The Gut Health Protocol For The 30-Day Challenge

by Dr. David Minkoff September 10, 2023 10 min read

The Gut Health Protocol For The 30-Day Challenge

Disclaimer: Neither this Protocol, or any article in the Gut Health Guide, make any claims as to treatment or cure of any disease or illness. This information, guide, and protocol exist only to help raise the overall health of our gut through nutritional means.


This is going to take some time to prepare, so I’m giving this to you here first.

We’re going to be addressing digestion, acid reflux, harmful micro-organisms, leaky gut and our colon bacteria (microbiome).

While this is key to longevity, hormonal balance, mood, stress levels, energy levels, mental ability, fat loss, muscle building and overall health, and you will feel much better by the end of it… it’s not for the faint of heart.

I want to be upfront about this. We will be killing off harmful bacteria, some you have had for years or even decades. Yes, they cause considerable damage over time, but when we kill them off you will also feel this.

You will go through reactions. Even if your gut is not in too poor condition.

This is because of how closely these harmful microorganisms are in touch with our cells, nerves and brain.

As these microorganisms die, you could almost say they “communicate their pain” to your brain. They certainly communicate their desires and cravings to our brain, which you feel when you get a sudden urge for sugar or junk food, and they communicate when they are “upset” as well.

So that’s one reaction. And you will feel it.

Secondly, when they do die off, they release two main things that can cause more reactions.

First, they release bio-toxins and free radicals that can harm our cells. This is why certain other supplements are part of this protocol, to protect our cells and speed up this process.

And second, both good and bad bacteria hold in actual toxins: glyphosate, heavy metals, plastics, PFAS and others.

When they die, these are released into the blood stream and must be removed.

While you may not experience all of these, as we try to take this on gradually, the die-off above can cause: some heartburn at the beginning, lowered energy levels, lethargy, extreme cravings for sugar, carbs or junk food, stomach upset, gas and bloating, trouble sleeping, foul-smelling bowel movements, diarrhea, headaches, brain fog, poor mood and even chills or flu-like symptoms.

These will be mild for some, and extreme for others. And truthfully, those who it’s the most extreme for need it the most and will experience the most benefit from it.

But this stage should only last about a week, two at the most, if you follow the protocol.

This protocol is designed to get you through this stage as swiftly and painlessly as possible. So keep to it.

Also note, you may feel you need more sleep during this protocol -- get the sleep. This is important. Your body needs more recovery time during this. 

It may even be smart to cut down on the number of days you workout during the week, just for a few weeks, to ensure your body and immune system are not overloaded.


This is the other part that will cause some discomfort.

While one part of the protocol is designed to kill off harmful microorganisms lowering your overall health, the other part is designed to both cut off their food source and to help repair the damage they’ve done over the years or decades.

If we continue to feed them the foods they thrive on, then no amount of work will remove them completely. So we need to cut this off.

At the same time we need to get the cells of our stomach and intestinal lining the nutrients they need to start healing, and we need to give the beneficial bacteria the nutrients that they need in order to thrive.

Therefore the diet will be most similar to a Paleo-type diet and may be quite radical compared to what you’re used to eating.

Some, whose digestive tracts are not in terrible shape, may be able to sneak in some of the items on the “No" list below. But for anyone truly needing a full gut address, I recommend sticking to the below foods as closely as you can.

It’s not that it may be hard at first. It will be. But the end result is more than worth it.


There are no macros or exact amounts of food to eat. Some days you may want to eat more and some days less. This is fine. We just need you keeping to certain foods and away from others.

Proteins: We need A LOT of protein. This is both to help heal the damage done and help build up the immune system which we need working at full capacity. It is also necessary for hormonal balance and microbiome health.

These proteins should be grass-fed and organic. We don't need to give the harmful bacteria any help in the way of food for them or more toxins that stress out the immune system more when it’s already overloaded.

PerfectAmino will also play heavily in this, below.

But there are no protein powders. The majority of these are more than 80% converted into sugars that feed these bacteria, and are partially indigestible for many.

Healthy Fats: Healthy fats are necessary for our cells, they make up half of the structure of each one of our cells. And some, such as coconut oil, help in getting rid of SIBO and candida.

These need to be non-processed fats: olive oil, avocados, butter, fatty fish, fatty meats, Omega 3 fats, etc.

Vegetables & Fruits: Vegetable are a must, at least at dinner and best if at lunch as well. Especially cruciferous vegetables. While these provide a very good source of fiber, which we need to keep or get things moving, they do much more than that and are quite vital.

Some low-glycemic fruit, such as an apple, is okay in the morning. However, the fewer carbs you can have on this diet, the better.

Nuts and Seeds: Raw almonds, flax seeds, sunflower seeds, pumpkin seeds and caraway are especially good on a candida or SIBO diet, but other nuts and seeds are okay as well as long as you do not have a known sensitivity to them.

Hydration is also key: Make sure you’re drinking plenty of water to help flush the bio-toxins and toxins out of your system.


No dairy except organic butter: For many, dairy is a mild auto-immune trigger. While some cream in your coffee isn’t too bad for some, for many it causes more troubles than they know. For the best results on this protocol, dairy should be cut out completely or kept to the absolute minimum. The only exception is organic butter. 

No grains: These not only feed the harmful bacteria, but the proteins in them (glutenen and gliadin) are one cause of leaky gut, as you'll see. So, while you may transition back onto them after the protocol, it is best to cut them out during the protocol for best results.

Absolutely no processed or packaged foods: No processed foods and no processed sugars. These directly feed, and for many are the cause of, the microorganisms we’re trying to kill off. This is the main place this protocol can fail, so this is important.

No nightshade vegetables: These can cause immune responses for many. You may have some in your diet and not notice any trouble from them. However, we will be putting a large load on your immune system for the first two weeks and something that normally gave it little trouble in the past can suddenly become quite a burden to it when it’s overloaded. So no nightshade vegetables.

No Sodas: These decrease the digestive ability of the stomach, both lowering the amount of nutrition you get from your foods and also making it easier for new microorganisms to slip through.


There are several different supplements for this protocol.

Some of these are involved in improving digestion and addressing heartburn, some for ensuring proper bowel movements, some for killing off harmful microorganisms such as SIBO, some to feed the beneficial bacteria we need, some to help repair the damage that has been done and even some to help make the reactions less severe.

Some are very helpful, while some are key:

1. GUT DEFENSE: The first is Gut Defense, and this is the hero of this protocol.

Gut Defense serves two functions. It helps kill off harmful bacteria, fungi (candida) and parasites. And it helps break down the bio-films these microorganisms create to protect themselves. This is necessary as these bio-films are a chief reason your immune system has not been able to get to them to kill them off already.

This is also where you will be feeling the chief amount of reactions, so we need to do this gradually.

Follow this sequence for the best results:

Phase One: Take 1 per day, at lunch, not dinner.

If you experience heavy reactions, then skip the next day. Then take it the day after and continue on. If heavy reactions occur again, skip a day again and so on.

Continue this until you have taken it daily for one full week.

Phase Two: Take 2 per day: 1 at lunch and 1 at dinner.

If heavy reactions occur, skip the next day completely. Then, on the following day, raise it back to 1 and the day after that raise it back to 2. Do this as many times as needed.

Continue this until no significant reactions have occurred for a week and you have taken 2 daily for one full week.

Phase Three: Increase to 3 per day: 1 at breakfast, 1 at lunch, and 1 at dinner.

If heavy reactions occur, skip the next day. On the day after that take 1, the day after that 2, and the day after that 3 again. Do this as many times as needed.

Phase Four: Carry on taking 3 per day. There is no need to increase beyond this level. Reactions should continue to subside more and more.

Note: Gut Defense should not be taken before bed as it may keep some people up.

Note: While you will notice the heaviest reactions in the first 1-2 weeks, and they should be gone or significantly lessened by the end of this challenge, both SIBO and candida do take time to fully address. It is highly recommended that you continue on Gut Defense for a total of four months to ensure all SIBO is fully addressed.

2. DIGESTIVE ENZYMES: These improve digestion in the stomach, both ensuring food and proteins are fully broken down so your body gets the needed nutrition from them, as well as helping to kill off new microorganisms trying to slip through.

This is necessary for this protocol, especially with the high amount of proteins and fats you will be eating. 

Most people don't realize how bad their stomach digestion has gotten until they try eating more meats or fatty foods. And for the first little while, they will need these digestive enzymes to fully digest these foods until the stomach comes back up to par.

Take 1-2 digestive enzymes with each meal, not before and not after unless you forgot. Start with 1 and increase to 2 if needed.

3. PROBIOTIC: This helps to replenish the beneficial bacteria needed in your colon for proper neurotransmitter and vitamin production, key for lowering stress, raising mood and getting better sleep.

Take 2 with lunch and 2 with dinner daily.

4. PERFECT AMINO: This serves two functions. Both to get your body the amino acids it needs to start healing the lining of the stomach and intestine, and to help feed the beneficial bacteria in the microbiome as the essential amino acids are their chief food source.

Take 3-4 servings of PA per day. Take 2 servings in the morning before food and 1-2 servings 20-30 mins before dinner.


Alright, those are the most vital supplements to take for this protocol.

However, there are some others that are quite important and which would be not only very beneficial, but very helpful when it comes to lowering the discomfort of bacterial die-off.

5. RELIEF AND METAL-FREE & CHEMICAL CLEANSE: Each help with the affects of bacterial die-off and from two different angles. Relief literally helps calm things down and provide direct relief from these affects, while Metal-Free acts to capture and remove the free radical, bio-toxins and toxins released by the dying bacteria to prevent their effects.

Relief should be taken at 3 per meal for severe reactions, and 3 per day for less severe reactions.

Metal-Free & Chemical Cleanse should be taken at one dropper per day.

6. GREENS: These are wonderful for a plethora of reasons, but the two key to this protocol are their antioxidant effect in fighting free radicals from bacterial die-off, and the fact that they are the other chief food source for our beneficial bacteria.

Greens should be taken at 1 serving per day.

7. MULTI COMPLETE: Your body will be going through a lot and needs all the help it can get. Multi Complete provides a full range of the vitamins our bodies need, in the quantities they need them in, to help our cells and immune system rebuild and function properly.

And they are key to the natural detox pathways of our body.

Take 4 tablets per day: 2 tablets with lunch and 2 tablets with dinner.

8. ELIMINATE: If you have any constipation trouble during this protocol, the first thing you do is take a magnesium supplement to get things moving, and ensure you are staying hydrated and taking electrolytes if needed.

But if this doesn’t work, then take Eliminate to help normalize bowel movements as per the directions on the bottle.

9. ELECTROLYTES: you may experience diarrhea during this protocol. This is natural. But with this can come electrolyte loss, giving headaches and dehydration. In this case just take a serving of electrolytes and ensure you’re drinking plenty of water.

10. SLEEP: If you’re having any trouble sleeping during the first week or two of the protocol, just take 3 capsules of sleep about an hour before bed and this should do the trick.

Alright, that’s a lot and you’ll need time to prepare. I’ll release the next article on Tuesday.

See you then!

Also, here you can find Discounted Product Bundles for the 30-Day Challenge. Just use code GUTHEALTH at Checkout.

And if you have any questions, make sure to join our VIP Group where you can ask any question you have and get only the best answers.

*These statements have not been evaluated by the Food and Drug Administration. These products are not intended to diagnose, treat, cure, or prevent any disease.