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Biofilm Protocol


Dr. Usman is the Director of True Health Medical Center in Naperville, IL where she specializes in treating biochemical imbalances in children with ADD and Autism. Dr. Usman is a DAN (Defeat Autism Now) doctor who has researched copper/zinc imbalances, metallothionein dysfunction and promotion therapy. She received her degree from Indiana University, completed residency at Cook County Hospital, and is board certified in Family Practice.

Dr. Usman is a member of the Professional Advisory Committe, Autism Society of Illinois.[1]


What Is Biofilm

What is Biofilm
What is Biofilm Biofilm is a self-made protective environment in which microbial populations hide from the body's immune system and anti-microbial therapies. Biofilm allows the bugs to evade surveillance of the immune system and our best attempt to throw antibiotics at them.
Role in Chronic Infections Biofilm communities can be 1000 times more resistant to antibiotics than free-floating bacteria.[2] The National Institutes of Health estimates that nearly 80 percent of chronic microbial infections are due to biofilm colonies.[2]
How is Biofilm Produced Resistant strains of microorganisms maintain their viability by producing a polysaccharide matrix that protects them from the hostile environment in which they are trying to survive. This extracellular matrix is called biofilm.[3][4]
Our normal flora also produce a natural biofilm, but resistant organisms produce their own biofilm which then takes over, preventing the normal flora from flourishing.[5]
Filamentous bacteria and Giardia lamblia (Enlarged view)
Filamentous bacteria and Giardia lamblia (Enlarged view)[6]

The biofilm produced by these resistant organisms can only be seen by electron microscopy and makes it difficult to culture these bugs.[5]

One image from the ASM collection (shown here), is a scanning electron micrograph (SEM) of the mucous layer of the small intestine of a mouse. The image illustrates how organisms live within the mucous  layer and on the villi. Note the way the mucous layer covers the villi and the relative depth of the layer.
One image from the ASM collection (shown here), is a scanning electron micrograph (SEM) of the mucous layer of the small intestine of a mouse. The image illustrates how organisms live within the mucous layer and on the villi. Note the way the mucous layer covers the villi and the relative depth of the layer.[7]

Where is Biofilm

Biofilm is also in the blood, as well as the gut and on the teeth.

Biofilm Formation

Generalized scheme depicting the development of gut biofilms.
Generalized scheme depicting the development of gut biofilms.[8]
Mucosal Layer
Mucosal Layer[8]

Potential Implication of Biofilm Formation in Patients with ASD


Dr. Usman - I presented a theory about the implications of biofilm production by resistant strains of bacteria/fungus in our ASD patients who have persistent dysbiosis to the Defeat Autism Now Think Tank Oct. 11, 2007
Dr. Usman - I presented a theory about the implications of biofilm production by resistant strains of bacteria/fungus in our ASD patients who have persistent dysbiosis to the Defeat Autism Now Think Tank Oct. 11, 2007
Biofilm Hypothesis
The abnormal production of biofilm by resistant strains of microorganisms may be a possible etiology of why many of our patients who do not have positive stool cultures for yeast or pathogenic bacteria do well when placed on antifungals and antibiotics, yet relapse when they stop.[5]

Why do so many of our ASD kids have persistent dysbiosis?

June 2007 - The literature search that I conducted with the help of Teresa Conrick, MS and Sonja Hintz, RN was quite convincing.[5]

Experiments done in vitro show that this polysaccharide matrix is negatively charged, and that it is held together by positively charged ions such as Ca, Mg, and Fe. Iron seems to play a big role in how these bacteria evade the immune system.
Further work on VRSA/MRSA and pseudomonas biofilms in vitro indicate that this biofilm may be penetrated by using a combination of EDTA and an antibiotic; the studies used Vancomycin for Staph and Gentamicin for Pseudomonas.
  1. We all know that the quality of our air, water and food is not ideal and contains numerous toxins and pollutants.
  2. Our children have a genetic susceptibility in their ability to handle this toxic burden.
  3. Research shows us that resistant organisms tend to grow in toxic, hostile environments, and after numerous rounds of antibiotics.
This theory might also explain subtypes of our ASD subpopulation who have abnormal behaviors, such as head banging or agitation, that seem to be gut pain related, yet again have negative studies.
The third subset that this seems relevant for is the group of children that have:
  • recurrent strep infections,
  • OCD,
  • perseverative, or repetitive behaviors who get worse in the spring and fall, yet may not test positive for strep.

Protocol Overview

The protocol that my staff and I developed was presented in its infancy at the October 2007 Think Tank. The Defeat Autism Now Think Tank is usually a forum where ideas are presented for discussion and further research. This protocol was not discussed in great detail (15 minutes was allotted for this discussion), and it was not meant for wide distribution at this time.

However, Dr Bradstreet presented it in his talk on New Advancements and clinicians and patients from all over the world are now asking for our protocol.


However, let me start with a few caveats.

First of all, this is brand new.

We have used this approach on about 60 patients.

The first two were Teresa's and Sonja's children - one with ASD/self injurious behavior and one with colitis, no ASD. Both initial patients are doing well.
However, this treatment has to be individualized for each patient's unique constitution and ability to handle both die-off and detox type reactions.
From our other patients we are seeing a variety of responses from decreased hyperactivity and stimming, to increased agitation, to no response.

Of course we may have a few bumps along our journey to recovery.

Breaking Down the Biofilm

To break down biofilm, Dr. Usman also uses enzymes such as serrapeptase, derived from silk worms, and nattokinase which penetrates the GI tract and gets into the blood where it breaks down fibrin.[2]

Biofilm requires formation of fibrin.

Probiotics and synbiotics - a combination of pre- and pro-biotics - crowd out bad bacteria, and also help disrupt biofilm along the mucus membrane.[2]

Awakening the Immune System

"When the film opens up, we do not know what is under there, and the immune system may not know what is under there, so you might get sick," Usman said. "And it is not always about killing the bugs. It is more important to change the gastrointestinal environment so the bugs don't grow."[2]

The big bumps with this approach are related to awakening the immune system to these organisms which it has not been recognizing. The body finally sees the bacteria or the candida that has been there creating other types of havoc all along. [9]

Acutely, patients may experience:

  • vomiting,
  • diarrhea,
  • high temps.

Rashes may appear, especially if the die off is sudden.

Heavy Metal Detox

The other theoretical issue is that the biofilm may be holding on to toxic metals such as aluminum and lead. As this toxic biofilm degrades, heavy metals may be released into the gastrointestinal tract for excretion. Our protocol was developed to address this possibility.[5]

People with high mercury levels in their bodies have more:
  • hormonal disturbances,
  • immune disturbances,
  • recurring fungal infections,
  • chronic bacterial infections [10]
see Main Article Mercury Toxicity and the Endocrine System

Next Steps

I urge all of you to have patience and wait for us to gather more data on this approach so that you are presented with the safest, most effective protocol.[5]

Remember, your doctor should implement this approach gradually with the unique needs of your child in mind. Because of the possibility for negative side effects, and the need to closely monitor the patients, and the possible use of pharmaceuticals, this treatment plan should be implemented only with the help of your physician.[5]

True Health Gut Biofilm Protocol(tm)

General Approach

This is a short-term treatment plan, we are using it for about 2-3 months.
Step Number Description Medications/Supplements
One Lysis and Detachment of the Polysaccharide Matrix (empty stomach, 30-60 min prior to Step 2)
  • Use of specific enzymes. (these are being refined and developed, as the enzymes we have available at this moment are not ideal)
  • Use of a chelator that can grab hold of minerals in the Matrix. (if not implemented appropriately this may cause mineral depletion in the body - do not attempt chelation without proper medical supervision)
Two Target the Microbe
  • Consider using antibiotics, herbals, or homeopathics.
  • (our office has had extensive experience with all three modalities, and have found that the choice "depends upon the kid". We are also researching a fourth modality that looks quite promising for eradicating these pesty organisms.
Three (This is the most crucuial - do not skip this step) Clean Up - Give 1-2 hrs after Step 2 if possible or at night
  • Here we use anything that can bind up the matrix (mucus), by products of die off, and potential metals in the gut.
  • Products include activated charcoal, alginate, clays, algaes, zeolites,.... we like pectin the best. Sometimes we use all of the above.
General Support
Other important factors
  • Probiotics, of course.
  • Anti-inflammatory agents such as EFA's, antioxidants, curcumin...
  • Natural fermented foods such as kefir, kombucha...
  • Healthful, non toxic foods (hormone- free, antibiotic-free, organic)

This protocol is still being developed and is not fully defined. We have only been using this for about 6 months in a specific subgroup of our patients.


Example Instance
Step Description Timing Medications/Supplements
Step 1 Detach Matrix Empty stomach 30 minutes before a meal or one hour after
Step 2 Target Microbes Wait 30-60 minutes
Step 3 Cleanup Wait 1-2 hours Activated charcoal
Duration at least 2 months.

Ultimate Goal

Remember, our ultimate goal is to restore the normal flora and the normal biofilm. This takes time and the process is slow. It took years for some our patients to reach this point, it may take time to reverse.

Dr. Usman's Protocol Update - Lyme Induced Autism Conference, 2009

A Cloaking Device

"All of our tough cases, the non responders - they show biofilms when we run their blood at Fry's lab," she explained. "Scientists are finding biofilms in polluted areas of our body - the teeth, mouth, adenoids, sinuses, and intestinal tract. The immune system recognizes a bug by proteins on its outer membrane. What happens when the bugs don't produce outer membrane proteins? Well, these bugs don't." Biofilms act as a unique cloaking device.[2]

MRSA Example

"Let's look at what happened when experts tackled the superbug, MRSA. One of the most effective drugs against MRSA is vancomycin. But they couldn't knock it out because there was a biofilm. However, when they combined the drug with EDTA, then the chelating agent pulled out the calcium, magnesium, and iron - all elements of biofilm - and dismantled the film."[2]

That raises the question of what supplements and nutrients may inadvertently feed the biofilm. "When trying to kill bugs, if you take calcium, you may not be making headway," Usman said. "Calcium, iron, and magnesium block our efforts to dismantle the biofilm."[2]

Iron Chelation

Another important resource is iron chelating compounds. "Outer membrane proteins" are easy for drugs to see, but they are not expressed when iron is present. "Our bodies make proteins, transferrin and lactoferrin, which mop up iron and block the ability of biofilm to form," she said. "But pathogenic bacteria secrete iron chelators to snatch up iron and thus compete with the transferrin and lactoferrin for what they need to survive."[2]

Learn More

Anju Usman, M.D. Lectures

Additional Material

URL Description NAC Reduces Biofilm Formation[11] Allergy Research Group - Biofilms Biofilms Biofilm Primer Amy Derksen, N.D. Lecture see minute 48


"…the autoimmune process can be arrested if the interplay between genes and environmental triggers is prevented by re-establishing intestinal barrier function...", - Mechanisms of Disease: the role of intestinal barrier function in the pathogenesis of gastrointestinal autoimmune disease. (Fasano, 2005)
  2. 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 Mary Budinger, Lyme-Induced Autism Conference Focuses on Biofilm and Toxicity, 2009
  3. Christopher Freeman, Maurice Lock, The biofilm polysaccharide matrix: a buffer against changing organic substrate supply, American Society of Limnology and Oceanography; 1998;
  4. Jeffrey B. Kaplan, Kabilan Velliyagounder, Chandran Ragunath, Holger Rohde, Dietrich Mack, Johannes K.-M. Knobloch, and Narayanan Ramasubbu, Genes Involved in the Synthesis and Degradation of Matrix Polysaccharide in Actinobacillus actinomycetemcomitans and Actinobacillus pleuropneumoniae Biofilms, Journal of Bacteriology, December 2004, p. 8213-8220, Vol. 186, No. 24 0021-9193
  5. 5.0 5.1 5.2 5.3 5.4 5.5 5.6 Autism-Mercury 213277
  6. Ken Rozee (, W. Costerton, K. Lam, Scanning Electron Micrographs of Mucous Layer of Mouse Ileum Showing Bacterial Growth - Part I; Jan 2002;
  7. Biofilms Primer
  8. 8.0 8.1 Brigitta Kleessen, Michael Blaut, Modulation of gut mucosal biofilms, British Journal of Nutrition, 2005, 93, Suppl 1. S35-S40
  9. Mark Cichocki, R.N., What is Immune Reconstitution Syndrome? Rebuilding the Immune System Can Cause Problems,; July 26, 2007
  10. Summers, A.O., Wireman, J., Vimy, M.J., Lorscheider, F.L., Marshall, B., Levy, S.B., Bennett, s., Billard, L., Mercury released from dental "silver" fillings provokes an increase in mercury and antibiotic resistant bacteria in primates oral and intestinal flora; Antimicrobial Agents and Chemotherapy, vol. 37, pp.825-834, 1993
  11. NAC Reduces Biofilm Formation; Wednesday, November 18, 2009 - Byron Richards, CCN
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