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How to Heal Your Gut: A Complete Guide

In this article you will learn:

  • Practically everything there is to learn about healing your gut

  • What the research says for common digestive problems

  • How to listen to your gut (literally) and heal so you can poop like a deity

The Details:

In this article we will review all of the priorities for healing your digestive center. In the words of the famous Dr. Bernard Jensen, Father of Colonics: “Death begins in the colon.” What this morbid quote also means is that life begins in the colon, too. This is why healing your center should be your first health priority. Use the following points along with your functional medicine doctor (or team) to develop a specific action plan that addresses your particular needs and your gut will thank you for many years to come.

Get an idea of your stomach acid levels.

The best way to do this is through a Heidelberg stomach acid test, but if you can’t find anyone in your area or it’s too expensive there are other means, although they aren’t as accurate (like the baking soda test) and may be inconclusive. There is a theory that blood type associates with stomach acid levels, with A being the weakest and O being the strongest. Observe how you react after heavy amounts of protein and fat and notice what foods, if any, cause you upset.

Get screened for irritants to your digestive tract so you understand what to avoid.

A food allergy panel is a basic start, but companies like Vibrant Wellness offer in-depth tests on wheat, dairy, seafood and lectins that all serve as valuable tools to inform you of any problem areas. If you have a moderate reaction to these foods, limit them or find a way to process them down so that you can minimize inflammation. For

example, removing the seeds of tomatoes or cooking them if you react to tomato

lectin. If you have a high reaction, even though it’s not an allergy, I would remove this

food and find a substitution. Personally, I would limit or eliminate wheat regardless

and limit your dairy intake to just grass-fed butter, ghee and healthy protein options

like kefir or grass-fed whey.

Establish a baseline of your gut health with a stool test.

Make sure that it gives you comprehensive data on the population breakdown of your microbiome, the inflammatory markers in your gut, whether you have parasites and other important pieces of information. Again, Vibrant Wellness has a Gut Zoomer that is incredibly thorough, but there are other brands out there that provide quality testing. Once you have your baseline, tweak your eating and supplementation accordingly and retest in 6 months or sooner (depending on how bad your initial baseline was) to see the difference.

Based on what you find in your first stool test, you will customize your eating and

nutrition protocols for the next go around. A good test that’s worth the money (like

the Gut Zoomer) will give you a detailed breakdown of your gut microbiome and

levels of inflammation and other important chemicals like pancreatic enzymes, short

chain fatty acids, whether you have undigested types of food, what type of bad

bacteria is growing out of control and so on. Sometimes, even with taking probiotics,

you may have certain specific strains that are low. This is normal because your gut is a

constantly evolving environment that is responsive to what you eat, do and put in

your body.

In these cases, see if you can find them in isolated supplements online or buy

something that has a high dose of those particular bacteria. I don’t eat dairy, and

occasionally I had to get probiotics containing specific strains found only in yogurt or

kefir, like lactobacillus bulgaricus, because I was deficient in them.

For other types of bacteria that aren’t available in supplement form, diet and lifestyle will be the main way to go about realigning yourself. Remember that high sugar and fat feeds Firmicutes, and soluble fiber (especially beans) feeds Bacteroidetes. While both are

important, you want more of the latter (Bacteroidetes type) because they support a healthy metabolism.

What I also like about the Gut Zoomer is that Vibrant will provide you with health

conditions that the bacteria in your gut are related to. Based on which bad ones are

out of control or which deficiencies you have in the good ones, you’ll know what

trends your gut is taking you toward and how to intervene appropriately.

Include some gut-supporting supplements into your routine.

I take a comprehensive digestive enzyme supplement to help break down my food along with the occasional betaine HCL with large meals since my stomach acid is naturally lower. If you take betaine HCL, make sure to dose it correctly and monitor yourself over time. Generally, you can start with 1000-2000mg and see how that feels. If you have a burning sensation in your stomach, drop down by one pill and try again. It is best to take this supplement halfway between meals or right after, as doing so beforehand may irritate your stomach or reduce the natural

acid it produces in response to food stimulus.

Besides these supplements, I also take probiotics, butyrate, lactoferrin and boswellia

to reduce inflammation in the gut and promote a strong microbiome. The OHS

supplement Opti GI is a light cleanse and also great for restoring the gut lining. You

can take it with meals or on an empty stomach morning and evening. I may also bring

in the powerful proteolytic enzyme supplement Optimal Acute in the morning and evening along with bromelain on an empty stomach to help clear away any biofilm present in my intestines, although be aware that bromelain may aggravate stomach ulcers so use it responsibly.

Most people aren't aware about the issues with biofilm, but digestive enzymes on an empty stomach are a good hack for it. Film develops on surface areas as a way for bacteria to do their thing. Your teeth and gums have biofilm, and it's a good thing, but if it gets too hard that turns into tartar and plaque which brings disease. The good bacteria in your gut is the same. It constantly fights against bad bacteria, and if you have had a history of gut imbalance then chance is you may have some unwanted biofilm that needs to be cleared. Excess biofilm from the bad guys can create problems with absorbing nutrients and inflammation, because it protects the bacteria from your immune system. Think of it like a little fort, a fort that you don't want in this case.

Some additional supplements to consider that are all research-based interventions

for treating inflammation, ulcers, gastritis and dysbiosis are:

  • The herb, forskolin, can stimulate stomach acid production significantly.(1)

  • Boron, or more specifically boric acid, has anti-ulcerative effects.(2)

  • Chamomile has been studied for its potential anti-ulcerative and anti-inflammatory properties on gut tissue.(3)

  • “Vitamin U” or methylmethionine, sourced from cabbage juice, is a great option for gastritis.(4)

  • Deglycyrrhizinated licorice (try saying that 3 times fast) is excellent for gastritis.(5)

  • Marshmallow root(6) and slippery elm(7) are also non-toxic, highly beneficial natural foods that heal the soft tissues in your body and digestive system and can be used long-term

  • Gamma oryzanol, a compound from rice bran oil, has shown great promise at treating ulcers and gastritis.(8)

  • Collagen protein can work to heal the tissues in your digestive system because it is high in certain types of protein like glycine and proline.(9,10)

  • Besides collagen protein powder, another great source for these healing benefits is high-quality bone broth. If you do get bone broth, make sure it is grass fed and has a high protein content per cup. Anything less than 10 grams just means it’s low quality despite the marketing claims. Bone broth needs to be thick, which means it is rich in proteins and nutrients for your gut, not to mention your tastebuds. Also, make sure it's from beef.

  • Chondroitin sulfate, hyaluronic acid, MSM (methylsulfonylmethane) and glucosamine, which are all-natural compounds primarily researched for joint health, have also been shown to help with gastritis and gut inflammation. (11,12,13) This product has all 3 and some more great stuff.

  • Finally, glutamine, oregano oil, ginger, NAC and aloe vera are some other great natural tools for healing your digestive system from inflammation, along with the eating principles outlined previously.

It’s important to know here that gastritis, which is inflammation of the stomach or

digestive tract, can be brought on by several factors. In general, the main ones are:

autoimmune (which leads to atrophic gastritis and eventually B12 deficiency because

your stomach can’t process B12 anymore), infection from the bacteria H. pylori,

bacterial overgrowth (like SIBO) or environmental factors like excess alcohol, chronic

use of NSAIDS or exposure to toxins.

Finally, a deficiency in vitamin B5 may lead to similar digestive complaints such as loss of appetite and stomach pain. Why all of this is important is it determines how you will proceed. For example, an inflamed stomach caused by H. pylori infection means you have to reduce your stomach acid levels temporarily (because this bacteria is acid resistant) and probably take antibiotics.

If, on the other hand, your stomach is getting irritated because of SIBO, this means you don’t have enough stomach acid and need to increase it by using betaine HCL and other tools to push the critters back down.

Some compounds irritate ulcers, like bromelain (which can stimulate bleeding) and certain foods should be avoided depending on what flavor of bullshit you’re dealing with. Finally, everyone’s tolerance and genes are different, meaning that other things listed here may cause you problems even though they’re fine for most people. Always do your research and know what variables are involved so that you know what to rule out and not go crazy trying to find the culprit.

Drink plenty of water, eat plenty of fiber and supplement with magnesium.

I recommend taking an extra 4-8 grams per day of psyllium husks to give your colon

lots of love and regularity. There are many great things about psyllium compared to

other sources of fiber and it’s just one of those easy and cheap interventions that has

an extremely skewed benefit to risk profile. It’s adaptive for both diarrhea or

constipation, has protective effects on your colon and it doesn’t ferment in your gut

like most prebiotic fibers.

This means that if you’re struggling with IBS, SIBO or a similar issue, getting the benefits of psyllium is still possible. Along with water and a quality chelated magnesium supplement, these simple strategies will lube you up on the inside and allow for Circulation to move things through you efficiently. If you’re going 2-3 times per day, your body is running like a Swiss clock and able to process food and detoxify easily.

Incorporate fasting as a way to heal your digestive system and let it reboot.

This can be a period of intermittent fasting, trying a water fast for 24-48 hours or doing a "done for you program" like the ProLon fasting program. All of these methods trigger the body’s healing mechanisms and give much needed rest to your colon.

Be mindful however that if you have stomach inflammation or ulcers, fasting may not be as useful since it leads to a gnawing stomach and potentially worsens the gastritis or ulcer. As always, consider all the variables and options available to you and customize your approach.

Beware of antibiotics.

Anytime you take an antibiotic, go on a “flora blitz” session

immediately afterward. I use this product after a round of antibiotics. Pump your body with these extra probiotics for a few weeks or so after the antibiotic to re-balance the system before opportunistic organisms like bad bacteria or Candida can take over.

Get a Squatty Potty or similar device so that you can poop like a true deity.

These simple tools allow you to assume the natural squatting position which in turn aligns your colon and puts less stress on the muscles down there for full evacuation with no residual. The result? If you’re following all of the principles laid out so far you will go so clean that you’ll hardly even have to wipe. No bullshit.

Tap into your gut...literally.

By gently tapping your belly button with one finger, you can stimulate blood flow into the digestive space and help move things along if you are feeling constipated or slow. This, along with your Squatty Potty, supplements and great eating habits are your weapons against almost any digestive woes for years to come.

Watch your fiber intake.

Today everyone is all about fiber, but too much can lead to overly large stools which can create serious problems with your behind - like anal fissures and irritated hemorrhoids. The perfect stool is soft and comes out effortlessly, so listen to your body as you improve your diet and also supplement with magnesium and other things. It's about finding the sweet spot, but ultimately always keep your stools soft to avoid any problems down there because prevention is the best medicine.

Invest in a professional who can do visceral mobilization techniques to straighten out the alignment of your organs and gut.

This can be a highly trained chiropractor or DO, an acupuncturist or a massage therapist who can do myofascial release. Structurally, the organs in your body are meant to move around but tension, lack of exercise, nutritional deficiencies, dehydration, internal misalignments and many other factors can affect their position and tone.

One simple example is your diaphragm. Although its main role is to help you breathe,

tension in your diaphragm can also upset the Alignment of your stomach and

contribute to pain in other areas of your body. This is because the fascia (the

connecting structure in between all your organs and muscles) distributes tension and

bears the burden.

It’s painful to release the diaphragm, because you have to get deep into your abdominal cavity, and only a trained professional should do this for you. Yet after it’s done, you’ll not only feel like you can breathe deeper, but your internal organs will shift back to their optimal arrangement and function better as a result.

Another example of alignment that is significant for digestive issues is the ileocecal valve. This is the gate between your small intestine and large intestine, and it’s

located about halfway between your hip bone and your belly button. Normally this is a

one-way street for food to go into your large intestines for further processing, but

various things can cause this valve to spasm or have a hard time opening or closing.

This is collectively referred to as “ileocecal valve syndrome” in the alternative community, although it is not recognized in modern healthcare. If your valve is closed and has a hard time opening, you will be constipated. For most people though, the valve is too open and this makes it easier for food to wash back up into your small intestine leading to bacterial overgrowth, toxins in your body and many negative long-term health effects.

It’s suspected that a malfunctioning ileocecal valve may be implicated in all kinds of symptoms like allergies, fibromyalgia, bad breath, indigestion, increased body odor, heart palpitations, irritable bowel issues, liver problems and migraines. It makes sense considering what we know about toxins and the digestive system, and it’s an often overlooked, but very important, area for healing your center.

Many things can contribute to an open or spasmed valve, but it’s just the usual

offenders that you already know about like toxins; parasites; having low stomach acid

(stomach acid triggers it to open and close); stress, which also disables its movement

and your stomach acid; antacids; inflammation in the gut; eating inflammatory foods;

not drinking enough water; not chewing your food properly and so on.

If your valve is closed, following a complete nutrition program will help it relax. Investing in your ability to relax in general will also help with your digestion. If your valve is open,

following the principles in this article will help you get it back in alignment.

First you have to eliminate stimulants and inflaming foods because they force your

colon to spasm or move faster. Snacking constantly will keep food moving through

your colon and not help the valve close and heal, so focus on a good diet, use the

products listed above to reduce inflammation and digest your food and stay

hydrated. Reducing your stress in either case is important, which is why eating

mindfully is one of the key principles I always emphasize.

When you are stressed, the signals interrupt the movement of your colon and valve, which can result in misalignments. This is why treating your emotional wounds and aligning your mind is another important step in the healing process.

Besides these good practices, working with an experienced professional who

understands the importance of organ alignment or how to massage the ileocecal

valve can be a priceless asset to your recovery.

Everyone’s considerations are different.

If you have a condition like SIBO, IBD, IBS, Crohn’s, ulcerative colitis, H. pylori infection or you’ve had your gallbladder removed, there’s still hope and ways to integrate diet, supplementation and mindset to heal your center for optimal health.

For people with inflammatory diseases, the focus should be on minimizing the inflammation by understanding what foods your body reacts to and supporting the colon with therapies and supplements that promote healing like we discussed previously.

If you have SIBO, or any similar derivative where something undesirable has

outgrown (like Candida or H. pylori), it will be a multidimensional dance between

several strategies. For general bacterial overgrowth, taking things like betaine HCL,

digestive bitters or forskolin will help to inhibit the upward crawl of bugs that aren’t

supposed to be in your small intestine by increasing stomach acid, as most of the time

SIBO-type issues are related to low stomach acid. Chewing your food mindfully is also

important, and you may have to spend a few weeks reducing foods that ferment

easily in the gut. This is called a “low FODMAP” diet, and while not something to do

for an extended period of time, it can help to take the pressure off and skew the

balance in your favor until things are more manageable.

Be careful with some gluten free alternatives as they use potato, pea or tapioca

starch. These will make you blow up if you have SIBO and it’s best to avoid them

altogether. Avoid prebiotic fiber supplements, but use a diverse array of probiotics in

the morning before you eat and in the evening 2 hours after your last meal. This will

help deliver reinforcements into your intestines and reshape your gut microbiome.

While you eat, the betaine HCL and digestive enzymes will ensure that your food is

properly digested and least likely to create more fermentation and overgrowth.

Adding the supplements mentioned previously along with your probiotics in the morning and evening will help to fortify your efforts during fasting hours for a comprehensive attack.

If you have an H. pylori infection or overgrowth, this too can be a tricky dance.

Common therapy is to take a few antibiotics at a time, along with a stomach acid

reducing medicine, so that you have the greatest chance of killing the bacteria and

letting your ulcer heal. Many people with an infection don’t have ulcers, and if you

have a history of stomach cancer in your family this is something to try to resolve as

quickly as possible.

Some natural treatments that may help with this are taking lactoferrin, proteolytic enzymes, probiotics, high-quality manuka honey and even UV light therapy in your stomach. If you do a course of antibiotics and stomach acid reducing medicine, make sure to blitz your gut with a ton of probiotics once you’re done so that you don’t have

overgrowth of other bad actors.

A detailed stool test will give you a clear picture of how you are doing in this area, how

your therapies are working and whether or not you have a particular issue. I like

Vibrant’s Gut Zoomer because it is exceptionally thorough and can give you many

points of specific action in an otherwise very murky problem. Remember, getting rid

of SIBO or any overgrowth is a pain in the ass because it’s not something that

happens quickly. It is a measure of your patience, habits and discipline.

It’s like there are two huge armies fighting an epic war inside your gut for domination (think Lord of the Rings but microscopically), and even though you are the terrain, you can’t intervene directly. You have to consistently support the good guys and be patient.

Even with everything I’ve shared with you, a full recovery from SIBO can take at least

a year or more of consistent habits, testing and targeted supplementation, with some

estimates being as high as 4 or 5 years.

Another common cause of digestive concerns are stomach acid reducing

medications. Unfortunately, most of the time this is a result of a misdiagnosis and will

only lead to more problems. There are many causes of heartburn and it’s not a sure sign that you have too much stomach acid, but likely the opposite. By having lower stomach acid, you digest your food poorly, which leads to gas and pressure on your esophagus or an overproduction of acid, which then burns the lower esophageal sphincter (LES) and gives you the sensation that acid is refluxing.

Therapy in these cases has to focus on digesting the food and reducing inflammation.

Acid inhibiting drugs are terrible for your body, as was plainly evident with the class

action lawsuit against Zantac. At the very least, they are further reducing your ability

to digest food for the long term. This only exacerbates your potential to develop

SIBO, nutritional deficiencies and other problems down the road.

Most mainstream doctors will not even bother with a Heidelberg acid test or consider the value of digestive enzymes, but will quickly prescribe you a stomach acid inhibitor instead. The products referenced here will help you break your food down and get

off of those pointless drugs, and a complete nutrition program alongside a mindful

diet will in general help remedy the situation.

My mother suffered for years with heartburn and was put on acid lowering medication, even though I insisted she probably had low stomach acid given what I know about myself as well as her own history and blood type. After finally convincing her to see a functional medicine doctor, take on some of the protocols laid out in this chapter and look for natural remedies, the problem went away easily and painlessly.

Besides misdiagnosed low stomach acid, yet another unfortunately common issue is

whether you’ve had your gallbladder removed. About 500,000 people get this done

every year and as a result lose a lifetime of support to process fats in their food. In

these cases, it is critical to help the liver, otherwise inflammation and bacterial

dysbiosis are sure to happen.

A relatively new supplement called TUDCA (tauroursodeoxycholic acid) has shown growing positive evidence as a safe and powerful way to support bile production in people without a gallbladder.(14,15) You can take a 250mg pill before your large meals and see how you feel.

OHS also has this great product with supporting herbs like dandelion, barberry and milk thistle, along with extra lipase (fat digesting enzyme) and chelated minerals for a comprehensive support formula for your liver. This is a great formula to use in the previous case of having heartburn from low stomach acid or a weakened LES.

Nevertheless, regardless if you have had your gallbladder taken out or not, if you are recovering from years of Burnout and poor diet or trying to lose weight, processing your food better is one of the key areas to focus on for recovery.


















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Disclaimer & Disclosure:

The information presented on this blog is not intended to treat, diagnose, or cure any disease or ailment. These statements have not been reviewed by the FDA and are not written by a licensed medical professional. Please consult your doctor before using any supplements or beginning any new health regimen, especially if you have any medical conditions. Furthermore, this blog may contain affiliate links to various products. Everything is vetted and tested by me thoroughly before recommendation, but in certain cases I may receive a commission if you purchase through the link. 

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