Leaky Gut, MTHFR, and How to Fix It

You are here:

Leaky Gut, MTHFR, and How to Fix It

digestive issues, intestinal permeability, food sensitivity testing, dysbiosis, endotoxin, methylation problems
There's no escape from leaky gut – it will affect each of us in some degree at some point in our lives. People with an MTHFR mutation or methylation issues are more likely to experience leaky gut in its more severe form. Here's an overview of how methylation and leaky gut are connected, and how to give your body what it needs to address it.

Dr. Doni Wilson discusses leaky gut, how it makes MTHFR worse, how it affects methylation, and easy steps to recovery.

digestive issues, intestinal permeability, food sensitivity testing, dysbiosis, endotoxin, methylation problemsMore and more, people today are discovering they have an MTHFR mutation (or SNP, single nucleotide polymorphism). However, they are often not told what to do about it – and if they are, the information is frequently incorrect.

That’s why over the past three years, I have developed a 5-step system to help people address MTHFR effectively. And you might be surprised to learn that step 1 includes optimizing your gut health. This is because anything that causes stress to your body will create methylation problems, especially if you have an MTHFR mutation, which already impairs methylation.

Just to recap what I’ve said in previous articles, methylation is the process by which your body converts B-vitamins (folate and B12) into SAM (s-adenosyl methionine). SAM is used in the production and breakdown of neurotransmitters like serotonin and dopamine. SAM is also used to break down histamine and to protect our DNA, and it helps our body make energy. So, SAM affects mood, energy, focus, and immune responses – which is why methylation is so important. For more information, you can read my article about methylation.

To improve methylation, we first need to remove the stresses that are inhibiting methylation. That includes toxins (as discussed in this recent article), and digestive problems such as leaky gut.

Thus, healing your gut is integral to improving methylation and, consequently, bringing your body back to optimal overall health. That is why in this article, I cover:

  1. Methylation and Leaky Gut
  2. How Endotoxins Can Make You Feel Ill
  3. How Endotoxins Can Make MTHFR Worse
  4. What to Do if You Have MTHFR and Leaky Gut
  5. How to Find Out if You Have Leaky Gut
  6. What to Do if You Have Leaky Gut
  7. What’s the Prognosis for People with MTHFR and Leaky Gut?

To heal leaky gut and improve methylation, you also need to address adrenal distress and optimize your stress response.

I’d like to invite YOU to attend a FREE Masterclass about MTHFR. You can sign up and watch it instantly here. In the masterclass, I discuss how addressing leaky gut, stress, adrenal distress, helps you to address MTHFR. You too can learn how to be healthy even though you are exposed to stress and have MTHFR.

Methylation and Leaky Gut

Leaky gut (also called intestinal permeability) is a condition in which the cells that line the intestinal wall are damaged and fail to keep undigested food and bacteria (and the substances bacteria produce) within the intestines, where they belong.

Instead, they can pass through the intestinal lining, where they trigger an immune reaction and cause inflammation, which can travel throughout your body. Toxins produced by bacteria can get into your blood stream, causing a range of other health issues.

Leaky gut is not a case of whether or not you have it – it’s about how severe is it.

When you think about it, there are so many causes of leaky gut, including stress, pesticides, and imbalanced gut bacteriawe will all have some degree of leaky gut at some point in our lives.

So, I encourage you to think of leaky gut as a spectrum, from mild to severe. Many people with leaky gut don’t display any obvious symptoms, while for others, it can be associated with distressing digestive issues.

People with MTHFR SNPs and methylation issues are more likely to experience leaky gut in its more severe form. That is because SAM is needed to make new healthy cells to line the intestines; and a person with MTHFR SNPs is less able to make enough SAM – especially when stressed.

As severity increases, people become more sensitive to the foods they eat. It can reach the point where no matter WHAT you eat, you feel unwell.

You may suffer from:

  • Headaches
  • Bloating
  • Fatigue
  • Congestion
  • Joint and muscle pain
  • Mood fluctuations
  • Decreased memory
  • Autoimmunity – such as Hashimoto’s and Rheumatoid arthritis

As the problem worsens, you may also experience histamine intolerance, which goes beyond basic food sensitivities, leading to allergic reactions like hives. And, because SAM is needed to help break down histamine, MTHFR SNPs also make histamine intolerance more likely.

At this stage, there will also be more severe imbalances in the gut bacteria in the microbiome. That is because the gut bacteria require a healthy gut lining in order to thrive. When leaky gut exists, the gut bacteria have a harder time staying balanced, and the wrong bacteria begin to thrive, creating even more symptoms, such as bloating.

How Endotoxins Can Make You Feel Ill

As gut bacteria get out of balance, they can produce endotoxins. Here’s how it happens:

  • There are trillions of bacteria in the gut, and they need to be in a nice balance, to keep us feeling good and healthy.
  • We feed the bacteria through the foods we eat. For example, fiber feeds our healthy bacteria. Fiber can be found in fruits and vegetables, as well as nuts and seeds. By contrast, sugar and undigested food can overfeed the wrong bacteria.
  • If we are feeding the bacteria the wrong food, or we are taking medications that disturb our bacterial balance, it can increase the level of “wrong” bacteria in the gut. This causes an imbalance (called dysbiosis).
  • These “bad bacteria” expel toxins (called endotoxins). If you have leaky gut, these endotoxins don’t just stay in the gut, but can travel throughout the body, via the bloodstream.
  • These endotoxins won’t necessarily send you to the hospital (like C.diff or salmonella bacteria), but they can cause weight gain, fatigue, and general poor health.

One kind of endotoxin on which many studies have been conducted1 is LPS (lipopolysaccharide), which can cause leaky gut by damaging the intestinal cells. LPS can also get out of the intestines and into your blood stream and nervous system, causing pain (muscle, joint, bladder, head) and “brain fog.”

How Endotoxins Can Make MTHFR Worse

Using LPS as an example, this endotoxin impairs the methylation process by blocking MAT (methionine adenosyl transferase).2

MAT is the enzyme that creates SAM. So, if LPS blocks MAT, you won’t get SAM, which is essential to methylation. inflammation caused by food reactions can also inhibit MAT. Thus, if you have both (inflammation and LPS), MAT will not function well, no matter your genetics.

People with MTHFR already have a genetic tendency to have less SAM. If you throw LPS and inflammation on top of that, it doesn’t matter how much folate or other supplements you take, as they will go nowhere if LPS and inflammation are blocking the process.

What to Do if You Have MTHFR and Leaky Gut

If you have leaky gut, before introducing any kind of methylation support, FIRST you need to address your leaky gut and any endotoxin issues.

If you already started taking folate (commonly recommended to treat MTHFR) and you feel worse (e.g. anxious or you have headaches), you should consider stopping the folate for now, and coming back to it only after you’ve healed the leaky gut issues. Click here to read a previous article on why some MTHFR patients feel worse when they take folate.

How to Find Out if You Have Leaky Gut

Whether or not you have started taking folate, it’s worth working with a practitioner to investigate whether you have leaky gut and/or dysbiosis. The first step is to take a food sensitivity test to determine whether any specific foods are irritating and weakening the intestinal lining.

Next, you need to do a stool test, which will show if there is an imbalance of bacteria in the gut. You will need to work with a practitioner for this. This test needs to include a DNA analysis of the bacteria, not just a culture.

Most mainstream doctors will not do this kind of stool test, so I strongly recommend finding a naturopathic doctor [If you want to work me me in particular, please set up an initial appointment here]. If the results show there are LPS-producing bacteria, I recommend addressing them with herbal approaches and spore-forming probiotics, not antibiotics.

What to Do if You Have Leaky Gut

The two most frequent questions MTHFR patients ask me about leaky gut are:

  • Can leaky gut heal?
  • Can I address leaky gut without medication?

The answer to both questions is YES.

People often worry they will never feel better, since they have felt ill for so long. But when we support your body methodically, you can not only address the leaky gut but also improve methylation within your body.

Below is a summary of the steps to take to heal leaky gut and remove “blocks” to methylation:

  1. First, based on food sensitivity results, change your diet to eliminate foods causing leaky gut – especially gluten – and inflammation.
  2. Then, introduce digestive enzymes such as plant-based pancreatic enzymes.*
  3. Next, introduce nutrients and herbs that help the intestinal cells recover such as in Leaky Gut Support powder.*
  4. Finally, introduce probiotics*, to replenish your gut supply of good bacteria including lactobacillus and bifidobacteria. Here’s a great product in capsule form.

By taking the above steps, and decreasing inflammation and LPS (and other endotoxins), you will make it easier not only for MAT enzyme to function more effectively, but methylation in general.

For more help changing your diet and implementing the process detailed above, you could start by following my 21-day Stress Remedy Program, which includes the products mentioned above.

What’s the Prognosis for People with MTHFR and Leaky Gut?

Very good! Patients often report experiencing better digestion, more energy, mood stability, and greater focus. They also sleep better and have less pain; and for women, fertility often improves by addressing leaky gut and MTHFR.

This makes sense when we realize that gut inflammation inhibits healthy ovary function (the subject of a future article), and pregnancy requires the production of many new healthy cells, all of which requires SAM.

I have also found that when MTHFR patients address their leaky gut issues, they often don’t require additional folate support (or as much as they used to) to optimize their methylation process.

I want you to know that healing is possible. I am confident because I myself recovered from leaky gut and histamine intolerance, and I have MTHFR SNPs.

If I can do it, you can too.

In some cases, it takes months or even years, so try to not get disappointed if it takes some time. The body is made of complex processes that are inter-related. What I can tell you is that things seem to go more smoothly and faster when we start by healing your gut.

Closing Thoughts

I know it can seem that there are so many issues in different parts of your body. My aim is to explain how they are all related, and how by embracing that fact, we can help your body heal faster. We can use the interconnectedness of our bodies to influence positive change. That’s why starting with your gut, with all the connections it has with the rest of your body, is so important.

I hope you found this article useful and informative. If you know anyone else who could benefit from this information, please feel free to share this article. To make sure you don’t miss out on future articles, please subscribe to this blog and you’ll receive a FREE starter guide I wrote about recovering from adrenal distress.

Or you may wish to work directly with me. Because fully addressing MTHFR mutations and methylation can be complicated, especially if you suffer from leaky gut, I have created a consultation and testing package that includes one-to-one appointments with me, health panels to help identify what needs to be addressed in your body, and follow-up sessions so we can make an individualized plan for you.

Here is more information about the MTHFR and Genetic Solutions Package.

Talk with you more soon!

–Dr. Doni
19th October 2017

*Please keep in mind that any and all supplements—nutrients, herbs, enzymes, or other—should be used with caution. My recommendation is that you seek the care of a naturopathic doctor (with a doctorate degree from a federally-accredited program) and that you have a primary care physician or practitioner whom you can contact to help you with individual dosing and protocols. If you ever experience negative symptoms after taking a product, stop taking it immediately and contact your doctor right away.


  1. Guo S, Al-sadi R, Said HM, Ma TY. Lipopolysaccharide causes an increase in intestinal tight junction permeability in vitro and in vivo by inducing enterocyte membrane expression and localization of TLR-4 and CD14. Am J Pathol. 2013;182(2):375-87.
  2. Ko K, Yang H, Noureddin M, et al. Changes in S-adenosylmethionine and GSH homeostasis during endotoxemia in mice. Lab Invest. 2008;88(10):1121-9.
Share this Post:
Master Your Stress, Reset Your Health by Dr. Doni Wilson



Order Now!
More from Dr. Doni

Related Posts

The 5 Burnout Types

Did you know there are 5 burnout types? They are based on your Stress Type®, which is how your adrenal function has been affected by