The Gut Health Protocol

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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 books Kill phase, followed
by the books Table of Contents.

Along with an easy to understand narrative and protocol, the book contains summaries and links
to 1,200 scientific studies that provide evidence for the protocols 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 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) and 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.
See fermented foods below.
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.
Heal the gut; including the permeability of the intestine (leaky gut), the mucosal layers, alleviate
intestinal inflammation and reestablishing a healthy microbiome.
Properly feed the 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 microbiome. 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
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 Protocols
Kill phase. The book actually has several protocols, each designed for a specific condition and
each backed up be numerous research studies.

Fermented Foods The Four Ks, and Probiotics Fermented foods, the poor mans dish and
the rich mans 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 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 stomachs 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 Ks are sauerKraut, Kimchi, Kefir, and Kombucha. But other ferments are also
beneficial, such as Miso, Natto, and any homemade fermented vegetables.
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.
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.
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.
Lactoferrin Lactoferrin binds iron so that pathogenic bacteria cant 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.
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)
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 dont know that you have parasites), the two main ones being Food Grade
Diatomaceous Earth and Wormwood.
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.
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.
Extra Virgin Coconut Oil EVCO for short, has been shown to be very effective against many
pathogenic strains of bacteria and yeast. Its also very good for general health and can be
consumed for life. It can be used in cooking or taken directly as a supplement.
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.
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.
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.
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.
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.
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)

Testimonials
Table of Contents
Introduction
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 Ks, and Probiotics
Benefits of Fermented Foods
Resistant Starch (RS)
Histamine Intolerance (HIT)
2) Food and Diet
Artificial Sweeteners
Fruit
Alcohol
Chewing Your Food Well
Chlorinated Water
I cant have dairy Who says you cant?
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
Ginger
Cinnamon Oil
Olive Leaf Extract
Oregano Oil
Berberine
Caprylic Acid
Kill Supplement Compounds
Strategy
10) Extra Virgin Coconut Oil (EVCO)
Strategy
11) N-acetylcysteine (NAC)
12) Colostrum
13) Lauricidin / Monolaurin
14) Zinc Carnosine
15) Milk Thistle
16) Larch Tree Fiber
Strategy
Chapter 2 Maintenance and Gut Repair
Butyrate
Butyrate Benefits:
Butyrate For Gut Health
Pain and Inflammation
Cancer Risk
Intestinal Disease Prevention
Methanogens / IBS-C / SIBO-C
Miscellaneous
Discussion
Clostridium butyricum (MIYAIRI 588)
Obtaining Butyrate From Food
Strategy
Fibers and Resistant Starch
Meet the Fibers
Foods High In Soluble Fiber
More Studies
Gut Bacteria Diversity Testing
Strategy
Turmeric / Curcumin
Glycine
l-Glutamine
Zinc Carnosine
Omega 3 Fatty Acids
Bone broth
Miscellaneous Gut Health Nutrients / Strategies
Mucogenics
How can you tell when youre getting better?
Strategy
Chapter 3 Other Herbal Tinctures & Supplements
Prescription Drugs
Chemicals
NOT recommended
Chapter 4 Nutritional Supplements
Vitamins
Minerals
Miscellaneous
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
Alkalization
Fungal Forms
Candida Spit Test / White Tongue
Candida Tests
SIFO Treatment / Supplements
Natural Nail Fungus Treatment
Strategy
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:
Treatment
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
Testing
Natural Treatment Options
Strategy
Chapter 13 GERD, Acid Reflux, and Heartburn
Strategy
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
Strategy
Chapter 16 Irritable Bowel Syndrome (IBS)
Chapter 17 Constipation
Consume the Right Kind of Fiber
Controlling Methane Producers
Traditional Medical Treatment
Strategy
Chapter 18 Inflammatory Bowel Disease
Chapter 19 Antibiotics
Antibiotic Risk Mitigation
Strategy
Chapter 20 Histamine Intolerance (HIT)
Symptoms
Histamine Safe Probiotics
Foods/ Drugs to Avoid
Strategy
Appendix A Additional Reading
Microbiome Health
Diet and Cravings
Bacteria
Antibiotics
Gut Health
Permeable Gut
Depression
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
Miscellaneous
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
Microbiome
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
Revisions
Index / Endnotes
KNOW ANYONE WITH GUT ISSUES? SHARE THIS PAGE:
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20 THOUGHTS ON
David Knight
JULY 22, 2015 AT 8:41 PM
Hi John,

Great book! Ive had an interest in SIBO for years both personally and professionally ( I
published Dr. Mark Pimentels Book, A New IBS Solution) Im in the process of updating the
book and would love to chat with you. Please feel free to contact me directly at
booktalk@sbcglobal.net or 818/788/4905. Thank you!

David Knight
Managing Editor/Publisher
REPLY
altamisal
JULY 26, 2015 AT 3:53 AM
Great summary! Shared at a forum for healing LPR/GERD.
REPLY
Tamara
AUGUST 28, 2015 AT 12:40 AM
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?

Thanks

Tamara
REPLY
herronj@theguthealthprotocol.com
NOVEMBER 14, 2015 AT 9:07 AM
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
(https://www.facebook.com/groups/The.Gut.Health.Protocol/) is where youll get a much faster
response (from myself and/or others).
REPLY
Tanja
JANUARY 18, 2016 AT 1:26 PM
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 killtime and diet
changes. If there is any other suggestions you have that would be great. Thank you
Tanja
REPLY
herronj@theguthealthprotocol.com
JANUARY 18, 2016 AT 5:46 PM
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 youve
fully read the book youll understand a lot more of the whys behind the protocol and the
Facebook group can help you even more.
REPLY
sharon
MAY 25, 2016 AT 9:57 AM
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.
REPLY
herronj@theguthealthprotocol.com
MAY 25, 2016 AT 9:02 PM
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, dont believe the hype about bacteria feed blastos,
they actually compete with them and good bacteria create an environment hostile to them. I
wouldnt worry about a colon cleanse either, the body takes care of that.
REPLY
Sander
AUGUST 1, 2016 AT 12:47 PM
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?
REPLY
herronj@theguthealthprotocol.com
AUGUST 3, 2016 AT 10:01 PM
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 cant individualize
this recommendation). Of course continue to work with your doctor as well and let them know
what youre planning to do.
REPLY
Joshua Finlay
OCTOBER 7, 2016 AT 2:51 AM
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?
REPLY
herronj@theguthealthprotocol.com
OCTOBER 7, 2016 AT 3:07 PM
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.
REPLY
jackiethrives
JANUARY 23, 2017 AT 1:17 PM
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.
REPLY
Anthony Lomangino
MARCH 14, 2017 AT 8:05 PM
Will this Book help with LPR?
REPLY
Marcia
JUNE 13, 2017 AT 9:10 AM
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.
REPLY
herronj@theguthealthprotocol.com
JUNE 13, 2017 AT 9:23 PM
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.
REPLY
graemejones
JUNE 15, 2017 AT 5:28 PM
Hello; does artemisinin kill the good gut bacteria?
REPLY
herronj@theguthealthprotocol.com
JUNE 15, 2017 AT 8:21 PM
I couldnt 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.
REPLY
Deborah Sevy
JULY 13, 2017 AT 7:54 PM
cant find anyone to ask questions about phages complete. can you help?
REPLY
herronj@theguthealthprotocol.com
JULY 18, 2017 AT 9:11 PM
Deborah,

Yes, you can reach out to me on Facebook, or join The Gut Health Protocol group, or email me
at
REPLY
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