Friday, February 19, 2010

Bowel indicators and biofilms

I have a long history of bowel issues starting from childhood, but the first time I actually got tested was in 1997.   A doctor who ran a business called Intestinal Success showed up at a workshop on color and vision that I was attending with Jacob Lieberman.  After some urging, I agreed to do a Comprehensive Stool Analysis.  Boy was I surprised at the results!  I had parasites, fungal dysbiosis, and bacterial dysbiosis.  Among the bacteria making hay in the sunshine of my toxic bowels were some species that, my doctor remarked, he never sees in anyone but the most debilitated people.  I looked (and still look) so strong and healthy to most people that even the doctor was surprised.

Ten years later, I had a clean CSA.  No strange, unwanted inhabitants.  Good indicators of adequate digestive enzymes and acid.  I was feeling FABULOUS, although I still wasn't quite recovered enough to go back to work.  But I was browsing the want ads and thinking of a strategy....
Still, there were indicators on other tests that all was not well down in the bowel.  Organic acid testing looks at 30-40 acids in the urine, depending upon the lab used, and several of those acids are classified as indicators of gastrointestinal health.  Ditto for urinary and plasma amino acids.  These tests indicated continuing issues with fungal and bacterial dysbiosis.   I figured there must be another reason for those results  (genetics perhaps?) and ignored them.  After all, I was feeling FABULOUS.  And for the first time in many years, I didn't care about testing, blogs, or ME-CFS forums.  I wanted to live another life - the life of a normal person, a life with friendships and parties, with walks in the countryside and bike rides, with writing projects and a house emptied of the piles of junk I'd accumulated during the past 6 years of relapse.

I haven't retested with a CSA since my relapse in October 2007.  I decided instead --now that cardiac symptoms have abated to a great extent -- to use the gastrointestinal markers on organic acids and amino acids as my guide.  For a finally learned something that makes sense of the discrepancy between stool tests and systemic fluids:  biofilms.

Biofilms are colonies of microflora that hide from the immune system under a film of minerals and polysaccharides.  Often they go into a cell-wall deficient state to make this possible.  Apparently, according to my friend in the Biology Department at our local college, they've been a hot topic in research for several years.

Dr. Usman first noticed that many of her autistic kids had a situation similar to mine: high urinary markers of dysbiosis but clean stool.  She hypothesized this was due to biofilms of gut organisms, and developed a protocol to trick the sneaky critters and catch them in their elusive game.   Her protocol consists of three parts:

  1. enzymes and EDTA on an empty stomach to break up the biofilm
  2. a half hour later, antimicrobials, both herbal and prescription
  3. an hour later, binders to mop up the toxins released

I researched biofilms and found that many other physicians had adopted the basic idea, some changing the timing, some the recommended enzymes, antimicrobials or binders.  I decided in early January to adopt a protocol.

The enzymes were the easy part.  Klaire Labs has marketed a product called Interfase which has the recommended combination of enzymes designed to break up biorfilms.  Interfase Plus also contains a small amount of disodium EDTA.  Since Dr. Yasko and others expressed some concern about this form of EDTA, I decided to order the EDTA chelator complex which she offers on her website. This product also contains garlic and malic acid.  Garlic is already a mild chelator and antimicrobial, and malic acid is particular good for binding aluminum.  I didn't see how either could hurt me.

The antimicrobials proved more challenging.  Back in Florida, Dr. Philips had given me a custom formula from Monastery of Herbs containing a slew of stuff ranging from wormwood to turkey rhubarb.  I hadn't done well with it, and although I was willing to slog through the symptoms of cramps and insomnia, when I showed up for neural therapy, my doctor remarked on how strange it was that my bladder meridian was stressed.  By the 2nd visit, it occurred to me to have him test these anti-microbials and, as soon as I got them out of the picture, I recovered.  Now you can understand why it took me 10 years to clean up the CSA.

Two months later, feeling stronger and transformed, I tried them again on the biofilm protocol.  Two or three days later I went in to see Doc.  "Now that you're stronger, we have to get you to hold between treatments," he said, and I knew it was the Monastery of Herbs combination that was sending me backwards.  I stopped them again.

I suppose I could try one herb at a time, but I've neither the patience nor the resources for that.  So instead of antimicrobials, I'm putting in positive things -- pro and pre- biotics.  Lactoferrin supports the colonization of healthy bacteria in the gut and robs iron from the pathogenic critters.  Saccharomyces boulardii competes with clostriadia difficile and other clostridia species that are apparently enjoying themselves at my expense according to the high levels of DHPPA consistently appearing in organic acids testing since 2005.  Lactobacillus GG, a unique strain of L. rhamnosus, is particularly good at inhibiting clostridium, reduces staph and strep in nasal passages, removes toxins from cyanobacteria (BTW: ciguatera toxin has been found in > 90% of people with ME-CFS by researchers in Hawaii), supports liver healing, and increases SIgA.  This seemed custom made for me so I purchased Allergy Research Groups formulation of it called Lactobacillus.  Then, I added Phloe, another ARG product, which is an extract from Kiwi fruit that has been shown in two human trials to increase gut motility, reduce flatulence, and improve gut microflora.  Yesterday, Doc sent me home with a liquid Acidophilus product that contains 250 billion per teaspoon.  So now I have a full pharmacy of health-inducing bowel products.

For the mop up part, I'm doing chitosan and buffered C -- when I remember.  That's the hardest part of this protocol!

No FABULOUS results yet.  The plasma amino acids sample of Jan 19 was drawn before I started the biofilm protocol and the urine amino results haven't come in yet.  I'd done colonics for a week before taking the blood sample, and my results were worse than 2 months previous, even though beta-alanine (a marker of fungal overgrowth) had come down.

Another marker, beta-aminoisobutyrate, was much higher, and since it has been consistently elevated for the past 3 years, I decided to research it.  What amazed me is that it is not just an indicator of bowel bacterial overgrowth.  It also, perhaps more importantly, indicates some metabolic issues involving a class of molecules called pyrimidines which are connected (through folinic acid) to the folate and methylation cycles.  This substance, beta-AIB, gets elevated when a liver enzyme that converts it to pyruvate works too slowly.  And since my pyruvate has shown low, low and lower since starting this test since 2002, I am guessing that I am one of the many people with a polymorphism in this liver enzyme (hepatic beta-AIB-pyruvate transaminase.

So I called the lab.  "What's the evidence for elevated beta-AIB as a gastrointestinal marker?" I asked.

"We see it often when there are bacterial issues," the customer service rep responded.

And so, onto the list of things to explore further -- when I have time and energy.

In the meantime, I'm going to continue with the biofilm protocol for another month and then redo the MAP through Dr. Yasko to see if my GI markers for clostridia have come down.  It's more than a marathon.  It's an odyssey.


  1. Hi Janis,

    Interesting post. I too am certain I'm dealing with major gut issues, and possible parasite issues, (and believe the gut connection to CFS/ME is huge).

    I was wondering if you've seen this article:

    This young pre-med student found that the ayurvedic herb 'haritaki' destroyed the biofilm that protects the pseudomonas bacteria.

    Haritaki is one of the three herbs in the ayurvedic formula "Triphala", used for thousands of years for intestinal problems.

    Just thought I'd throw it out there in case you hadn't heard of it.

    best regards,


    (for some reason I wasn't able to comment using my wordpress account...?) :)

  2. Thanks for the good info, I am an acupuncturist in an integrative medical practice and we have many patients with Lyme, CFS and biofilm issues. It is amazing how much great info comes from the patients themselves. Keep up the good work and feel better.


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