22d • PROTOCOLS 🔬🧬
Biofilm protocol 🦠
Biofilms are a HUGE global health concern as they are rising in prevalence year on year, in hospitals biofilms are even more abundant and are associated with pathogenic bacterial strains such as E. coli, salmonella, klebsiella, MRSA and others. Once they colonise the GI tract - or any epithelium such as the nose, sinuses or throat they can result in bacterial infections which can be extremely difficult to get rid of. Modern medicine offers antibiotics for infections, and this can be highly effective, however most do not affect the biofilms and the bacteria within them - only creating collateral damage to our own DNA, Mitochondria, paneth cells, goblet cells and deplete nutrients such as Coenzyme Q10. This guide should lay out a path for those who think they are dealing with biofilms.
(This is not a substitute for medical interventions and it is not medical advice. If you think you have a serious infection please seek medical attention. This is for informational purposes only.) Thank you
Here's what were going to do (In 3 stages):
- Remove/ Limit the substrates needed for the bacteria/ fungi to make biofilms
- Interrupt bacterial communication
- Begin breaking down biofilms
1 - Remove the substrates needed for the bacteria to survive
First off, I am not saying that completely cutting out a food group like FODMAPs, Sugar or Resistant Starch is the answer, but reducing the fuel availability (for a period of time) can be beneficial as this will give the bacteria or fungi less energy to use to carry out metabolic processes such as generating biofilms. This may mean just reducing the intake of a particular substrate such as FODMAPS/ Resistant Starch/ Sugars e.g. fructose by 20-80% for a short period of time. The amount of reduction needed will depend on the severity of the issues.
I would recommend limiting the food substrate that causes the most discomfort/ symptoms as this indicates the pathogen is metabolising and interacting with this. For some people this will mean lowering specific FODMAPs such as oligosaccharides/ fructans (e.g. garlic, onions) or sugars such as high fructose fruits e.g. pears, mangoes, grapes.
Important note: this is to be used as a tool in the short term e.g. 4-6 weeks (can be less or more) to reduce symptoms + biofilms + proliferation + inflammation whilst we break down biofilms and use antimicrobials.
2 - Interrupt bacterial communication
QS - AKA Quorum Sensing is one of the most underrated yet least spoken about topics in gut health.
Anybody with stubborn bacterial or fungal infections, dysbiosis, biofilm buildup, IBD and IBS probably has unaddressed issues with Quorum Sensing (QS).
QS is the process which bacteria and fungi use to communicate with each other. This allows them to coordinate things like biofilm production, toxin release and production of virulence factors. In simpleton terms: if you aren’t addressing Quorum Sensing then you’re essentially allowing bacteria and fungi to form protected biofilm colonies, avoid the immune system and release inflammatory toxins into the gut.
Some of these most potent Quorum sensing inhibitors include herbs and flavonoids such as:
- Quercetin (found in blueberries, apples and red onions)
- Allicin (found in garlic)
- Rosemary
- Turmeric
- Cinnamaldehyde (Cinnamon)
- Clove
- Skullcap
- Resveratrol (found in grapes)
- EGCG (found in green tea)
- Oregano
Adding a few of these to your protocol can make it far more effective at getting rid of biofilms, preventing more biofilm build up and also lowering bacterial resistance to herbs and antibiotics. Many of these herbs (except oregano) can increase beneficial bacteria and reduce inflammation too.
3 - Begin breaking down biofilms
There are 4 main parts to target:
- The EPS (Extracellular Polysaccharide Matrix)
- Structural proteins
- Extracellular DNA
- Heavy metal ions
The EPS (Extracellular Polysaccharide Matrix) makes up 90% of the biofilms weight, so breaking this down is a critical step to making bacteria susceptible to antimicrobials. The EPS is largely made up of proteins secreted by bacteria, they can also use these surface proteins to attach to the gut lining.
Here are some beneficial enzymes that can help break down different parts of the biofilms EPS:
Cellulase breaks the 1-4 glycosidic bonds that hold together the skeleton of the EPS matrix together.
Amylase works by hydrolising the complex carbohydrate molecules that are part of the biofilm matrix
Proteolytic Enzymes
Serrapeptase and Nattokinase degrade the protein components of the EPS matrix. By breaking the structural “cement” that holds the biofilm together, they expose the trapped microbes to immune cells and antimicrobials.
- Serrapeptase, derived from beneficial bacteria found in silkworms, has long been recognised for its anti-inflammatory and protein-cleaving properties.
- Nattokinase, produced from fermented soybeans (natto), supports circulation while helping dissolve fibrin and protein debris often found within biofilm layers.
Structural proteins such as amyloids and lectins stabilize the biofilm architecture by connecting bacterial cells to the surrounding matrix. Proteyolytic enzymes such as nattokinase, lumbrokinase, serrapeptase, protease, peptidase and lysozyme are some of the most researched protein degrading enzymes which act as biofilm agents.
NAC (N-Acetyl-Cystine) is another key compound known for its mucolytic (mucus-dissolving) properties. It works by breaking the sulphur bonds that give the biofilm its thick, mucus-like texture. Research shows NAC can also reduce bacterial adhesion and inhibit the formation of new biofilms, making it a multi-faceted compound against biofilms.
How? NAC can penetrate the bacterial membrane, increase oxidative stress, and halt protein synthesis. It cleaves the disulfide bonds found within the extracellular matrix of the biofilm - disrupting the physical structure of the biofilm.
When combined, proteolytic enzymes and NAC form a potent first-line attack, one that breaks through the film’s outer defences, making it easier for antimicrobials to reach bacteria within biofilms.
Extracellular DNA promotes structural integrity and facilitates the exchange of genetic information among biofilm-residing bacterial cells. Collodial silver is a great biofilm disruptor in this regard as it can penetrate cell membranes and
Heavy metal ions - metal ions are used by bacterial biofilms to hold the structure of biofilms together.
EDTA (Ethylenediaminetetraacetic acid) is a powerful chelator of cations such as calcium, magnesium and iron) removing the structural stability of the biofilm matrix, creating pores and causing it to disintergrate.
Some other honorable mentions include:
- Berberine
- Monolaurin (found in coconut oil)
How to use Binders effectively
Binders are a very helpful tool in reducing die off symptoms, inflammation and reduce liver burden when using antimicrobials.
The main benefits of using binders are:
- Reduced heavy metal exposure (especially when using antimicrobials)
- Bind endotoxins such as LPS before they can initiate high levels of inflammation
- Bind to mycotoxins to reduce exposure and damage
- Disrupt biofilms
Some of the most commonly used binders include:
Zeolites - binds to heavy metals (lead, arsenic, cadmium, mercury), mycotoxins (toxic fungal by-products), May be better for yeast overgrowths, absorbs histamine, doesn't bind to minerals. Low risk of constipation
Activated Charcoal - Non specific binder, can be used to mop up gasses, endotoxin, oestrogen, bile acids and drugs, It's effective, cheap, broad spectrum binding effects. Can cause constipation in some individuals.
Bentonite Clay - Also a non selective binder, works by using a negative charge to attract positively charged particles like heavy metals, Alfatoxins. Bentonite clay can also bind to minerals like zinc an magnesium and medications.
Enterosgel - Studied improvements for IBS-Diarrhoea, very potent binder of endotoxin - LPS (37mg of endotoxin per 22.5g dose), can bind to bile salts (Taurocholic acid & Glycocholic acid) and C. Diff + Shiga like toxins from pathogenic bacteria.
One of my all-time favourite binders is MCP - modified citrus pectin:
- Reduced serum heavy metals (lead - 560%, 150% cadmium, 130% arsenic increased urinary excretion)
- Binds endotoxin - LPS
- Binds heavy metals in the gut
- Interrupts biofilms
- Bind mycotoxins
- Lowers inflammation (Gallectin 3)
- Prevents biofilm reformation
- Feeds beneficial bacteria
- Easily tolerated
MCP is one of the safest, gentle binders that also come with a whole host of other benefits such as increasing beneficial bacteria such as Bifidobacteria, improving stool quality on the Bristol stool scale in patients with IBS-Diarrhoea, and doesn’t bind as much to beneficial minerals.
Note: take all binders away from medications to prevent them stopping absorption
I would take binders ideally away from food and supplements (and medications), more than 45 minutes before food - more than 2 hours after food. If taking antimicrobials then take the binder 45 minutes to 1 hour after to prevent die off symptoms.
Detoxification support
If you don't want to deal with die off symptoms, or cause excess stress to the liver and spleen, prevent inflammation then I would recommend supporting your body's detoxification systems before jumping into antimicrobials. Here's the steps you need to follow to do this:
Drink 2-3L water a day 2L if you are a woman, and 3L if you are a man - with electrolytes (sodium, potassium, magnesium) to support the clearance of toxins via the liver and lymphatic system
Support the lymphatic system by doing the Big 6 Lymphatic by Dr Perry Nickelson (I have put this into the "Protocols" section on the home page. You can also just look this up on YouTube if you want a video demo. You can also do lymphatic hops to help move stagnant lymph.
Support Liver detoxification as the liver has to process:
- Lipopolysaccharide (LPS/endotoxin) from Gram-negative bacteria
- Ammonia
- Heavy metals
- Histamine
- Acetaldehyde
- Secondary bile acids
- Dead bacterial proteins and nucleic acids
Phase 1 Liver detoxification needs: B2, B3, Magnesium, Iron, Vitamin C, and glutathione, vitamin E, CoQ10, NAC, selenium as antioxidants to support this phase.
Phase 2 Liver detoxification needs: glycine, cysteine, glutamate to complete glutathione conjugation + sulfur amino acids, cysteine, methionine and Cofactors: molybdenum, vitamin B6 to add sulfate groups + UDP-glucuronic acid, Magnesium, B vitamins for glucoronidation. Can also use Calcium-D Glucarate here to support this process. Methylation also needs B9, B12, B6, B2, Choline, Betaine, Methionine, Creatine and Magnesium + Pantothenic acid (Vitamin B5), Acetyl-CoA and Protein for acetylation + Glycine, Taurine, Glutamine, Arginine for Amino acid conjugation.
Phase 3 Liver detoxification needs: Taurine and Glycine for bile acid conjugation, choline for phosphatidyl choline for bile, magnesium and water for optimal bile flow. Bitter herbs and TUDCA can help bile flow to eliminate toxins.
Summary (putting it all together into actionable steps):
- cook with herbs and spices to reduce quorum sensing and bacterial virulence, potentially use a supplement to block QS like quercetin if needed
- optimise Vitamin D levels through sunlight or supplementation to 100nmol/L
- break down biofilms with 1-3 biofilm disruptors such as NAC and proteolytic enzymes that suit your needs
- use antimicrobials that are right for you and your issues (safeguard/ gentler herbs or more potent)
- bind the toxic by-products and manage die off symptoms
- focus on lymphatics, liver support and hydration
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Biofilm protocol 🦠
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