🤹‍♂️ Health goals slipping through your fingers? Get back on track with 1:1 health coaching
Printer icon

You And Your Gut Flora

Gut flora
The goal of this article is to tackle gut and gut flora problems and what to do about it. Granted, following a Paleo diet will often provide great relief for whatever ailment you’re dealing with. Also, other than being very strict with the diet, complete elimination of dairy, egg whites, nightshade vegetables, nuts and seeds and limiting fruit intake should be a priority, as discussed in our articles about dealing with autoimmune diseases and about the benefits of egg yolks.

With all these tactics implemented though, some problems related to the gut often still persist and can prove to be a real challenge to deal with. This article will dig deeper into the subject and will recommend a general strategy to cope with many gut and gut flora issues. Note that each problem usually also requires a special approach, but the general ideas discussed here usually apply broadly.

Here is a summary of the subjects discussed here:

Note that in case of a hard to treat condition, I would tackle the problem with a shotgun approach. This basically means that I would eliminate any possible offending foods at the same time as I would try and maximize my immune system strength, gut healing and good flora rebuilding. Forgetting a step or doing things only partially often leads to poor results unfortunately. I’ve been dealing with tough problems myself and it sometimes seems that even the stars have to be aligned to start seeing progress, so hang in there and do everything possible to regain health as soon as possible so you can laugh about it afterwards.

The importance and many functions of the gut and gut flora

Your body is the host to over 100 trillion bacteria, most of them in your gut and you have way, way more bacteria in your body than human cells. In this sense, we could say that we are more bacteria than human.

The gut is the principal area of your body where exchanges are made between you and the exterior world and where nutrient uptake takes place. Consequently, the gut is also the major area of contact with toxins and pathogens.

Since most diseases start in the gut, the present subject is extremely important to overall health. Our body understands the major role of the gut on our health and concentrates over 70% of our immune system in it.

Our gut bacteria is so intrinsically related to the health of the gut that we cannot talk of gut health without focusing on having a healthy gut flora.

Upset StomachThere are many things that can go wrong with the gut and gut flora that can manifest in the gut itself, but also elsewhere. Some of the most well known gut problems are IBD (inflammatory bowel disease), IBS (irritable bowel syndrome), GERD (gastroesophageal reflux disease), Crohn’s disease, ulcerative colitis, celiac disease and SIBO (small intestinal bacterial overgrowth). On the opposite side, autism and schizophrenia are two mental disorders that have strong ties to gut flora problems.

For their part, autoimmune diseases first start with damage done to the tight junctions at the epithelial cell level in the gut, which inevitably leads to a leaky gut, which itself permits foreign proteins to enter the bloodstream. The body then manufactures antibodies against those foreign proteins, but the problem is that some of those proteins often mimic proteins already present in the body, like in the thyroid gland or the pancreas for example. This mimicry, coupled with the newly formed antibodies, makes the body attack its own tissues. In the case of the thyroid, we’re talking about Hashimoto’s thyroiditis or Grave’s disease and in the case of the pancreas it’s type 1 diabetes.

Finally, inflammation that starts in the gut often leads to inflammation elsewhere in the body like the joints or arteries.

You can see that maintaining a healthy gut is of much importance for the prevention and healing of many ailments and for general well-being. In maintaining a healthy gut and immune system, the gut flora has many functions, namely:

  • Proper nutrient uptake
  • Protection against pathogens, viruses and opportunistic bacteria
  • Nutrient creation (e.g.: Biotin, vitamin K2, butyric acid, …)
  • Preventing systemic and gut inflammation
  • Proper metabolism and weight regulation

Here are some pointers at what leads to a disruption of the gut flora:

  • NSAIDs (Non-steroidal anti-inflammatory drugs)
  • Antibiotics
  • Birth control pill
  • Food toxins mostly from grains and legumes
  • Excess carbohydrate and fructose consumption
  • Inflammation from excess total polyunsaturated and omega-6 fat consumption
  • Infections
  • Chronic stress
  • Lack of sleep
  • Improper nutrient intake and deficiency in some critical vitamins and minerals
  • Weak immune system (often caused by all of the above)

Grey zone food groups to eliminate

The possible problems caused by vegetables of the nightshade family, nuts and seeds, fruits, dairy and egg whites have already been discussed in my article on dealing with autoimmune and digestive problems as well as my article about egg yolks, but a reminder is always in order. In short, in dealing with a gut or gut flora ailment, you should eliminate all these items for a while. When reintegrating them, the best way to do it is one by one to be able to tell if one of them causes problems.


Vegetables of the nightshade family include eggplants, tomatoes, peppers and potatoes. Tobacco is also part of the nightshade family. Those newly introduced plants to human consumption, anthropologically speaking, contain glycoalkaloids, which are compounds capable of damaging the integrity of the gut barrier and further exacerbating inflammation and a leaky gut. Otherwise perfectly healthy and nutritious, those vegetables should be eliminated from your diet when dealing with gut issues.

Nuts and seeds

Even though nuts and seeds were available to our fellow ancestors, they can still cause problems in today’s already damaged guts and immune systems. Even healthy people should eat nuts and seeds in moderation. After all, caveman would gather a few here and there a few times per year, not eat a whole jar of butter made from them. Most contain levels of phytic acid, which bind nutrients and make them unavailable, further exacerbating malabsorption and malnutrition already caused by the gut ailment.

Granted, the phytic acid levels in nuts and seeds are much lower than in most grains, but it’s still there nonetheless. The second point to keep in mind with nuts and seeds is their high polyunsaturated fat (PUFA) content, especially omega-6 fats. Remember that PUFAs are fragile fats that oxidize and become rancid easily, further exacerbating free radical damage and inflammation in our bodies. Furthermore, a high ratio of omega-6 to omega-3 fat is calling for trouble. Strive for a very low total PUFA content in your diet by eliminating nuts and seeds, all vegetable oils except coconut and olive oil and by eating grass-fed and pastured animals. Keep a good omega-3 to omega-6 balance by eating wild fatty fish like salmon and sardines frequently.


While fruits are found in nature, contain essential nutrients and are made by plants and trees to actually be eaten so the seeds can be spread, the story is not as pretty as most fruitarians would like you to believe.

First, most fruits widely available today are bred for a higher and higher sugar content, at the detriment of vitamins, fiber and antioxidants.

This is not just a random thought that’s spread around Paleo diet circles. A simple trip in the wild will show you that most wild fruits are small, tart and fibrous.

In addition to that, fruits are supposed to be available in limited quantities and only at certain times of the year.

The problem with all that, as it relates to the gut and gut flora is the amount of the sugar fructose in fruits. You probably already know that fructose should be kept to a minimum on a Paleo diet. This is especially important when dealing with issues in the gut. While fructose can’t be metabolized by most cells in the body and is sent to the liver directly, it’s a very good source of food for all the bacteria, fungus, yeast and pathogens in your gut. Fructose, even in small amounts, is like putting gasoline on a fire when your gut flora is already disrupted. Furthermore, fructose will exacerbate oxidative stress to your cells and issues with insulin sensitivities, weakening the immune system even more, which is a really bad idea.

Egg whites

As mentioned in my article on the multiple health benefits of egg yolks, egg whites also contain anti-nutrients and protein inhibitors. They are also a very frequent allergy. The antinutrient avidin binds to biotin and makes it unavailable to the body. This is bad news for people with disrupted gut flora because biotin is normally produced by a healthy flora so a person with an unhealthy flora is almost always already biotin deficient.

Other grey zone food groups

Some dairy products like butter, cheese and yogurt as well as coffee, dark chocolate and alcohol are often sporadically consumed by people following a Paleo diet, but they should all be eliminated as they can all cause problems. Pure butter fat from grass-fed animals is highly beneficial though. It’s called clarified butter and it’s easy to make at home.

Dietary approach to heal the gut and keep a strong immune system to fight the ailment

Healthy digestionWhen dealing with gut and gut flora issues, the situation can easily turn out to be an uphill battle against a vicious cycle. An already leaky and inflamed gut will make it harder to absorb nutrients properly, which will lead to major deficiencies and in turn make it very hard for the gut to heal itself or to soothe the inflammation. You can probably see how this can turn out to be a very bad situation to be in. You’ll therefore have to pay a special attention to getting enough of some critical nutrients in the healing process. Furthermore, some nutrients like calcium and iron should be limited until your gut flora gets in better shape and you’ll see why latter.

Vitamin D

As discussed before, vitamin D is extremely important for proper calcium metabolism and bone structure, but it’s also very important to keep a strong immune system, to suppress autoimmune problems and to produce special antibacterial peptides that help fight off undesired bacteria, fungus and viruses.

In fact, it has even been shown that a deficiency in vitamin D alone can be the cause of the gut flora problem in the first place.

I recommend taking all the natural sunlight you can get as well as eating fatty fish like wild salmon or sardines regularly and probably a supplemental dose of 4,000 or 5,000 IU of vitamin D3 per day for most people.

Vitamin K2

As discussed in my article on the virtues of butter, vitamin K2 is a very important micronutrient and most people are deficient, especially those with a disrupted gut flora because vitamin K2 is normally produced by the gut flora.

Vitamin K2 also prevents against vitamin D toxicity and activates the proteins created by vitamin D and vitamin A for proper utilization of calcium.

Some food sources of vitamin K2 include butter from grass-fed and pastured animals, goose liver, duck liver and egg yolks. Some fermented products like natto and cheeses are also high in the MK-7 form of vitamin K2.


Magnesium is a mineral that’s important for more than 300 enzymes to work properly and is needed for proper digestion and elimination. A magnesium deficiency causes a slower bowel emptying which leads to malabsorption and constipation, and those are all contributing to gut flora problems.

Magnesium is also very important for proper and restorative sleep, vitamin D function and immune system function, three things that you want on your side when trying to heal the gut and rebuild a good gut flora.

Most people’s diets are deficient in magnesium because our soils are now deprived of magnesium and our water supplies are softened, which reduces the magnesium content.

Natural sources high in magnesium include spinach, swiss chard, halibut, chinook salmon and pumpkin seeds. If you decide to go with a supplement, I recommend taking from 200 mg to 500 mg per day in a form like magnesium citrate, chloride or glycinate, which are much better absorbed than the cheaper magnesium oxide form.

Vitamin C and other antioxidants

Vitamin C is a major antioxidant that most mammals produce by themselves and don’t need from external sources, but we lost that ability and need to get it from food.

A lot of people on a Paleo diet will argue that eating a low carbohydrate diet prevents vitamin C deficiency because carbohydrates compete with vitamin C for absorption in the cell, but in a state of disease or infection, simply avoiding a deficiency is not a good idea.

Vitamin C as well as other antioxidants like selenium and vitamin E are very important and used heavily when the body is dealing with an infection or is trying to heal tissues.

Studies have even shown that some infections otherwise very difficult to cure have been cured in record time with high dose vitamin C. It’s likely that our ancestors had access to wild plants that had a very high vitamin C content and getting that much vitamin C from external sources might be a reason why we lost the ability to produce it ourselves.

The rose hip and sea buckthorn fruits are very high in vitamin C, much more than any other citrus fruit or berry. If you decide to supplement, it can prove to be a good idea to choose a buffered vitamin C because vitamin C alone (ascorbic acid) can be quite irritating. I like sodium ascorbate or magnesium ascorbate as sources of supplemental vitamin C. Magnesium ascorbate is a good way to get more magnesium at the same time.

The chief antioxidant of the body though is called glutathione and is produced mainly by the liver. It’s important to help the body maximize its production of glutathione. Vitamin C as well as N-acetylcysteine (NAC) are useful to help the body produce glutathione.


Iodine, a bit like magnesium, is another one of those nutrients that are pretty low in most people’s diets mainly because our soils are so poor in it nowadays, but also because a lot of what surrounds us inhibits its absorption. Some examples are chlorinated water and bromine found in fire retardants in household products, carpets and mattresses.

The problem is even worse for people on a Paleo diet who eliminated refined iodized salt from their diet. This is often the only source of iodine in one’s diet nowadays. A simple solution is to use a natural sea salt combined with seaweed flakes, which should be available at most health food stores.

Iodine deficiency is known for being a major cause of hypothyroidism as the hormones produced by the thyroid gland are composed, in major part, of iodine, but it’s also really important for proper immune function. Hypothyroidism causes a poor immune system, constipation and slows wound and tissue healing so any hypothyroidism state should be well taken care of to achieve success in healing gut flora problems and bowel diseases.

Iodine is also a very potent antifungal, antiviral and antibacterial compound and was used extensively both externally on the skin and internally before antibiotics became popular. In this sense iodine can be part of the direct arsenal against undesired gut pathogens.

One common fear when taking supplemental iodine is the aggravation of an autoimmune disease of the thyroid gland. This is a valid concern and iodine supplementation should be started on a really low dose of about only 1 mg per day and increased very slowly. Furthermore, it’s a good idea to get tested for the presence of thyroid auto-antibodies as well as making sure to be off of any grains or legumes for a few months before taking larger doses of iodine.

The best natural source of iodine is seaweed. If you decide to supplement, I recommend a formulation that includes both iodine and iodide.

Foods that heal

Micronutrients taken individually to prevent deficiencies or to provide a surplus when the body is dealing with ailments is a great idea, but whole foods will always win when it comes to nutrition. Bone broths, egg yolks and organ meats like liver should be an integral part of your diet, especially when dealing with gut problems. Be careful with egg yolks, they’re not always tolerated very well.

The carbohydrate question

There is much debate going on about whether one should consume carbohydrates at all or what type of carbohydrates to consume when dealing with gut flora problems.

Some people will advocate complete carbohydrate avoidance and a near zero-carbohydrate diet, while others recommend at least some amount of carbohydrates to feed glucose to the cells and therefore speed up healing.

Yet again, some, like the proponents of the specific carbohydrate diet (SCD) recommend avoiding all sources of starch, while others recommend just about the opposite to prevent consuming large amounts of the toxic sugar fructose.

While each group brings good points, I think that in the end a universal approach is hard to take and that each problem will need a tailored approach. In other words, you’ll have to experiment for yourself.

A zero-carbohydrate diet is a good way to starve the bad bacteria in your gut, but it will also starve the good ones so you’ll have to play around to find a balance between starving the bad guys and feeding the good guys. There is also the possibility that a long term zero-carbohydrate diet, especially when the body is dealing with pathogens or an infection, could lead to deficiencies or hypothyroidism. Hypothyroidism is a sure way to aggravate gut flora problems. Furthermore, I’ve seen reports of some people having their fungal infections get worse on a zero-carbohydrate diet.

In theory, natural sources of starch like yams, sweet potatoes, cassava and chestnuts should be beneficial because they consist of glucose molecules attached together without any toxic fructose. In practice though, starch can be hard to digest and further aggravate overgrowth of bacteria in the small intestine.

Try it out yourself, reduce your carbohydrate consumption to near zero for a while, then incorporate a limited amount of natural starchy carbohydrates like sweet potatoes or yams for a while. Then try out having some carbohydrates, but only formed of simple sugars like those found in fruits. In this last test, berries and stone fruits like peaches, prunes and apricots have a better glucose to fructose ratio than most other fruits. Monitor how you feel in those three tests and go from there. Also consider cycling through zero-carb periods and periods with limited amounts of carbs.

Biofilms, their role in gut flora problems and how to deal with them

Healing the gutOpportunistic bacteria and pathogens that take over when the gut flora becomes unbalanced create strong mesh-like structures called biofilms where they reside, hide from the immune system, thrive and multiply. Those biofilms are formed with the help of metals like calcium, iron and magnesium as well as carbohydrate structures called polysaccharides. These metal and mucus structures act as a shield and make it very difficult or even impossible to attack the residing intruders with antibiotics or probiotics alone.

Pathogens also have a strong affinity to iron and some pathogens and infectious diseases can be controlled only when deprived of iron. With that said however, iron is a vital constituent to life and to your cells so being in an anemic state is not a good idea. It’s a catch 22. One strategy that might prove to work well is supplementing with lactoferrin or apolactoferrin. Lactoferrin is a protein found in human milk that has antiviral, antibacterial and antifungal properties. It’s present in greater quantity in colostrum, the first food that a newborn gets, so there is reason to believe that it’s really important to the development of a healthy gut flora in infants. Lactoferrin has a strong affinity to iron and binds to it so it can get delivered to the cells instead of being robbed by pathogens to further build their biofilm. The antiviral and antifungal properties of lactoferrin probably come from its iron binding capacity. Apolactoferrin is lactoferrin that has been deprived of iron so it has an even stronger affinity to it. Even if you decide to take lactoferrin, taking iron supplements or going out of your way to get more iron is probably not a good idea. Of course, in most cases, you should continue eating iron-rich liver for the multitude of much needed nutrients it brings.

As for calcium, apart from being a major mineral used in the formation of biofilms, it’s also a competitive inhibitor to magnesium. Most people, especially people with gut and gut flora issues, are greatly deficient in this critical nutrient. Granted, magnesium is also used in biofilms, but it’s just so damn vital that I don’t recommend any magnesium deprivation. In fact, more magnesium could help remove some of the calcium in those biofilms, which is a good thing. As for the dangers of limiting calcium, well, in your healing period your body can make up for it by pulling it out of your bones.

Dealing with biofilms

Of course, other than limiting calcium and iron, you’ll want to implement a strategy to disrupt the structure of the pathogenic biofilms in order for antibacterial and antifungal products as well as probiotics to take effect in eradicating the bad guys.


It has been demonstrated that some enzymes that have the ability to digest fibrin and polysaccharides can help disrupt the strong protective walls that form the biofilms when taken on an empty stomach. Nattokinase, serrapeptase and lumbrokinase are three enzymes that have the ability to digest fibrin. Hemicellulase, cellulase and glucoamylase have the ability to digest the polysaccharide matrix found in biofilms and special formulations like Candex are available to do just that.

Those enzymes should be taken on an empty stomach or else they will simply digest your food instead.

Chelation and EDTA

Once the enzymes start doing their job of breaking open the biofilms, you can consider products that chelate the metal ions and heavy metals often found in those biofilms. One such agent is called EDTA and has the ability to chelate heavy metals such as lead and mercury, but also metals like calcium, magnesium and iron out of your body. This can be both good and bad because you absolutely need to get rid of the metals that form the biofilms, but EDTAs can also further aggravate deficiencies in those minerals. One strategy is to take EDTAs on and off in order to replenish your body in nutrients as best as you can.

I think that a sodium or magnesium based EDTA is a better idea than a calcium based one. One such product that can prove helpful is a magnesium di-potassium EDTA in suppository form called Medicardium.

A gentler way to chelate or get rid of the metals found in biofilms are vinegars and acids like citric acid, which can dissolve or bind those metals.

Antifungal, antiviral and antibacterial substances

Once the enzymes have started eating on the walls of the biofilms and the chelating agents have started removing the heavy metals and minerals from these, it can be a good idea to attack the pathogenic flora that’s now exposed to the world. Two strategies to do this are antifungal and antibacterial agents as well as probiotics. Consult the following section for more on probiotics.

In a lot of cases, taking a antifungal and antibacterial substance is a much better idea than going on a course of antibiotics because there is less chance of experiencing negative side effects or of having pathogens become resistant to them.

Some antifungal or antibacterial agents will be better at dealing with certain kinds of pathogens and alternating between them is a good idea. If you don’t know the specific nature of your problem, you’ll probably have to do a lot of self experimentation with those agents to find the better ones.

Here is a short list of some of the most well known or studied antibacterial, antiviral and antifungal agents: Olive leaf extract, citrus seed extracts, Kolorex (horopito), iodine, bee propolis, Manuka honey, oregano oil, undecenoic acid and caprylic acid. All those are available in health food stores on online.

Herxheimer reaction and dealing with it

One way to know if your probiotics and biofilm disruption efforts are working is to monitor for a Herxheimer reaction, also called die-off. A die-off reaction is a set of negative symptoms that happen when a large portion of detrimental bacteria is being killed all at once and toxic byproducts are being released in your blood. In that case, your detoxifying organs like the liver and kidneys are overloaded with toxins and you can experience a set of symptoms like strong headaches, excess mucus, fatigue, lethargy and flu-like symptoms. You can even really get the flu if the reaction becomes too strong.

In a way, this die-off reaction is good news because it means that bad things are leaving your body, but in reality that reaction can become really hard to deal with.

One way to deal with it is to go more slowly with the biofilm disruption and probiotic approach. When problems are bad enough, it can mean starting with a really small dose of probiotic and increasing very slowly over the course of months.

Another strategy to reduce the load of toxins in your body and to prevent reabsorption of those toxins is to take toxic binders, also often referred to as mopers, that have a strong surface area for toxins to bind to. Two such products are citrus pectin and activated charcoal.

Finally, one last strategy is to take hot baths or saunas in order to sweat and let the toxins leave your body by another important detoxifying organ, the skin. If you go through this route though, care should be taken to consume enough electrolytes like sodium and potassium as they are lost heavily in sweat.

Approach to rebuild a healthy gut flora


To properly heal from a problem originating from a gut flora disruption, it’s not enough to simply eradicate detrimental bacteria, fungus or yeast. Good bacteria should be consumed in large quantities around the same time as the bad bacteria is being eradicated, otherwise the bad bacteria could just grow back and take over again.

It’s important to understand though that our guts are composed of a complex array of thousands of different species of bacteria and that the formulations sold in stores that only contain a few strains of bacteria are not enough to rebalance the gut flora alone. Rather, what they can help with is repositioning the gut in the acidic environment it needs to be able to help the good guys thrive and take control.

Probiotic sauerkrautIt should also be noted that it’s not always black and white and that the good guys can become the bad guys when in an improper environment. In fact, bifidobacterium and acidophilus overgrowth is possible. Saccharomyces boulardii, a normally beneficial yeast, can also cause problems in people with yeast or fungal problems. Kefir, which contains a complex array of normally beneficial bacteria and yeast can also have the same negative effect.

People suffering from SIBO (small bowel bacterial overgrowth), for example, have a problem where too much of the bacteria that normally colonizes the colon has taken place in the small intestine. Self experimentation is one of the choices you have when it comes to the right beneficial bacteria for your specific problems. In that case you have to listen to what your body tells you very carefully. The real way though to know what’s going on in your gut is with a stool test like the Metametrix GI Effects stool test. Such a test can be ordered by your doctor or can be ordered online on a site like Forrest Health, when you’re not lucky enough to have a doctor that’s well-educated on the matter. Also note that such a test can only detect problems happening mostly in the colon, where most of the gut’s bacteria resides, but won’t detect bacterial overgrowth in the small intestine. For this, you would need a lactulose breath test where you ingest a pill of lactulose, an indigestible sugar, and your breath would then be analyzed to find out if an unusual amount of hydrogen gas is produced.

In general, I’ve found that lactobacillus bacteria like acidophilus should be beneficial for most everybody and should probably be the type of bacteria with which you start. Custom Probiotics and GI Pro Health are two places online where you can find formulations containing only acidophilus bacteria.

Otherwise, if you find other strains like bifidobacterium to be helpful as well, some of the better products available out there are VSL#3, a probiotic delivering 450 billion bacterias per dose, as well as Primal Defense and LB17, which contain very hardy strains of a multitude of bacterial species. Care should be taken with those however, especially if you’re not sure of the nature of your gut flora problem. Most people today tend to blame Candida albicans for all their gut flora related problems, but matters are often much more complex and Candida overgrowth is not always the major cause of the problem.

Naturally lacto-fermented food like naturally fermented sauerkraut will contain high amounts of beneficial lactobacillus bacteria and should be taken regularly alongside a supplemental probiotic to help matters even more. The only potential problem is that the acidic and salty nature of those fermented foods can further irritate inflamed digestive tracts.


FOS (Fructooligosaccharide) and inulin are considered prebiotics and are indigestible fibers that are supposed to feed the good bacteria and help it thrive and grow.

Even though I haven’t found any compelling arguments or science against prebiotics, self experimentation has shown me that they can actually be very detrimental and they will also absolutely feed bad bacteria, especially in the case of overgrowth of bacteria in the small intestine.

Care should therefore be taken when trying out prebiotics and they should be discontinued if matters get worse. Some gas and bloating can be expected in the beginning, but you should stop consuming prebiotics if your digestive problems get worse.  Some natural sources of prebiotics are Jerusalem artichokes, chicory root, leeks and onions, with Jerusalem artichokes and chicory root being much better sources than onions or leeks.

Timing of probiotic consumption

If you’re trying to disrupt biofilms and kill off detrimental bacteria with antibacterial substances, you should always keep in mind that those will unfortunately also make life difficult for the beneficial bacteria.

Because of this, care should be taken to take antibacterials away from the probiotic and you should even consider stopping antibacterial agents for a while if you suspect them of blocking the beneficial bacteria and keeping it from taking over.

A word on fecal transplants

The strains of bacteria in our guts are so diversified that sometimes probiotic supplements have a very hard time bringing our flora back to normal.

Fecal transplants are fecal matter of an healthy donor introduced in the colon of a person with a bowel disease in order for the gut bacteria of the donor to colonize the unhealthy gut. This is possible because most of what aids in the formation of stools is bacteria from the colon.

In the case that your gut flora disruption is happening in the colon and not in the small intestine, fecal transplants might be very beneficial. It might sound a bit disgusting, but for those dealing with such problems the disgusting factor rarely matters very much.

I won’t go into too much detail about fecal transplants and I’m not an expert in the matter, but some well informed doctors are now starting to offer it as a way to treat ulcerative colitis or Clostridium difficile infections.

I’ve seen some reports of people healing in an almost miraculous fashion with it, but then again not much information on the ability of fecal transplants to disrupt biofilms is available at the moment.

Possible useful supplements

Here I’ll cover a few of the available supplements known to either help heal the gut, soothe inflammation or help with specific problems that are related to the gut flora. Note that the other possible important supplements like antioxidants, probiotics and natural antifungal and antibacterial herbs were covered in the sections on healing the gut, rebuilding the flora and on dealing with biofilms.

Slippery elm and marshmallow root

Slippery elm and marshmallow root extract are two mucilaginous herbs that have demulcent properties and that can help soothe the digestive tract by providing an extra layer of mucus.

Peppermint oil

Studies have shown that peppermint oil offers help and relief to those suffering from IBS (irritable bowel syndrome).


Glutamine is an amino acid that can be really helpful to heal an inflamed and irritated gut.

Bromelain and turmeric

Bromelain is a natural compound found in pineapples that reduces inflammation and that helps digest protein. Turmeric, a spice used extensively in India, also helps soothe inflammation.

Those two supplements can help soothe inflammation, which should make it easier to absorb nutrients and in turn help heal the gut faster. Bromelain helps absorb nutrients even more because of its protease enzymatic potential. Very fragile and irritated gut barriers can become further irritated by protease enzymes though so go slow and be careful with it.

D-mannose and cranberry extract

If you’re dealing with a urinary tract infection (UTI), see your doctor. However, in preventing further infections or to help get rid of them naturally, cranberry extracts and the sugar d-mannose can be of a really good help. D-mannose is a sugar that doesn’t get metabolized in our bodies, but rather binds to Escherichia coli (E. coli) in the bladder and gets out in the urine. Therefore, if you’re dealing with a UTI caused by E. coli in your bladder, d-mannose can prove very useful.

HCL and pepsin

Most people suffering with GERD (gastroesophageal reflux disease) are not dealing with an overly acidic stomach environment, but rather an under acidic one where bacteria can thrive, ferment food and produce gas that then gets out of the stomach and into the esophagus with some of the stomach’s acid, causing the symptoms of GERD.

If you’re suffering from those problems, it would be a good idea to try to actually increase your stomach’s acidity so your food can be properly digested and bacteria can be killed by the acidity. Supplements with HCL (hydrochloric acid) and pepsin are a good way to do that, but should be discontinued when your own stomach’s acids become normal again. You should take HCL with meals that contain proteins and a good way to figure out the amount needed is to slowly increase the dose by increments over the course of multiple days until you feel a sensation of warmth from taking them and then reducing the dose just under that amount that gave you the warmth.

Don’t take HCL if you have an ulcer, gastritis or an otherwise irritable bowel as it can irritate a stomach that has a disrupted mucus membrane. In that case, you might be dealing with the H. pylori bacteria and the following two supplements might prove helpful.


DGL (deglycyrrhizinated licorice) is a supplement of licorice where the glycyrrhizin, a potentially harmful compound, has been removed. DGL can help soothe inflammation and irritation and has also been shown to be useful in healing ulcers.

Mastic gum

Most ulcers are caused by a bacteria called Helicobacter pylori (H. pylori) and that bacteria can also contribute to a lower acidity of the stomach and heartburn or GERD problems.

It’s believed that more than 50% of the population have H. pylori, but it’s asymptomatic in most cases. When it does become symptomatic, mastic gum, a resin from the Pistacia lentiscus plant, can be very helpful in eradicating it.

Of course, mainstream medicine will prescribe a course of antibiotics when dealing with H. pylori problems, but those aren’t without consequences and can further aggravate other problems, so trying the natural route before is always a good idea.

Probiotics like lactobacillus and bifidobacterium are also helpful in controlling H. pylori.

Putting it all together

In summary to this rather long article, an approach to health and repairing gut flora problems and bowel diseases should be taken on multiple levels.

The first level to take care of is the nutritional one where you avoid any food that can potentially cause problems. This of course includes any grains, legumes or vegetable oils, but also egg whites, fruits, nightshade vegetables, nuts and seeds for most cases.

Then, care should be taken to obtain proper nutrition. Some of the critical nutrients are vitamin D, vitamin K2, magnesium, vitamin C and iodine. Those also happen to be low on most people’s diets, even people following a Paleo diet. Nutritious whole foods like homemade broth, liver and egg yolks should be consumed regularly.

The next step is to try to disrupt bacterial biofilms present in the gut with multiple strategies including avoiding calcium and iron, taking special enzymes on an empty stomach, chelating the minerals and heavy metals that form the biofilm’s structure and taking natural antifungal, antiviral and antibacterial agents.

Finally, it’s important to rebuild a healthy gut flora with an high dose of beneficial bacteria. The right type of bacteria to take will depend on your specific problem, but usually lactobacillus bacteria is a very good starting point.

Photo of Ashley Noël

Hi I’m Ashley, I’m an ADAPT Certified Functional Health Coach

Get coaching around:

  • transitioning to a Paleo diet
  • reaching your fitness goals
  • getting through those hurdles
    • limiting sugar, gluten, carbs
    • eating out
  • overall life satisfaction

I can’t wait to help you make lasting lifestyle changes