Smarter Gut Repair
(November 2025)
​This article does NOT constitute medical advice. Consult with your physician before making any changes to your medical plan.
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Those of us that have experienced chronic disease want to feel better as soon as possible. One of the main ways to repair the gut in chronic disease is to use a medical diet like carnivore, keto, GAPS (Gut and Physiology Syndrome), or SCD (Specific Carbohydrate Diet). These diets are designed to starve out bad bacteria that only feed on starch and sugar, while our good bacteria can survive by eating mostly protein and fat. However, our ever-deteriorating lifestyle and environment have brought about new quasi-pathogenic microbes that have changed the game in the last 10 years. Microbiome specialists like William Davis, Mary Ruddick, Suzanne Dekota, and Sabine Hazan have been looking closer at the arise of mucous eaters in the gut.

The mucous of the gut is essential for the planting of our good microbes. But when the quasi-pathogenic bacteria (like strep, staph, klebsiella) become overgrown they can eat the mucosal lining of the gut. When this happens then diets like carnivore and GAPS won't solve the whole problem, and our birth microbes can become starved by the medical diet while these quasi-pathogens proliferate by eating our mucous layer that the birth microbes depend on for their existence.

What do we do? First, we have to feed our birth microbes. I will provide a list below of what foods they need.
Second, we need to get a GI MAP to see if we have any of the quasi-pathogenic mucous eaters and to see what our birth microbe population looks like. Third, we need to treat out gut with very specific probiotics that will push out the very specific mucous eaters. 

1.) Feed the Birth Microbes: Specific microbes eat specific foods. You don't need a lot. Just a sprinkle is enough to feed to the birth microbes according Mary Ruddick. You can use more as you heal. The following foods will feed most of the birth microbes in most people. You can get them as powders and mix, say, a tablespoon of each of them together in a container. Then just add a quarter teaspoon per day to your food of beverages. Increase as you can tolerate them. I just mix them in a little water and drink them. I will list each food with a link to the one that I purchased:
     - Green banana resistant starch
     - Inulin
     - Shrimp shells (chitosan)
     - Acacia fiber
     - Arabinogalactin
     - Colostrum
     - HMO (human milk oligosaccharide)
     - Fucose
     - Psyllium husk

2. GI Map​: I ordered my test from DHA Laboratory. Here is the link.

3.) Pushing Out Mucous Eaters: This will take a little work. Once you get the results of your GI Map you will need to look up the specific names of the microbes that are over-grown in your gut and then find which microbes will push them out. Once you know which microbes will push them out then you can purchase those microbes and feed them the specific food that they eat. To make it cheaper and to quickly grow these beneficial microbes you can culture some of them into a yogurt so you don't have to keep purchasing them. Just use a couple tablespoons of your last yogurt to make the next batch. Refer to William Davis's book called Super Gut for recipes and instructions for culturing your own yogurt.

This approach to healing the gut microbiome is a more targeted strategy than most other approaches.

Probiotics like Bacillus subtilis and some Lactobacillus strains (such as L. plantarum and L. rhamnosus) are showing promise for controlling Staph and Strep in the gut. Bacillus subtilis has been shown to significantly reduce Staphylococcus aureus colonization. Lactobacillus plantarum can stimulate mucus secretion to protect the gut and help expel pathogens, while Lactobacillus rhamnosus can strengthen the mucus barrier and reduce inflammation. 
Specific probiotic strains

• Bacillus subtilis: Research indicates this probiotic can eliminate over 95% of Staphylococcus aureus colonizing the body without disrupting other beneficial microbes.
• Lactobacillus plantarum: This strain stimulates mucus secretion, which protects the gut, and helps expel pathogens like Staphylococcus.
• Lactobacillus rhamnosus: This strain is known to improve gut lining integrity by strengthening the mucus barrier and has been shown in studies to reduce Staphylococcus aureus adhesion to intestinal cells.
• Lactobacillus paracasei: This strain has been shown to survive in the GI tract and reduce the counts of staphylococci and streptococci in the gut.
• Streptococcus salivarius K12: This oral probiotic has demonstrated the ability to kill Streptococcus pyogenes in lab settings. 

How they work

• Strengthening the mucus layer: Certain probiotics, like Lactobacillus rhamnosus, can increase the thickness of the protective mucus layer in the gut, making it harder for bacteria to adhere to the gut lining.
• Expelling pathogens: Probiotics like Lactobacillus plantarum can actively help remove harmful bacteria from the gut.
• Producing antimicrobial agents: Some Lactobacillus strains produce antimicrobial substances that can kill or inhibit the growth of various pathogenic bacteria. 

Important considerations

• While preliminary research is promising, much of it is still in the early stages, and more studies are needed to confirm these effects in humans.
• For specific health concerns, it is important to consult with a healthcare provider to discuss the best course of action, which may include probiotics alongside other treatments. 

Specific probiotics like Lactobacillus rhamnosus GG and Bifidobacterium lactis Bb-12 are known to enhance the gut's mucus layer and inhibit pathogens, making them beneficial for controlling mucus-eating pseudopathogens. Saccharomyces boulardii is another key probiotic yeast often used in conjunction with antibiotics, and it may help by reinforcing the intestinal barrier and enhancing the immune response. 
Probiotics for a stronger mucus barrier 

• Lactobacillus strains: Strains like Lactobacillus rhamnosus GG (LGG) have hair-like structures called pili that help them adhere to the mucus layer and epithelial cells, strengthening the barrier. Other Lactobacillus species, such as L. johnsonii LJ1 and L. casei Shirota, have also shown the ability to inhibit pathogen adhesion in studies.
• Bifidobacterium strains: Various Bifidobacterium species, including B. lactis Bb-12 and B. longum, can bind to the mucus layer and have been shown to reinforce the intestinal barrier.
• Akkermansia muciniphila: This bacterium naturally degrades mucins for energy, which can provide fuel for the host's gut lining, but its use as a probiotic may depend on specific needs. 

Probiotics to support immune function 

• Saccharomyces boulardii: This probiotic yeast is particularly useful for its ability to enhance the immune response, which can help the body fight off pathogens. It is often used alongside antibiotics because it is a yeast and is not affected by them.
• Lactobacillus casei (431 strain): Studies have shown this strain can boost the immune response and help with the convalescence from diarrheal diseases. 

Considerations

• Combined use: Combining multiple probiotic strains, such as B. lactis Bb-12 and L. rhamnosus LGG, may provide synergistic benefits by inhibiting pathogens more effectively than a single strain alone.
• Individual variation: The effectiveness of probiotics can vary depending on the individual's specific microbiome and health status.
• Consult a professional: It is important to consult a healthcare provider before starting any new supplement regimen, especially when dealing with gut issues and pseudopathogens. 

Cultivating Into Yogurt:
​Lactobacillus rhamnosus GG and Bifidobacterium lactis BB-12 can be cultivated in yogurt, as BB-12 is a widely used probiotic in commercial yogurts, and studies show that LGG can also be added to yogurt to create a functional food. Both strains are compatible with the conditions in yogurt production, which typically involve culturing with traditional yogurt starter cultures like Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus. 
How they are cultivated in yogurt

• As a starter culture: These probiotic strains can be added to the milk along with the traditional yogurt starter cultures to create a yogurt with probiotic benefits.
• For improved survival: Some methods, like the one described in ScienceDirect, involve "stress-adapting" the bacteria before they are added to the milk. This process can improve their survival rate during the yogurt production process and storage.
• For product stability: Research has shown that strains like BB-12 can remain viable in yogurt-based drinks for up to 30 days, indicating a stable product with a consistent probiotic population. 

Considerations for making probiotic yogurt

• Traditional starter cultures: Yogurt is traditionally made with a combination of Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus.
• Bifidobacterium BB-12®: This strain is already used in a number of dairy products, including yogurt, infant formula, and cheese.
• Other strains: While L. rhamnosus GG is less common than B. lactis BB-12, studies show it can be cultivated in yogurt. 

Important note

• The information provided here is for informational purposes only and does not constitute medical advice. Always consult a healthcare provider before making any changes to your diet or health regimen.

This article does NOT constitute medical advice. Consult with your physician before making any changes to your medical plan.