick.  At the worst all we get is information, but often enough that suffices to reassure us that we are barking up the right tree (bacterial dysbiosis).  Then we can move with more confidence toward bigger steps aimed at flora restoration or replacement.

The short protocol is simply to use the 15-dose prescriptions and do 3 days of 3 to 5 doses of Gentamycin and Vancomycin given together daily – accompanied by a concurrent antifungal medication – and see what happens.  If the results are very good in terms of systemic or central nervous system effects and one has a strong instinct toward continuing longer to observe and consolidate the effect, then a treatment of up to 9 days is OK so long as the looseness of stools is tolerable.  If the results are truly dramatic then consideration of a longer treatment is not out of the question but usually shifting to the probiotics and fiber will give a sense of whether repopulating the gut with a better flora is in the works.

A risk significant risk of this protocol accompanies mention of it to a medical professional such as your sister’s doctor-husband who might have a virtual melt-down at the mere mention of it.  Gentamycin is not in common use as an oral medication so his assumption would be that you are submitting your child to intravenous gentamycin and its very significant risks.  Caution must be exercised to explain carefully that your use of both genta and vanco is ORAL and that both are non-absorbable; with risks that are limited to killing good germs in the digestive tract.  Those risks are not insignificant but may be tolerable as may those associated with the other non-absorbable antimicrobials I mentioned above.  A trial of Flagyl in a research study inspired by Ellen Bolte’s insightful observation of her son’s autism’s possible connection to Clostridia showed improvement in the children treated for 6 weeks.  The improvement did not persist.  The information gained from the improvement did, however, open our understanding of gut-brain connections that continues to widen with more recent experience that will surely be discussed on these pages with more questions like yours.

Question:  Has what I have described been submitted to a double blind placebo controlled randomize study in children in the autism spectrum?  Answer: No, and not like to be so anytime soon.  The basic principles that would underlie the decision to try such a protocol in an individual child are however founded on good science that now firmly supports the notion that the microbiome – the collective ecology of the digestive tract’s germs – is a powerful influence in health and disease.  Its depletion consequent to the use of antibiotics and modern hygiene is now emerging as a serious consideration in many chronic illnesses.  More reason to hesitate to nuke the microbiome with something like Genta/Vanco but such a step may have a place in a protocol that includes efforts to “re-florestate” the gut afterward.


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I totally agree with Dr. Baker, but I would mention that there is a risk to the treatment, because you could select out for vancomycin resistant organisms which is a serious problem today. As an ID person I should also mention that Gentamicin is with an I and Tobramycin is with a Y - go figure.

We use Candex, lots of biotin, and Pau d'Arco here with good results. Three times a day and then we give probiotics in the evening. GSE works great too, but those with phenolic issues (such as my son) can't handle GSE. We tried the prescription stuff for years, but these natural supplements have brought better results.

Why not try DO?

Thank you for the spelling. I have had it wrong for years! Dr. Hift: Do you agree that the reistance problem is separable between the general emergence of resistance and the potential for it to arise in during a short course of treatment in an individual? And that while both are of concern, the latter tips the decision scales lightly when the stakes are high?

The Candex, biotin, etc. are appropriate for yeast problems, but the question related to Clostridia.

Thank you Dr. Baker and to you all for your suggestions. As I am in Israel, I am not quite sure how to go about getting these medications. Could you be more specific, Dr. Baker, as to how these medications are dosed? If I would have a more detailed protocol, I could approach our family doctor - who is very supportive but limited in her knowledge of biomedical treatments - to assist us in obtaining these medications. Also, what is "DO" that was suggested - I am not familiar with the term.

I had C. Diff. for a year before I found a way to finally get it out of my system. I had tried Vancomyacin and some of the other meds listed above and it didn't work. I was very sick. I finally found a woman in Cushing, WI. who helped me to rid my body of C. Diff. this was 10 yrs. ago. Her e-mail is She used a combination of very potent probiotic type supplements and they worked! If you have further questions, please e-mail me. Best of Luck~

Dear Leah, Jon Pangborn, PhD and took the job of summarizing the first meeting of parents, practitioners, and scientists (some of us combining these roles) in 1995. Autism Research Institute published a pamphlet describing protocols for laboratory assessment of autistic children. Recommendations included consideration of tests that might be useful for driving decisions for a particular child as well as for gathering data that would help us get a better grasp on the biochemistry, immunology and toxicology of autism. Over time the re-editions of our book turned to description of treatment options aimed not at "autism" but at children as individuals. Unfortunately the word "protocol" stuck to the book for a while and gave a mistaken impression. Biomedical treatment is aimed at the individual, not the disease. After retiring Dr. Pangborn has re-written his part of the book which will be published by Autism Research Institute very soon. It will provide you with guidance. Autism: Effective Biomedical Treatments by Pangborn and Baker is now out of print. I am considering how to make my part available with an update from the 2007 addendum. Checking Amazon I see that among the dozens of books on autism only a few address medical or biomedical issues with the kind of specificity that you seek. In a way that is reassuring because the biomedical approach is more a way of thinking than a set of protocols. The thinking begins with the two questions embracing the notion that nature's strong impulse toward healing is favored by discovering unmet special needs: 1. to get essential or accessory nutrients, accessory nutrients, rhythmic integration, and light and love in their various forms and/or 2. avoid allergens and toxins. I am also unfamiliar with “DO.”

Two years later and we are back stuck on the clostridia again. I re-found the genta/vanco protocol you once gave us. I also found a DAN! doctor here in Israel willing to help implement the protocol. We need more specific doses for the two antibiotics in order to implement. Would you be willing to give us these details or give th directly to our doctor? We can be reached at