Biofilm Protocol Explained

Biofilm Protocol Explained


A biofilm is a mucous film that forms protective layers over bacteria and fungi colonies. Common in nature, the film covering rocks in a river bed and the film on your teeth are examples of biofilms. Biofilms can either promote health or illness, depending on the bacterial makeup and the size of the biofilm. Toxic bacteria and fungi within biofilms are difficult to eradicate because layers of mucus and minerals in the biofilm protect them.

Often, children previously treated with the probiotic have improved, but as soon as you withdraw treatment, the symptoms return. The reason this happens is that the probiotic treats only the surface, not those bacteria and fungi hidden deep within the biofilm. In order to get to these protected pathogenic organisms, the treatment has to disrupt the biofilm and establish the new biofilm with healthy flora.

The goal of breaking down the biofilm with the toxic substances and replacing them with healthy flora is to reduce the total number of bacteria to a healthy level. One of the protocols we use in our clinic is SPS 30 or Interface Plus and Metal Magnet for the cleanup agent.

Biofilm protocol instructions can vary a bit depending on the supplements and medications used in the protocol. Two concepts are common to most biofilm protocols. The first is that the you must give the enzyme used break down the biofilm when the child’s stomach is empty and then allowe some time to work before adding the other killing agents. The second concept is that the enzyme must remove this debris with the cleanup agent. These cleanup agents by nature bind up almost everything, so you have to give them separately away from vitamins, medicines, and other nutrients.

Basic steps:


  • Break down the biofilm with the use of specialized enzymes.
  • Wait 30 minutes for the enzymes to break down the biofilm.
  • Add in anti-bacterial and/or antifungal agents.
  • Provide a source of replacement flora.
  • Repeat the process two times per day.
  • Once a day usually at bedtime, add in a binding agent to clean up the debris.


Supplements you will need:


  • Enzymes designed for biofilms: either SPS30, Interfase, Nattokinase, Lumbrokinase, or Interfase Plus
  • Antibacterial/Antifungal Agents: (Pick one or two from the list) Biocidin, ProEnt2, Olive leaf extract, grape seed extract, Candibactin AR or Candibactin BR, ADP (not suitable for small children due to the strong oregano smell and taste)
  • Clean-up or Binding Agent: (Choose one) GI-Detox, Metal Magnet, Extox, Toxin Free, Activated Charcoal, Tru Fiber, Modified Fruit Pectin, or other binding agent.


Morning and Afternoon

Give enzymes first thing in the morning on empty stomach. It’s essential that you don’t give the enzymes with food, because the enzymes would just break down the food and not the biofilm. If you must, a very small amount of food will to help get the enzymes into the child. Other medications may be given at this time, as well. Give the enzyme again later in the day, again at least 30 minutes before a meal and at least one hour after a meal. The next step is to wait 30 minutes to allow the enzymes time to break down the biofilm. Then, give your choice of antibacterial/antifungal agents; these can generally can go with food. We usually use a combination of a couple of agents one that has activity against bacteria and another with antifungal activity together. This step is repeated twice a day.

Evening or Bedtime

This is usually the best time to give the binding agent. The important thing to remember about binding agents is they bind everything, including medications and supplements, so you need to give them separately and away from everything else. Do not give any other supplement or medication within one hour before giving a binding agent. The binding agent will help bind up heavy metals and other debris and reduce the severity of Herxheimer reactions. You may see a Herxheimer reaction when you first start the protocol. A Herxheimer reaction is a flu-like feeling the sudden release of toxins from dead bacteria cause . If the Herxheimer’s reactions are too severe then you have to reduce the dose of the killing agents for a few days or stopped all together.


A bowel antioxidant is very helpful at reducing symptoms during the protocol. Oxyperm is a antioxidant designed for this purposed and is our preferred agent. You can omit it, but the protocol generally works better with Oxyperm.


Dr. Stephen Smith


Treating autistic children for over 15 years