Evidence-Based, Simplified Nutrition and Lifestyle Strategies

Gut Healing Protocol List

Gut Supports that You Need Right Now

Gut Healing Protocol List

I focus on root-cause healing. Oftentimes that means healing the gut with a meat-based elimination diet. Gut health is so critical I wrapped Carnivore Cure around a meat-based elimination diet. Diet alone will not get us to optimal health but it will get us pretty close.


In nutritional therapy, we prioritize North to South healing as fundamental for root-cause healing. If you think of the digestive process, north to south would essentially start with a focus on the mouth and upper GI area and end with bowel or urinary movements. You may have large intestine dysbiosis but it may stem from having insufficient stomach acid in the upper GI.


If you take anything away from this article, focus on North to South for root-cause healing.


Why Meat Alone Doesn’t Always Work

Most of my clients have been eating a meat-based diet for months before working with me. Once they started eating a meat-based diet, their general digestive symptoms improve but not fully. You can read some of the symptoms of an unhealthy gut here.


Essentially, if you still teeter between loose stools and constipation weekly, get nauseous with too much fat and still burp or have indigestion after a meat-based meal, you probably need some gut support.


If your digestive process isn’t functioning at capacity, it won’t be able to break down your foods into the raw materials it needs to fuel (and heal) the body. It doesn’t matter how great your food quality is if you can’t absorb the nutrients.


As part of my initial consult intake, I have my clients fill out food and mood journals, medical history, and most importantly a symptom burden nutritional assessment. This assessment helps me to identify the root cause and how best to support my client. The results are based on the individual client’s needs and that’s what makes the assessment powerful.


Although my practice is fully booked, I allow several ad-hoc symptom burden assessments monthly. Currently, this is the closest I can get to support you on a one-on-one basis.



Starting the Gut Healing Process

I always recommend working with a qualified practitioner before starting new diets or supplemental protocols.


The following supplements are some temporary supports I use with my clients. These are general supports that focus on healing locally (e.g., stomach vs. liver vs. small intestine) but until we figure out the root cause, it is not an exact science. No specific supplement works for everyone but these are some of my go-to’s with my hundreds of clients.


Gut-Support Meat-Based Transition List


Upper GI Support

  • Betaine Hydrochloric acid (HCl) is very effective but it is not for everyone. HCl should not be taken if you are using any kind of anti-inflammatory medications such as corticosteroids (e.g., Prednisone), ibuprofen, and NSAIDs on a daily basis. These drugs can damage the gastrointestinal (GI) lining. Adding HCl can then increase the risk of gastric bleeding and ulcers.
  • Almost 90% of Americans are deficient in hydrochloric acid. Betaine HCl helps to provide more digestive support and hydrochloric acid to support better digestion and absorption of foods. Hydrozyme supports the gut with supplemental Betaine hydrochloride, Pepsin, Pancreatin (digestive enzymes) along with other known synergists. If you need stronger support you can try Betaine Plus HP that has a greater amount of Betaine HCl and Pepsin.
  • If you can’t take HCl, try digestive bitters over the HCl. Digestive bitters can stimulate HCl naturally (albeit not as effective). MegaGuard balances H.Pylori helps with bile flow supports normal digestion and balances stomach acid. The bitters and herbals help to promote normal digestion, regulate stomach acid, and reduce occasional digestive discomforts such as gas, bloating, and indigestion.
  • Apple Cider Vinegar (ACV) rarely works for my clients because they usually have some yeast or fungal overgrowth (e.g., candida). If you don’t have any overgrowths, ACV might be enough for some natural GI stimulation. Take 1 tbsp of ACV with a little bit of water 10-20 minutes before your meal. Limit your water consumption. We need our upper GI to have enough stomach acid to break down our foods and kill off any pathogens. We also need our stomach acid to be highly acidic (pH of 1.5-2.5).


You can see why alkaline waters (pH of 8.5-9.0) with our meals are a horrible idea. Studies show that drinking alkaline water will raise the pH of our stomach acid by 0.5 pH for at least 30 minutes. If you really want to drink alkaline waters, drink them away from meals.


pH Scale and Examples Table


Liver + Gallbladder Support

  • The liver produces bile to help digest and absorb fats. If you’ve been low-fat or eating limited animal fats, you may temporarily need these supports to help with loose, immediate stools. Ox bile seems to work in half my clients. Beta Plus supports bile production and fat digestion. Beta Plus is recommended when the need for supplemental bile salts is indicated or when the gallbladder has been removed. Consistent loose stools can be a sign. Beta plus supports healthy bile production. Bile serves as a fat emulsifier, allowing fat to become water-soluble and better absorbed.
  • Digestive enzymes work well. We’ve slammed our pancreas with excess insulin production and now cannot produce enough digestive enzymes to break down our foods, especially fats and proteins. There are different types of digestive enzymes, including proteolytic enzymes. These digestive enzymes mimic the ones in your body. And just in case you’re concerned, taking more digestive enzymes or HCl will not shut down your own body’s production of them.


When taken with food, Intenzyme Forte helps to support the inflammatory processes, pathways of protein metabolism, hormone processing, and immune system support. The digestive enzymes support the breakdown of proteins, fats, and carbohydrate digestion. Interestingly, proteolytic enzymes are also an outstanding and highly effective remedy for systemic or localized inflammation and discomfort such as muscle soreness. When taken away from meals, this digestive enzyme support becomes an inflammation and pain reducer for muscle soreness.

  • If you continue to have loose stools, sometimes herbals and fish oils can help with overall liver support. The better liver function you have, the better you can produce bile for fat breakdown and toxin removal. You can also try larger doses of supplemental choline and riboflavin.


Take one at a time and move up to the proper dose slowly. You don’t want to overwhelm the system and you also want to rule out what is helping and what is not helping.


Gut-Support Meat-Based Transition List


Small Intestine

The small intestine houses most of the body’s immune cells. The small intestine is also where most of our nutrients get absorbed. This is why the health of the small intestine is critical.

  • For small intestinal healing, my favorite has been IPS, but it has shellfish so not everyone can take it.


Carnivore Cure goes into much more detail about the cascading and interdependent process that is the digestive system.


I shared healing supports but there are also toxin removal or eradicating supports. I first like to heal the body before attacking the body. This doesn’t hold true for all diseases but for many, it does. One way we support the body with less proliferation of toxins is by sticking to a cleaner diet while we strengthen the body. Attacking first is rarely my modus operandi.


Some general eradicating supports (like antifungals) are oregano oil (which doesn’t usually help with strong imbalances), caprylic acid (MCT Oil, C8), MSM, Saccharomyces boulardii, dill, and garlic.


Large Intestine

If you’re worried about antinutrients, most supplements, unless an extract, have most antinutrients removed.


Most of our research has only been done on the bacteria of the microbiome. We are only beginning to scratch the surface.


Most of the microbiome is in our large intestine, specifically called the cecum. Bacteria, fungi, viruses, and other microscopic living things make up the microorganisms (microbes) of our microbiome. These microbes exist in our intestines and our skin. (Why I’m not a fan of hand sanitizers. You can read my article, here).


Marshmallow root, slippery elm, and licorice root are herbals that can support both the small and large intestines.


Some recommend butyric acid but unless I see butyric acid low on a real stool test, I don’t recommend it as most supplements are made from plant fibers.


Remember, these are general supports, and supports will vary based on sensitivity and individual needs.


Large intestine parts

Image Source: Recording forces exerted on the bowel wall during colonoscopy: In vitro evaluation – Scientific Figure on ResearchGate.



Ah, probiotics. So many strains, so many promises, and so very confusing.


Let me make it really simple.


No one really knows what strains are the best for us. We mapped the human genome, studied populations of people’s guts that are healthy (and sick), and decided what strains are likely good for us.


We just don’t know definitively.


There are people that promise strains, counts and numbers, and different patents and stickers but nothing is for certain. See the example with akkermansia muciniphilia, for example.



Too little Akkermansia muciniphilia has been shown to correlate with obesity but too much akkermansia muciniphilia correlates with multiple sclerosis (MS). And there’s no simple probiotic to take to increase akkermansia muciniphilia. Instead, we are told to consume polyphenols but another study shows that fasting and ketogenic diets (not rich in polyphenols) support akkermansia muciniphilia.


See the dilemma?


I have two clients that both consume meat-based diets and both recently took stool tests. Well, one had moderate to high amounts of akkermansia muciniphilia and the other client had extremely low levels. Both are on the lower weight and within the BMI range.


Clinical life is never the same as research. I try to marry the two but it’s rarely one to one.


We just don’t know what exact probiotics or strains are ideal for the gut, especially for someone that eats a meat-based diet. But generally speaking, there are basic umbrella probiotics (not specific strains, per see) that have shown efficacy in my practice.


What Probiotics to Take

Did you know that most probiotics don’t live and survive in the body? They just work while taking it. Yes, most of the common probiotics only work to support gut healing while taking it. That doesn’t mean they don’t work, they just aren’t forever and why eating a clean diet is critical.


The only probiotic that can live and proliferate in the body is spore (soil-based) probiotics.


The major umbrella probiotics that essentially cover the majority of the strains are:


There is one product listed with prebiotics but half of my clients do not do well with these fibers. So they take the lactobacillus and bifidobacterium without them.


If you’ve taken antibiotics or had traveler’s food poisoning, you may want to try my full probiotic restart kit. It’s a very powerful probiotic kit that has helped many of my clients. My youngest client was 5 months old. These probiotics are safe for infants but make sure to start with smaller doses and introduce them slowly, one by one.



All probiotic supplements and immunoglobulin can be taken without the capsule.


With these probiotics, using a binder or an immunoglobulin can help usher out the endotoxins released from the die-off when the probiotics do their magic. (like lipopolysaccharides (LPS)).


LPS is an endotoxin from the outer membrane of Gram-negative bacteria, found in the portal venous blood and triglyceride-rich, low-density lipoproteins.


I see people throw around the term endotoxins but basically, we take probiotics, they crowd out the bad gut bugs, and when the bad bugs are killed off, they release toxins within the body. Sometimes these toxins are LPS. The binders and IgGs can help the immune system mop up and remove these toxins.


Gut healing protocol list


Closing Thoughts

I’ve shared specific products that have shown efficacy in my hundreds of clients, not because they are 100% the answer.


Gut healing is not just your diet. It’s a large part of healing as we can tame the immune response to food toxins (e.g., plant-based foods). But the truth is that we see people eat some plant-based foods and have decent gut health. Genetics absolutely plays a role in gut health. Some people just win the genetic lottery and can do anything with their health and thrive.


But not all of us.


Not most of us.


But as the study of epigenetics believes that our lifestyle determines what genes are turned on/off, we can play to our strengths. Eating a meat-based diet can do wonders for your gut. Some of you may need to tweak your microbiome bugs and eat favorably to your genes but usually, there are bigger levers to pull.

  • Reducing stress is critical to gut health. If we have chronic stress in the body, it creates chronic, low-dose inflammation. This can be mental stressors, trauma, and even physical stress.


Stress is toxic.


Our immune system is weakened with constant stress.


Our gut is more permeable with constant stress.


Our endocrine health (hormones + thyroid, etc), shuttles most raw materials to produce cortisol. Too much cortisol is never good.

  • Get quality sleep. We need sleep. It’s where our memories get organized (search: sleep spindles) and we detox. We sleep almost 33% of our life. So why do we always push sleep to the last priority?


Exercise and movement have as much power as taking an antidepressant. A meat-based diet is healing but healthy doses of movement make it even better.

  • Focus on strengthening your gut. Your entire body (and mental health) will thank you for it.


Where does my food go after I eat it


You can always start with my gut-healing kit as it has the most general supports to get started on a gut-healing protocol.


Whatever you do, remember to support the gut from north to south. Gut healing can be complicated but I hope I’ve given you the support to make it a bit more digestible (pun intended).



w️ith ♥ and hope for healing,



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DISCLAIMER: The content is for educational purposes only. While I am a nutritional therapy practitioner, I am not providing medical advice. Whenever you start a new diet or protocol, always first consult with your trusted practitioner.

Nutrition with Judy


  • michael rothman md
    March 29, 2024 at 6:56 am

    Judy, the information on your site is world class. I am a medical doctor with more than 30 years of experience, and your site is my go to for much research.

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