Gut issues are at the heart of everything you will be working on when it comes to your health. Your digestive system is vital for taking in the nutrients that you need and eliminating the toxins and byproducts that you don’t. The gut is closely linked to both the nervous and immune systems – like a tripod, if one of those systems goes down the others are going to follow. As I’m not a doctor this post is not designed to diagnose or treat your gut and health issues. What I want to do is bring up some important topics in the areas of gut health and digestive disorders and help you to think a little bit about how these might be related to problems you are experiencing. If your doctor or health practitioner isn’t talking to you about your gut it’s time to find another one.

balance body
A good place to start is a discussion about how MTHFR relates to gut issues. I think that many people come to an awareness of their MTHFR status because they are having health problems. People who feel great don’t tend to rush out and get expensive genetic tests unless they were simply curious and found a cheap way to sequence their genomes. We seek the root causes of our problems because we are having them. So chances are you are reading this because you’re not feeling well and you think you might have a MTHFR gene mutation. Or you know you have one (or more) and are ready to get to the bottom of your accompanying illnesses. Gut issues are at the root of many bodily dysfunctions and it is often advised that one needs to work on the gut before beginning other treatments, including revving up methylation when it’s been stalled by enzyme deficiencies. Quite a few gut issues are genetically linked to MTHFR and, as unaddressed MTHFR gene mutations can stall the body’s detoxification and elimination process, gut issues are prone to follow.

I’ve mentioned the importance of good gut health in previous posts but now I’d like to focus on common disorders of the gastrointestinal (GI) tract, testing and what health professionals are saying about these disorders and how they interact with other MTHFR-related health conditions. If you’re looking for more information about symptoms and treatment just follow the links to more information written by these practitioners. Every one of us is different and is dealing with a different mix of toxins, symptoms and pre-existing conditions. I urge you to find a competent doctor who can evaluate the issues in your particular case and develop a personalized diagnostic and treatment protocol for you. Some of us react well to the generally advised supplements and protocols while others have special circumstances that require more attention and novel treatments. Self-diagnosis and treatment can only get you so far sometimes so please don’t hesitate to seek help if you aren’t getting better.

What GI Issues Might I Have?

Please remember that you can have no symptoms and still have a GI issue. Of course, sometimes the signs of these disorders are very obvious. You might feel sick after you eat or you may have a child with autism spectrum disorders who is demonstrating reactive behaviors. Other disorders present as something other than a GI issue (rashes, neurological symptoms, fatigue, etc). I discussed inflammation recently and some of the major causes of this problem are gut issues, which can sometimes be silent. Some of the most common disorders are irritable bowel syndrome (IBS), Celiac Disease, Crohn’s Disease, GER/GERD, ulcerative colitis, diverticular disease, gastritis, H. pylori, ulcers, candida, parasites, small intestinal bacterial overgrowth (SIBO)/small bowel bacterial overgrowth syndrome (SBBOS) and food sensitivities. Constipation, diarrhea and gas are also common problems but usually have a root cause. All of these issues can lead to the very dangerous situation of leaky gut, which is also caused by toxins, medications and certain foods.

Why Isn’t My Doctor Talking About This?

There are many doctors who will be able to talk to you about GI health and its importance but these tend to be the naturopathic doctors or those who are working with neuroimmune and autoimmune diseases. Our society pays very little attention to the gut. We’re inundated with junk food, chemicals, drugs for digestive (and other) problems and a lack of general understanding about the importance of GI health. Let’s think for a moment about something as simple as the Western toilet. As Dr. Bernard Jensen discusses in Dr. Jensen’s Guide To Better Bowel Care, the modern toilet is an “ergonomic nightmare” (150). If you’ve traveled to Asian countries or even France you may have encountered (and probably shied away from) the squat toilet. Well guess what? Squatting is the most healthful position for elimination. It supports the internal organs in the correct place during the process and prevents problems like hemorrhoids, hernias, varicose veins, ileocecal-valve dysfunction, incomplete elimination and sigmoid strictures. The modern toilet was invented by a watchmaker and improved by a cabinet-maker, not anyone who knew anything about health and medicine (150-154). And yet we are stuck with it. So if we can’t even get this very important aspect of furniture and plumbing correct as a society, what hope do we have of assigning significant importance to problems of the gut?

Gut healing also doesn’t happen overnight. There is no drug you can take or quick-fix you can make to heal your GI system. Perhaps this is why many doctors know or care little about proper gut health. And with our modern diets and lifestyle almost all of us are going to have some degree of GI dysfunction. What you must know and understand is that if you have any hope of completely healing yourself you must address your gut issues.

How Common GI Issues Cause Problems

Aside from the uncomfortable symptoms that those with IBS or chronic constipation or diarrhea are familiar with, GI diseases can lead to inflammation, autoimmune disorders, neuroimmune disorders, cancer and other illnesses. Dr. Jess Armine recently did a presentation on chronic illnesses and the gut and discussed leaky gut in particular. This is a good talk to listen to as he describes the physiology and functions of a normal healthy gut and then goes on to talk about how to assess and repair the damage.

Leaky gut syndrome is getting more and more attention lately. Essentially this means that the lining of your GI tract has holes in it, which allow toxins and molecules that are not broken down properly to “leak” out into the bloodstream. The body then mounts an immune response causing inflammation. Leaky guts also have absorption issues, which means that the person can end up with nutritional deficiencies.  All of this puts stress on the liver and can lead to gut dysbiosis (microbial imbalances). Leaky gut syndrome has been linked to diseases like diabetes, metabolic disorders, depression, anxiety, adrenal fatigue, migraines, addiction, premenstrual syndrome, cardiovascular issues and ADD/ADHD. Dr. Armine notes that if you have a leaky gut you will have issues with the blood brain barrier and leaky mitochondria as well.

I think it’s prudent to assume you have leaky gut as most of us do to some degree. It would require the cleanest of diets and optimal health to avoid problems with the GI tract. The best way to proceed, as always, is to start looking for the root causes of the problem. The good news is that the things that are causing your gut stress are likely also the overlapping causes of other health issues. Our bodies cannot be separated by organ or system because everything works together as a whole. Informed parents of autistic children will likely be very educated about issues of the gut because much of the aggravation caused to the nervous systems of autistic children arises in their guts. Dr. Amy Yasko and Dr. Nancy Mullan explain this very well in this article about gastrointestinal balance and neurotransmitters. I think I have mentioned before that all of us can learn a lot from the research and education around autistic children. Because they are so small and undeveloped, these children unfortunately receive the full effects of systemic imbalances and pathogens. But many adult conditions arise from very similar problems. The difference is that we have fully developed brains and immune systems. So when I refer to literature relating to autistic and spectrum disorder children on this site you can still likely learn a lot from it and much of it will apply to you as well.

In this excellent article, Dr. Tim Jackson describes how hormones can be disrupted by gut dysfunction. This will be of particular interest to thyroid patients and those suffering from weight gain and autoimmune disease. Chemicals, bacteria and stress are all contributors to systemic illness that often starts in the gut.

Causes Of GI Issues and Leaky Gut

The primary causes of gut dysfunction are food intolerances and toxins. Toxins can be either organic (yeast, parasites, bacteria and other pathogens) or inorganic (generally pesticides, chemicals and unnatural additives, preservatives, etc). You’ve probably been wondering why one of the most common recommendations is to go gluten, casein (dairy) and even soy-free. Gluten and casein are the two most common problematic elements because they are large proteins that are difficult for the body to break down. Gliadin is the toxic component of gluten and reactions are very common even for people who don’t have Celiac disease or a known sensitivity. Dr. Armine discusses how the wheat products of today have exponentially higher gluten content than they did in the past as a result of genetic modification. Casein, which is found in dairy products, is also problematic for many people even though they would not call themselves lactose intolerant or allergic to milk. The two most common forms of casein are A1 beta-casein and A2 beta-casein, the former of which is found in Holstein cows and usually more reactive for sensitive guts. This is all explained well in the linked article to the Nourishing Hope website.

Many other forms of food pose a challenge to people, however, and limiting only gluten and casein may not be enough. Hundreds of foods can cause a delayed sensitivity reaction anywhere from four to 24 hours (sometimes even later) after ingesting it. This can make it very tricky to figure out which foods are troubling you. Dr. Kendal Stewart discusses this in his podcasts and also describes how heavy metals can cause food sensitivities and nutritional imbalances by interrupting the functions of minerals in the body. He recommends that people go completely organic in order to prevent the ingestion of toxins and pesticides from one’s diet and to avoid sugar, especially if you have gut dysbiosis. Be sure to avoid processed foods because while those may be gluten-free they can also be loaded with additives, preservatives and sugar. Glutamic acid (more commonly known as MSG) is a powerful stimulant that causes problems for many people as it is hidden in foods and disguised on ingredient labels.

Hormonal and neurotransmitter imbalances can also lead to digestive problems. Low cortisol, for example, can cause you to end up with chronic gut inflammation, hypoglycemia and environmental sensitivities. Mutations in the COMT gene can cause IBS due to too much dopamine. If you’ve begun to explore your personal genome you may already be analyzing some of your single nucleotide polymorphisms (SNPs) and discovering some areas where gut issues and gene mutations overlap. As more and more SNPs are discovered and analyzed we will be learning much more about how our genetics are impacting specific aspects of health.

Stomach acid imbalances are another causal factor and can also lead to gut issues, and the symptoms of high and low stomach acid are very similar. Drugs actually make the situation worse. Most people are familiar with the problems of too much acid such as heartburn, reflux, ulcers and indigestion. But low stomach acid can also cause problems when undigested food leads to an overgrowth of organisms like yeast and bacteria, eventually causing a leaky gut. And if you have SIBO some of the common suggestions for improving digestive health may even cause further inflammation of your gut. So diagnosing health conditions correctly is central to your treatment, which will be discussed in the next section.

Finally, parasites, bacteria and other organisms can wreak havoc on your GI system. I’ve discussed pathogens in another post on viruses and neuroimmune disorders and it’s important to test for those whenever you’re dealing with a nagging health issue. We are all exposed to viruses and bacteria but those with gut and immune dysfunction are more prone to invasion and inflammation from unwelcome pathogens. One important gut-related bacteria to consider is Helicobacter Pylori (H. pylori). This is a very common infection and impacts many systems in the body. It has been tied to vitamin and mineral deficiencies, hormonal imbalance, insulin resistance, fatigue, autoimmune disease and more. I think this post by My Gutsy provides an excellent overview of H. pylori infections with some additional resources.

If you’ve been reading through and listening to the links in this post you might be feeling like the cause and effect relationship between many of these issues seems blurred and even confusing. Unfortunately when dealing with issues of the gut there is often a vicious cycle and gut problems can be very difficult to tackle. Be prepared for a long battle but assured of the victory if you enter it and win.

Testing and Treatment

The first step in your action plan should be to find a starting point, which means working with a knowledgeable health practitioner to determine what your major root cause issues are and working on those in the logical order. I can recommend a few GI tests here that regular doctors may not be aware of but some of them are not covered by all insurance plans. It makes sense to work on things in the correct order so that you don’t make a misstep and cause your symptoms and problems to worsen. Working through them in the right order also ensures the avoidance of some frustrations. For example, the co-host on Dr. Stewart’s podcasts is a mother of an autistic child. When she did the food sensitivity testing her son came up positive for 150 different food allergies. After working on his immune system many of these sensitivities resolved and Dr. Stewart recommended to only commence that testing at a certain point in the treatment protocol. Assessment of your GI issues needs to happen relative to your other health programs and treatments.

If finding a practitioner is proving difficult, or if you just want to become more informed about gut issues and how to figure out what you’re dealing with, this is an excellent and thorough article that goes in-depth on the topic of “How To Fix Your Gut.”

Some helpful tests that I’m aware of are:

Genova Diagnostics/Metametrix DNA Stool Analysis With GI Effects – examines gut bacterial groups, diagnoses potential sensitivities and looks for absorption and inflammation biomarkers along with reliable parasite detection. Useful for diagnosing GI issues.

US Biotek Laboratories Antibody Assessment Panels – provide a comprehensive report on food sensitivities and other allergens that you are reacting to.

ELISA/ACT Biotechnologies offer a variety of tests for common allergens including medications, toxic minerals and metals, foods and other potential toxins.

Cyrex Laboratories offer a variety of tests and arrays that are relevant.

Dr. Stewart recommends simple saliva pH strip testing for affordable ongoing monitoring once you’ve done the initial testing – if your body is acidic you are likely having a flare-up or infection.


Jensen, B. (1999) Dr. Jensen’s Guide To Better Bowel Care. New York, NY: Avery.

10 thoughts on “Things That Plague Us: Gut Issues

  1. Loei

    Great website! Ok, so my questions is have you healed your self and your gut. And where would I find a doctor who would work with me that I can afford? Because I know I have gut issues. And have high sulfur in my urine.


  2. jenny hurrion

    Hi Andrea, I have just been diagnosed with mthfr (2 bad genes) feeling very confused about it all at the moment but really want to do what I can to improve my health.
    I am in my early 50’s & was feeling very sore in my neck & shoulders, (inflammation) my Dr did some blood tests& the results weren’t good. She has told me to try a gluten/dairy free diet, trying the gluten free but don’t think I can go completely dairy free, does it matter if I occasionally eat gluten?
    I also have to stay away from anything containing synthetic folic acid, does this mean that all flours, rice pasta & bread contain it? Do you have a list of foods which can replace any of these?
    I am reading your blog, it is helping me to understand a lot better. Thankyou .


    1. Andrea Post author

      Hi Jenny – I would certainly try to eliminate all gluten and dairy if that is what your doctor recommends. Everyone is different. The only way to know if you have intolerance to the proteins in gluten and dairy (casein) is to get specific testing for food sensitivities. Most conventional flours and foods containing them will be enriched with folic acid, yes. You can find unenriched flour in both gluten and gluten-free varieties at places like Whole Foods. There are all kinds of substitute flours and pastas, etc you can try, brown rice pasta, unenriched flour, gluten free flour blends etc. Check out the special diets section of your supermarket. Good luck!


  3. Kelly

    I’m sorry, but I found this to be disappointing. I thought there would be more discussion of how the MTHFR polymorphism relates to gut issues…


    1. Andrea Post author

      Well, sorry to disappoint you, Kelly – I’m not a primary researcher so I can only work with the information that is out there and I couldn’t find any direct studies. All of this research is very new. If you find something please do be so kind as to post it here so others can learn. Thanks so much for your feedback!


  4. Krista

    This is just fantastic, Andrea, and echoes much of what my doctors are saying. I have most of the symptoms you described and it’s only been through addressing gut issues that I’ve found any relief. The medications just made me worse. I’m so glad to be in this place now with the hope of getting and feeling better. 🙂


  5. mamaglee

    What a fabulous post Andrea. Thank you for all the details and links to further info and tests. Just discovered I have the MTHFR gene from both parents the one with the 6 in it. Am working with a functional medicine doctor. The testing takes a long time. Adrenals shot, thyroid not functioning properly, parasite, high blood pressure, excess bloat and weight, depression, cancer survivor, sensitive to chemicals, etc. I’m also doing brain retraining which helps a lot. Much gratitude for all you do and share. Sincerely, Mamaglee


    1. Andrea Post author

      Ugh, yes the testing does take awhile. But it sounds like your doctor is being very thorough, which is wonderful. Best wishes for a speedy recovery and thank you so much for your very kind comment! =)


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