Summary of “The Gut Health Protocol”

The full version of “The Gut Health Protocol – Second Edition” is available on Amazon in both Paperback and Kindle formats. What follows is a summary of the book’s “Kill” phase, followed by the book’s Table of Contents.

The Gut Health Protocol - Kindle Cover

Along with an easy to understand narrative and protocol, the book contains summaries and links to over 1,200 scientific studies that provide evidence for the protocol’s efficacy. The actual protocol is in plain language and easy to understand. It is the product of over three years of reader suggestions after draft versions were posted to our Facebook group and comments on the first edition. If you need more evidence of efficacy see some just a few of the many testimonials it has received. It is my hope that this book will serve as a valuable tool in your quest to restore your gut to normal and help you to go armed with great information the next time you visit your doctor.

This summary is intended to give people a basic protocol that they can use to improve their gut health and assist with treating a bacterial or yeast imbalance. The actual book offers far more detail and plans tailored to specific conditions, such as Small Intestinal Bacterial Overgrowth (SIBO), Small Intestine Fungal Overgrowth (SIFO, or Intestinal Candida), SIBO-C (constipation), IBS, Acid Reflux, h.Pylori, etc. With research studies quoted every step of the way. The full book also includes recipes, instructions, and references that will greatly ease the burden of this, or any, such protocol.

Goals of the Gut Health Protocol:

  • Disrupt the biofilm created by opportunistic / pathogenic bacterial and yeast. This is one of the major methods pathogens use to protect themselves from our immune system, natural remedies, and even antibiotics.
  • Kill the pathogens, both free-floating and those that have adhered to the intestinal wall, using natural herbs, enzymes, and competition pressures from the probiotic bacteria found in fermented foods. Do this while killing as little good bacteria as possible.
  • Establish an environment in the entire gastrointestinal tract that is hospitable to beneficial bacteria (including our heritage strains passed to us by our mothers); while creating an inhospitable environment to opportunistic / pathogenic strains.
  • Populate the gut with a wide diversity, and high culture count, of beneficial bacteria. This serves many purposes, including the goals above, and helps to prevent pathogens from recolonizing.
  • Improve stomach and gut motility (keep things moving along). This not only helps prevent constipation and the feeling of being full all the time, but it also helps wash pathogenic strains out of the small intestine. Undigested food is a major cause of SIBO and “leaky gut”. Undigested food and unabsorbed sugars can also ferment in the gut, causing inflammation, bloating, and making leaky gut even worse. These need to be move to the colon as quickly as possible (while we work on solving those issue too).
  • Heal the gut; including the permeability of the intestine (leaky gut), the mucosal layers, alleviate intestinal inflammation and reestablishing a healthy microbiome. Leaky gut is one of things that make us feel the sickest.
  • Properly feed the good bacteria of the small and large intestine. This provides many benefits to the host (you) and helps prevent a reoccurrence of the disease state.
  • Preventing the return of opportunistic / pathogenic organisms.
  • Creating educated host organisms for our microbiomes. These host organisms will educate other hosts so that both the host colonies and the microbiome colonies thrive. The host organism is you, and you should be educating others, including your doctors.

Symptoms of SIBO and SIFO

The symptoms of Small Intestinal Bacterial Overgrowth (SIBO) and Small Intestinal Fungal (Yeast) Overgrowth (SIFO) are very similar and are listed below. It is also very possible to have both. There does seem to be a lot more “brain fog” and a feeling of being slightly drunk with SIFO.

SIBO / SIFO Symptoms:

  • abdominal fullness
  • diarrhea
  • constipation
  • indigestion
  • abdominal pain
  • cramping pain after meals
  • gas / bloating
  • abdominal distension
  • flatulence
  • weakness
  • fatigue
  • eczema
  • excessive fullness after a meal

Mostly SIFO (in addition to above):

  • “Brain Fog”
  • Feeling slightly drunk most of the time
  • psoriasis and eczema
  • Overwhelming cravings for sugar and refined carbohydrates
  • Tongue, nail and skin fungal infections.
  • For women, frequent vaginal candidiasis (vaginitis) infections
  • Depression, anxiety, mood swings


The Very Basic Protocol

What follows is a very trimmed down version of what is contained in The Gut Health Protocol’s “Kill” phase. The book actually has several protocols, each designed for a specific condition and each backed up be numerous research studies.

  1. Fermented Foods – The Four “K”s, and Probiotics – Fermented foods, “the poor man’s dish and the rich man’s medicine” are very important for the treatment of SIBO and SIFO (fungal overgrowth), even if antibiotics are used. If you have problems with digestion or constipation, fermented foods are probably one of the best things you can do to help correct the situation. If you have frequent heartburn, GERD, and acid reflux it is often due to weak ineffective stomach acid (this will be explained more in section 6 below); fermented foods help heal the stomach’s ability to manufacture stomach acid (HCl). They contain beneficial organic acids – lactic acid helps the gut control pathogenic bacteria and promote the growth of probiotic bacteria. E.g. Kombucha can contain: acetic acid, ethanol, gluconic acid, glucuronic acid, glycerol, lactic acid, usnic acid. The Four “K”s are sauerKraut, Kimchi, Kefir, and Kombucha. But other ferments are also beneficial, such as Miso, Natto, and any homemade fermented vegetables.
  2. Food and Diet – It is very important that you follow a very low sugar diet, including avoiding most fruits, and very low carbs for at least 3 weeks; you can start adding carbs back two weeks after you are having mostly good bowel movements. After that you should avoid sugar as much as possible and avoid wheat; sugar and carbs feed pathogenic gut bacteria, and wheat worsens an already inflamed intestine. These recommendations are not based on any current fad or farfetched theory, everything, again, is based sound scientific study. Many people will be able to return to eating carbs once the gut infection is eliminated. The book outlines several diets that may help, including my own Gut Health Diet designed specifically for healing.
  3. Exercise / Sleep – A very limited amount of exercise is necessary to balance hormones, burn excess glucose, and to signal the body to raise metabolism. Exercise can be limited to nothing more than brisk walks, though some mild resistance training is beneficial. Sleep is far more important than people give it credit. Studies have shown that by simply increasing the amount of sleep one gets that it can cause them to burn additional calories and even lose weight.
  4. Biofilm Disruption – The biofilm created by pathogenic bacteria can interfere with nutrient absorption in the small gut and is often inflammatory. The biofilm is basically a home for a community of bacteria and yeast. This home can protect them, not only from our immune systems but from medications such as antibiotics and antifungals. The biofilm can be quite tough and is often reinforced with minerals such as calcium and iron. On the other hand the biofilm created by probiotic (symbiotic) bacteria is anti-inflammatory and beneficial to gut health. This section outlines the various strategies for defeating pathogenic biofilms and is useful even if taking antibiotics. The primary recommended supplement is a product called Interfase Plus.
  5. Lactoferrin – Lactoferrin binds iron so that pathogenic bacteria can’t utilize it, but your body can. In fact Lactoferrin makes iron more bio-available for humans. This one function alone makes lactoferrin very important to stopping bacterial and yeast gut infections. It is also a biofilm disrupter (see above), so this further adds to its effectiveness. Lactoferrin is found naturally in human breast milk. A number of studies (outlined in the full book) show the efficacy of supplementing with lactoferrin for several gut infections as well as for general health.
  6. Betaine HCl and Digestive Enzymes – Many people with gut infections end up not being able to properly digest their food. This is due to several factors, the primary reason being that the toxins produced by pathogenic bacteria damage your stomachs ability to manufacture stomach acid and utilize digestive enzymes. This section outlines how you can successfully supplement these natural substances. Once your gut heals most people can actually stop taking them. The section also explains why antacids (such as protein pump inhibitors) are usually not a good idea. Again, the full book contains several research studies linked and summarized. (Amazon)
  7. Parasites – As icky as it may sound many people with gut issues have parasites as well as some other underlying infection. This section covers the primary treatments (which can be used even if you don’t know that you have parasites), the two main ones being Food Grade Diatomaceous Earth and Wormwood.
  8. Soil Based Organisms (SBO) – In addition to the probiotics found in fermented foods SBOs are a probiotic found in the soil. When we lived closer to nature we consumed SBOs daily on the food we ate and even the air we breathed when farming. Today we live in a much more sterile environment and most people do not have an adequate population of these organisms (primarily probiotic bacteria and yeasts). Adding an SBO can help eliminate pathogenic strains, help prevent their return, and help heal the gut. Prescript-Assist if the primary SBO recommended.
  9. “Kill” Supplements – These are primarily herbs that can help kill pathogenic bacteria and yeast. We want to be sure to use supplements that harm pathogenic strains more than probiotic strains (by blocking or interfering with processes unique to those strains). Many scientific studies backup the efficacy of these herbs and, in some cases, even show them to be more powerful than prescription antibiotics. Because a full understanding of this topic is important you should read this section of the book carefully.
  10. Extra Virgin Coconut Oil – EVCO for short, has been shown to be very effective against many pathogenic strains of bacteria and yeast. It’s also very good for general health and can be consumed for life. It can be used in cooking or taken directly as a supplement.
  11. N-acetylcysteine (NAC) – NAC has been shown in several studies to reduce pathogenic bacteria, and is a biofilm disrupter. It can also detoxify certain toxins and can help reverse some of the damage done by antibiotics.
  12. Colostrum – Colostrum helps rebuild your immune system and can naturally fight pathogens in the body. It also helps heal the gut and fights
    intestinal inflammation.
  13. Lauricidin / Monolaurin – Made from coconut, monolaurin supports a healthy immune function and helps break down the biofilms of SIBO and candida albicans. It is also reported to kill lipid-coated viruses.
  14. Zinc Carnosine – Studies show that people get over SIBO and h.pylori quicker when taking Zinc Carnosine. It is also very useful for healing the gut and combating disease associated inflammation and leaky gut.
  15. Milk Thistle – Milk Thistle, or silymarin, has been shown in dozens of studies to be supportive of the liver and help detox the blood. This is important when killing a lot of bacteria as mild toxins are released by the bacteria during this process. This helps with “die-off” symptoms.
  16. Larch Tree Fiber – Larch Tree Arabinogalactan fiber is added starting the 3rd week of the “kill” phase. This is necessary to start rebuilding the microbiome (the good bacteria). This process will continue during the Healing & Repair phase in Chapter 2.

The Gut Health Protocol book goes in to a lot more detail on each of the above recommendations. Chapter 2 starts the gut repair and healing phase of the protocol and is extremely important to feeling better and long term success. Many of the symptoms of SIBO are actually caused by inflammation and leaky gut, these are addressed in Chapter 2.

The chapters on the other various gut conditions recommend supplements that are tailored to those conditions, thus speeding recovery and reducing the chances of gut irritation. The large amount of research quoted in the book is also very helpful in understanding your condition and secondary issues caused by it.


Table of Contents (Second Edition)

Table of Contents
Chapter 1 The Gut Health Protocol
Goals of The Gut Health Protocol
Our Gut, An Overview
Digestive Timeline
Our Microbiome
Gas Production
The Basic Gut Health Protocol
1) Fermented Foods, The Four “K”s, and Probiotics
Benefits of Fermented Foods
• Resistant Starch (RS)
• Histamine Intolerance (HIT)
2) Food and Diet
Artificial Sweeteners
Chewing Your Food Well
Chlorinated Water
“I can’t have dairy” – Who says you can’t?
Suggested Diets
• The Gut Health Diet
• Paleo / Primal / Ancestral Diet
• Paleo Autoimmune Protocol Diet (AIP)
• Specific Carbohydrate Diet (SCD)
• Low FODMAP Diet
• The Whole30 Diet
• Elemental Diet
• Blood Type Diets
3) Exercise / Sleep
4) Biofilm Disrupting Enzymes (SIBO & SIFO)
5) Lactoferrin
6) Betaine HCL and Digestive Enzymes
HCl Challenge
Digestive Enzymes
Normal Stomach pH
Normal Intestinal pH
Proton Pump Inhibitors (PPI)
7) Parasites
Parasite Treatment Options
Blastocystis hominis
8) Soil Based Organisms (SBO)
9) “Kill” Supplements
Natural “Kill” Supplements Listed by Risk/Benefit
Garlic / Allicin
Cinnamon Oil
Olive Leaf Extract
Oregano Oil
Caprylic Acid
Kill Supplement Compounds
10) Extra Virgin Coconut Oil (EVCO)
11) N-acetylcysteine (NAC)
12) Colostrum
13) Lauricidin / Monolaurin
14) Zinc Carnosine
15) Milk Thistle
16) Larch Tree Fiber
Chapter 2 Maintenance and Gut Repair
Butyrate Benefits:
Butyrate For Gut Health
Pain and Inflammation
Cancer Risk
Intestinal Disease Prevention
Methanogens / IBS-C / SIBO-C
Clostridium butyricum (MIYAIRI 588)
Obtaining Butyrate From Food
Fibers and Resistant Starch
Meet the Fibers
Foods High In Soluble Fiber
More Studies
Gut Bacteria Diversity Testing
Turmeric / Curcumin
Zinc Carnosine
Omega 3 Fatty Acids
Bone broth
Miscellaneous Gut Health Nutrients / Strategies
How can you tell when you’re getting better?
Chapter 3 Other Herbal Tinctures & Supplements
Prescription Drugs
NOT recommended
Chapter 4 Nutritional Supplements
Chapter 5 Small Intestinal Bacteria Overgrowth (SIBO)
SIBO Symptoms
SIBO Causes / Risk Factors
SIBO Treatment / Supplements
SIBO Testing
Chapter 6 Intestinal Candida Albicans Overgrowth (SIFO)
SIFO Symptoms
SIFO Causes
Fungal Forms
Candida Spit Test / White Tongue
Candida Tests
SIFO Treatment / Supplements
Natural Nail Fungus Treatment
Chapter 7 Ileocecal Valve
Chapter 8 “Natural Antibiotics”
Colloidal (or Nano) Silver
Grapefruit Seed Extract (GSE)
Chapter 9 Biofilm and Quorum Sensing (they can hide, and “talk”!)
Quorum Sensing
Chapter 10 Fructose Malabsorption
FM Symptoms:
Chapter 11 Motility and the Microbiota
Chapter 12 Leaky Gut Syndrome and Enteritis
Lipopolysaccharide – LPS
Fermented Foods
Turmeric / Curcumin to Treat LPS
Symptoms of Leaky Gut
Causes of Leaky Gut
Natural Treatment Options
Chapter 13 GERD, Acid Reflux, and Heartburn
Chapter 14 Gastritis
Treatment Options
Chapter 15 Helicobacter Pylori Treatments and Studies
Causes of H. pylori
Testing for h. pylori
Natural Treatments / Supplements
Hybrid Treatment
Possible PPI / HCl Treatments
Supporting Evidence
Antibiotics / Triple-Therapy
Chapter 16 Irritable Bowel Syndrome (IBS)
Chapter 17 Constipation
Consume the Right Kind of Fiber
Controlling Methane Producers
Traditional Medical Treatment
Chapter 18 Inflammatory Bowel Disease
Chapter 19 Antibiotics
Antibiotic Risk Mitigation
Chapter 20 Histamine Intolerance (HIT)
Histamine “Safe” Probiotics
Foods/ Drugs to Avoid
Appendix A Additional Reading
Microbiome Health
Diet and Cravings
Gut Health
Permeable Gut
Traditional Food and Recipes
General Nutrition
Appendix B Using Probiotics In The Treatment of SIBO
Appendix C Gut Health Protocol Supplement Chart
Appendix D Recipes
Fermented Food Recipes
Kefir Instructions – 2 Quart Mason Jar
Gut Healing Golden Kefir
Kombucha Instructions – 2 Quart Mason Jar
Simple Sauerkraut – Airlock Method
Fermented Bean Dip – 2 Quart Jar
FODMAP Friendly Kefir Ranch Dressing
Gut Health Green Smoothie
Broths, Soups, Stews, Chiles
Beef Bone Broth
FODMAP Safe Texas Chili
Golden Turmeric Paste
Golden Sludge
5 Minute Homemade Mayonnaise
Appendix E How to make your Own Ball Jar Airlock Lids
Appendix F Histamine Safe Sauerkraut
Appendix G MTHFR
Appendix I Eczema
Intestinal Permeability
Probiotics/ Prebiotics
Appendix K Bacteria Strains Found In Probiotics
Appendix J Carbohydrates in the Human Diet
Appendix Q The Gut Health Diet Foods
Allowed Foods
Avoid Foods
Appendix X Acknowledgments
Appendix Y Glossary / List of Abbreviations
Appendix Z Disclaimer and Usage Permissions
Usage Permissions
Updates and Discussion
Note Regarding Studies In This Book
Index / Endnotes

20 thoughts on “”

  1. Hi John,

    Great book! I’ve had an interest in SIBO for years both personally and professionally– ( I published Dr. Mark Pimentel’s Book, ” A New IBS Solution”) I’m in the process of updating the book and would love to chat with you. Please feel free to contact me directly at or 818/788/4905. Thank you!

    David Knight
    Managing Editor/Publisher

  2. Hi John,

    I purchased your book and getting ready to start the gut health protocol for sibo/sifo. Do I need to take both the Allibiotic adding capyrlic acid and the candida support in phase 1?



    1. Tamara, yes, the Allibiotic should be taken with the other supplements listed. You can start slowly and work up to the full dose listed on the bottle to help avoid some of the die-off symptoms but remember that die-off means that it is working.

      Sorry for the slow reply, the Facebook Group The Gut Health Protocol ( is where you’ll get a much faster response (from myself and/or others).

  3. Hi John,
    I purchased your book and am definitely ready to improve my digestive situation. I had to remove my gallbladder 2 months ago and I think I am suffering from a bad gastritis/duodenitis (possibly due to bile reflux). I find myself eating a very bland diet (have lost quite a bit of weight) as I am not sure I can handle much else due to nausea and abdominal pain, unfortunately this also means I am eating a lot of carbs( white rice, potatoes, yams), bananas are also a staple as they they feel gentle. I have cut out dairy and sugar (other than fruit:apples, pears). My H.pylori test is pending. Do I still follow the full protocol especially in regard to the “kill”time and diet changes. If there is any other suggestions you have that would be great. Thank you

    1. Tanja,

      I think you just joined the Facebook support group, that is a great resource for information. The reasons behind gastritis and enteritis are very important. But the nice thing about this protocol is that is food and nutrition based and very unlikely to do harm, many people with gut issues do have at least some SIBO and/or intestinal yeast (SIFO). So certainly worth a try. Results of the h.pylori test are also important for what direction you branch off during or after doing the basic protocol. The fruit and carbs are almost always a bad thing while healing. I think once you’ve fully read the book you’ll understand a lot more of the “whys” behind the protocol and the Facebook group can help you even more.

  4. hello, ive had blasto hominis parasite for a long time and have been suffering with nausea, no apetite, depression/anxiety etc. I have done a organic colon cleanse and a 16 day parasite cleanse also (wormwood, black wanut hull, cloves) i have cut carbs, sugar, dairy almost completely. I take l-glutamine, magenisum, hawaiiwan spirulina, oregano oil, zinc, apple cider vinegar, all on a daily basis. Nothing is getting rid of it! What else is there to do? I am losing hope and the depression is taking over my life. Please help.

    1. Staying very low carb while supplementing Nigella sativa (black seed extract), Gincer, Garlic, Wormwood (Now Foods Green Walnut Oil Wormwood Complex works well Amazon), and cinnamon bark oil. All have scientific evidence of efficacy. You then want to build up your microbiome to compete with the parasites, don’t believe the hype about bacteria feed blastos, they actually compete with them and good bacteria create an environment hostile to them. I wouldn’t worry about a colon cleanse either, the body takes care of that.

  5. Hi John,
    What if you have a lot of trouble digesting fats, cant handle a low carb diet (creates anxiety and depression) and you have an enterococcus bacteria that feeds of your protein?

    1. Digestive enzymes and ox bile may help for digesting the fats. Low carb related depression may be low soluble fiber (which is often very low on low carb diets), supplementing soluble fiber may help. Are you referring to Vancomycin-Resistant Enterococci (VRE)? Otherwise I would assume antibiotics would have taken care of it by now. If so this is where a natural protocol may help! Antibiotic resistant bacteria are not resistant to natural treatments. The new second edition of the book outlines a protocol that may help many people with this condition (I can’t “individualize” this recommendation). Of course continue to work with your doctor as well and let them know what you’re planning to do.

  6. Like a large number of people, I find that my sleep suffers without adequate carbs. What would be the ideal carb source for the killing phase? Something like dextrose/pure glucose?

    1. Joshua, yes, a small amount of pure dextrose/glucose.

      In the Repair and Healing phase the soluble fiber may be all you need. When our microbiome is impaired so are our hormones. Over time you should need less and less sugar / carbs for good sleep and thyroid.

      1. Get the dextrose organically sourced, as glyphosate residues from conventional grains can impair other gut healing initiatives, opening the tight junctions between gut wall cells.

  7. Hi, I have H.Pylori. Been taking Interfase Plus for three weeks now. I believe it is working well because my tongue that was heavily coated is much improved. No more heavy coat. I can actually see my tongue in the mornings! However, I have suddenly become very weak after three weeks. No energy. My body feels drained.

    Is it possible that the Interfase is also depleting my body of needed nutrients? I read about the benefits of monolaurin. Can i take it along with the interfase or can it be taken alone and give the interfase a break? I am also taking Zeolite powder. Thanks for your response.

    1. Interfase Plus needs to be taken between meals on an empty stomach, just take the monolaurin with food. Interfase Plus can bind to minerals, I recommend that people not take it for more than month unless advised by their doctor (for this very reason). You should read Chapter 15 in The Gut Health Protocol if you have it.

      You may want to consider taking a liquid ionic mineral supplement. Good State makes several good liquid mineral supplements that are very easy for the body to absorb, two you may want to consider are Ionic Trace Minerals and the Ionic Calcium and Magnesium.

      h.Pylori will probably need more than just Interfase and monolaurin, it can be rather difficult to get rid of.

    1. I couldn’t find any research studies showing its effect on beneficial bacteria. It is used mostly to kill parasites. However, I did find studies showing that it does kill some gram-positive and gram-negative anaerobic bacteria. Since its method of action seems to be to create free radicals from iron it is probably harmful to many strains of bacteria it comes in to contact with.

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