Have you ever considered that gut bacteria can influence your genes?  That thought might sound strange, but that is exactly what the latest research is showing us.  It is becoming ever more apparent that who and what lives in our gut has a huge influence on our methylation cycle.  The compounds that come from the microorganisms in the gut are known to influence our brain chemistry, hormones, blood sugar, sleep cycle, and much more.  Far from being a quiet neighbor in our gut, the gut microbes have a huge impact on the function and expression of our genes.  You’ll see below that there are three nasty gut-toxins in particular that can really damage the methylation cycle. In a recent post I outlined how our genetic SNPs in the COMT and MAO pathway lead to increased levels of adrenalin, which in turn leads to increases in pain and anxiety.  Anxiety is something we have all felt; but many people are living trapped in a world where they cannot find peace because of constant worry, panic and pain.  And while those genetic variations we carry certainly do influence our perception of pain and our feelings of anxiety, there is another part of the story that needs to be mentioned – the gut origin of anxiety and methylation problems. Again it might not make sense at first glance that gut bacteria can influence our methylation cycle.  But as I pointed out in a post titled MTHFR and the Stress-Gut Connection, we know that gut bacteria also have a methylation cycle.  In other words, that which helps optimize our methylation cycle so we can grow and repair also helps microbes grow and repair. When we take methylation vitamins it is like dumping fertilizer into our gut.  We expect that the fertilizer, the B-vitamins, goes into our bodies but the gut bacteria will eat it first.  When bacteria and yeasts eat our fertilizer first, they grow stronger while we become progressively malnourished.  This is a main reason why people who take vitamins and eat healthy foods still have their symptoms flaring up or aren’t getting better.  It means something in the gut is eating all that fertilizer and making them sick.  A perfect example of this problem can be found by looking at how SIBO impacts our methylation cycle:

  • SIBO causes iron-deficient anemia, low protein and malnutrition in general
  • SIBO makes it hard to gain weight, and slows the growth of children
  • SIBO increases blood folic acid and folate levels, interfering with MTHFR pathways
  • SIBO decreases absorption of B12 and fatty vitamins like A, D, E and K leading to poor methylation and chronic disease

Now obviously SIBO is a more severe form of this problem, but it does illustrate the point.  When the gut is imbalanced and overgrowth with bacteria and yeast, we simply cannot optimize our health or our genes. I don’t want you to get the idea that gut microbes and bacteria can only harm us.  The truth is that without the proper bacteria in our gut we cannot survive.  We absolutely depend on those organism to provide our bodies with nutrients to create health.  So while the microbes and bacteria we are going to discuss are necessary for health, anything that is good can become toxic if it begins to get out of balance.  And this gut imbalance is the driving force behind so many symptoms that make people with methylation issues chronically sick. Remember that the gut consists of a tube that is 26 feet long and about as large as half a tennis court!  Considering we have over 22,000 genes and we have 10 times as many bacteria as we have individual cells, its no surprise that the gut bugs can influence our own cells.  The thing to keep in mind when looking at the gut-methylation connection is that not all genes are created equal.  In other words, some genes are very sensitive to what happens in the gut while others are not.

Methylation genes which are very sensitive to gut problems:

  • COMT – Catechol-o-methyltransferase
  • MAO – Monoamine Oxidase
  • MTR – Methionine Synthase
  • SULT – Phenol Sulfotransferase

As you will see these genes take it on the chin when the gut has gone awry.

Typical Variant Report Showing COMT, MAO, MTR, and SULT SNPs:

MAO and COMT Variants

MTR and SULT Variants

* NOTE: for the genes shown above red or yellow means they are slowed down.

** NOTE: only one SNP needs to be present to impact these genes, although often there are multiple DNA SNPs for a given gene in a single individual.

Not only do gut bacteria product vitamins that we need, they also produce toxins that disturb our methylation cycle and lead to things like anxiety, tension, insomnia, pain, fatigue, and brain fog.  Taking methylation support vitamins can save your life, and we have a long list of patients who have benefited enormously from the right blend of methyl nutrients.  However if your gut is dumping toxins into your body when you take vitamins then it will slow your progress considerably. There are three very important methylation-destroying gut toxins which can increase anxiety, pain, insomnia, brain fog, headaches, and more – phenols, aromatic amino acids, and aldehydes.  That fact alone should make everyone take extra care of their gut.  But when we consider how the bacterial environment in the gut influences our methylation cycle, we can see that gut infections can halt progress in someone who is trying to fix their methylation problems.  Just look at all the different ways bacterial byproducts can impact our methylation cycle:

The Big Three Microbial Byproducts that Impair Methylation:

1) Phenol compounds

Phenols come from plants and bacteria.  Some phenols like resveratrol and green tea catechins are have enormous health benefits.  But because of their similar shape, these and other phenol compounds compete with estrogen and adrenalin/dopamine for metabolism through the COMT pathway; therefore if the imbalanced gut is causing more phenols to leak into the body, it will slow the clearance of estrogen and stress hormones.  This increase of adrenalin/noradrenalin will more pressure on the COMT and MAO systems, two pathways that are genetically slowed in many people.

So if the gut is producing a lot of phenols (during SIBO or other gut infections) then the body cannot detox stress hormones and estrogens very well.  The reasons is that the phenols sit in the same parking space in the COMT enzyme as does adrenalin, dopamine, and estrogen. High phenol levels from the gut can lead to pain, anxiety, insomnia, fatigue, low thyroid, fibroids, endometriosis, weight gain and more just by interferring with the COMT pathway and putting excess pressure on the MAO system.  But that is not all that gut-derived phenols can do.

Phenols are also metabolized through the sulfation pathway and they can lower sulfate levels.  The SULT1A1 and SULT1A2 genes are responsible for taking a toxin, neurotransmitter, bile acid or hormone and gluing it to a molecule of sulfate.  This is the sulftate transfer that is so important to Phase II detox.  All phenols whether they come from the gut or the diet are processed through the SULT pathway.  When phenols are metabolized this way they remove sulfate from the body.  And sulfate is often lacking in people with imbalanced methylation and chronic disease.

Individuals with SULT SNPs have a SLOWED sulfation pathway already, and when phenols from the gut enter the body in high amounts it slow down their phase II sulfation even more.  In this way lots of phenol production from the gut bacteria can greatly impair your detox system increasing sensitivity to smells, foods, chemicals and more.  The phenol connection to methylation is the idea behind the Feingold Diet for the treatment of Autism and other neurological and developmental issues.

2) Aromatic Amino Acids

Aromatic amino acids which are produced by gut bacteria are necessary for proper brain and nervous system function.  You’ve likely heard of the aromatic amino acids – they are tyrosine, phenylalanine and tryptophan.  These are the protein precursors of our dopamine, adrenalin, noradrenalin, serotonin and melatonin neurotransmitters.  These chemical messengers regulate sleep, attention, thinking, and multitudes of other critical processes.  Too much or too little of these amino acids can have a large impact on our brain and our methylation cycle.

While we can get these aromatic amino acids in our diet when we eat protein, the gut microbes also produce these key biomolecules.  Yes, bacteria in the gut produce the amino acids we use to make our neurotransmitters and this is why the gut is often called the “second brain”.  The bacteria use something called the Shikamate pathway to produce tyrosine, phenylalanine and tryptophan – molecules that can heavily influence our nervous system through neurotransmitter production.

If there is an overgrowth of bacteria such as with SIBO and other gut infections then we can predict there will be an excess of adrenalin, dopamine, and serotonin.  The more bacteria we harbor in our bodies, the more aromatic amino acids will be produced.  If we have too much tyrosine/phenylalanine we can end up with too much adrenalin and dopamine.    And so excess gut bacteria can lead to symptoms of overmethylation by way of too much tyrosine, phenylalanine and tryptophan.

However, when we eat GMO foods grown with Round-Up, we can also have our gut become sick and infected.  We now know that the active ingredient glyphosate destroys the Shikamate pathway in bacteria.  Without this pathway working, the good bacteria in our bodies will die off and more aggressive forms will take their place.  An MIT researcher with 170 published papers under her belt has shown the connection between glyphosate and autismHer theory is that as healthy gut bacteria are destroyed by Round-Up, our detoxification system goes awry and our nervous system can malfunction.  You don’t need me to tell you that everyone should avoid GMO foods and eat organic as much as possible.

3) Aldehydes and Alcohol

Yeasts such as Candida produce these are toxic molecules which are similar in shape and function to formaldehyde, a known cancer-causing toxin used in thousands of products.  Aside from DNA damage, aldehydes are known to inhibit the methionine synthase enzyme MTR which is required for the recycling of homocysteine and the production of SAMe.  Another issue with aldehydes is that they are broken down by the exact same enzymes that also break down our neurotransmitters.  And if you have two molecules competing for the same parking space (the same enzyme) then you are going to slow down the breakdown of those molecules, causing symptoms and upsetting the methylation pathways.

When the body has a problem with yeast and aldehydes, it also has a problem with alcohol.  We know that yeasts such as Candida produce alcohol.  And we know that alcohol causes loss of zinc, magnesium and b-vitamins – a common pattern we see with people who have a gut infection.  But the damage doesn’t end there.  The ethanol (alcohol) that Candida produces gets turned into aldehydes inside the body, which can break DNA strands and lead to cancer and cell destruction.

So after the alcohol depletes you of zinc, magnesium, folate, niacin and other b-vitamins, it gets turned into an aldehyde which damage cells and blocks the breakdown of dopamine, serotonin, adrenalin and histamine.  Because aldehydes, histamine, dopamine, serotonin and adrenalin each get metabolized through the aldehyde detox pathway, excess aldehydes causes increased levels of stress hormone and neurotransmitters.  This is a recipe for anxiety, pain, insomnia and more.

As I have shown, gut byproducts that increase the levels of stress hormones – phenols, aromatic amino acids, and aldehydes – will tend to cause anxiety and many other symptoms of overmethylation.  When these stress hormones rise inside the body, people with COMT and MAO SNPs will experience side effects of these powerful hormones.  Since we cannot change our genes, we must change our environment to take the pressure off those genes.  This strategy has been the most promising in treating methylation issues which don’t respond well to b-vitamin therapy. Clearly the issue with gut health and methylation is a complex one, and it can have a huge impact on our health.  It is a fact that our gut microbiom provides us with important nutrients that we otherwise wouldn’t get in our diet.  Yet it is also true that an excess of or the wrong kind of yeast and bacteria can upset our methylation cycle and make us sick.  There is a reason that seasoned practitioners look first at the gut to make sure that is working properly.  If we are getting too many phenols, amino acids, and aldehydes from our gut into our body, you will not be able to optimize methylation by using supplements.  In cases like these you must heal and balance the gut first. Healing the gut is simple, but it takes hard work.  It requires effort, focus, discipline and of course the right advice, supplements and diet.  But it doesn’t have to take a long time.  I have a program that can dramatically change the gut in as little as 10 days.  After helping people all over the country and the world improve their digestion, I can save you time and help you get better results.  If you would like my help in your quest for optimum health and methylation then contact me today! Yours In Health, Dr. Rostenberg By studying the current peer-reviewed research, Dr. Rostenberg has discovered powerful, natural strategies to restore your gut and heal your body.  He can help you uncover the genetic or root causes of your health problem and find a natural solution!  If you would like help with your gut function to improve your methylation and reduce/eliminate your symptoms, please contact Dr. Rostenberg at Red Mountain Natural Medicine today. Phone 208-322-7755. Email Website


  • January 6, 2015 Reply

    Marie Dyer

    I enjoyed your article very much. I am a nurse that works with helping people regain their health in Alberta Canada and I was wondering about working with you to help my clients. Most of my clients are on the lower end of the pay scale but I really agree with your approach. I have never solved a gut issue in 10 days so I feel strongly you can really help me as I personally have these weak methylation genes. Some B vitamins make me sick.
    I am extremely grateful to you for taking the time to share your information in this article.

    Would love to connect with you.
    With gratitude and appreciation,

    • January 18, 2015 Reply

      Dr. Rostenberg

      Hello Marie,

      Thank you for taking time to contact me. My apologies for a slow response we have been dealing with a new website and hiring and training new staff the last couple of weeks. Your comment is important to me and I would also like to connect with you. The gut holds the key to so much of our health and wellness. And when we look at the methylation cycle we can see that it too is greatly influenced by gut dysbiosis. The best way to get in touch is to email my front office at and request a 10 minutes complimentary consult. When we speak just remind me of our exchange here online and we can discuss how we might be able to work together. My office phone is 208-322-7755 if you prefer to speak rather than type. I look forward to speaking with you.

      Yours in Health,

      Dr. Rostenberg

  • January 7, 2015 Reply

    Beth Kuykendall

    I got my genetic genie results back and have some questions regarding those.

    • January 18, 2015 Reply

      Dr. Rostenberg

      Hi Beth,

      Thank you for taking time to contact me. My apologies for a slow response we have been dealing with a new website and hiring and training new staff the last couple of weeks. I help people all over the country and world make sense of their genetic report and find natural solutions to their health problem. I would encourage you to reach out and connect with me. The next step is to contact my front desk at or via phone 208-322-7755. My staff will walk you through the details of how I can help you.

      Yours in Health,

      Dr. Rostenberg

  • March 23, 2015 Reply


    Dr. Rostenberg,

    I really appreciate your insight on healing methylation. I’ve had two big surgeries within past two years that required general anesthesia and rounds of antibiotics. My gut flora has been damaged and I do not have regular bowel movements anymore as I used to. I am extremely interested in 10 day gut recovery protocol. Could you please let me know what I need to do to gut my health back? I would sincerely appreciate your response.

    • March 24, 2015 Reply

      Dr. Rostenberg


      Thank you for taking time to ask your question. Your gut has been through a lot but it can and will get better. I have a safe, powerful and effective 10-day program that I use in my office to help patients dealing with similar issues. I will email you the protocol personally so you can have a chance to read over it. Please let me know if you have any other questions!

      In Health,

      Dr. Rostenberg

  • April 10, 2015 Reply


    I recently had two surgeries which required me to take preventative antibiotics. I did not wish to take them, but was convinced I had to by the surgeons or the surgeries would not be done. I cannot get my gut health back in order ever since. I am at a loss as to what to do. I have been taking my probiotics, drinking kvass, to no avail. I have the C677T heterozygous gene mutation. I also have biopsy diagnosed Celiac disease, so am 100% gluten free, and pretty much grain free. I would very much appreciate your response.

  • June 4, 2015 Reply


    Hello, Dr. Rostenberg!

    So, truly, there is no way for any to eat and take supplements for methylation and mitochondria support and get better without first doing a program with the candibactin? Would it be wise to test for SIBO or gut imbalance first? Thank you!

    • June 5, 2015 Reply

      Dr. Rostenberg

      Hi Shelley,

      When the gut is not healthy and there is an imbalance of bacteria/fungi/virus/parasites, it becomes very difficult to benefit from methylation support. What happens is the gut bugs will eat your vitamins, and then poop out toxins that may make the body even more toxic. This is the reason that individuals with a methylation problem, who also have a gut infection/imbalance, must treat the gut first. By doing the Candibactin and other gut products before methylation support, you increase the odds that the methylation support will be effective.

      In Health,

      Dr. Rostenberg

  • November 15, 2015 Reply

    Jennifer Townsend

    I have overgrowth of E-Coli, and according to my bowel screen, no beneficial bacteria in my gut. I have had gall bladder removed and have had three years of anxiety, insomnia, diahorrea, UTI’s and am now following the diet, no alcohol, no sugar, no wheat. Supplements of Golden Seal, Echinacea, cranberry, and am a lot better. Sleeping at least 6 hours a night, diahorrea has stopped, however UTI’s are still occurring. I am interested in the 10 day programme, but being under a Naturopath am concerned about whether this would conflict with her program.

    • November 16, 2015 Reply


      Hi Jennifer,

      Thanks for your comment! I suggest you reach out and speak with my team about your UTI and health concerns. We have helped many, many women with chronic UTI issues. Having had your gallbladder removed tells us a lot about some methylation and estrogen-related issues that your body has experienced. The If speaking to us on the phone to guide you directly is not something you wish to pursue at this time, then the 10-day program is a fantastic way to restore your gut. To fix the gut we have to do multiple things simultaneously and do them correctly. That is what the 10-day program is designed to accomplish. We have used this program hundreds of times. It works! Regarding your concern about “offending” other doctors or conflicting with them, look at the issue from a doctor’s point of view. All we want is for you to feel better and make gains in your quest for health. Any doctor that gets upset because a patient does their own research and finds answers from different sources is being cruel to their patients. At the end of the day you want to feel better, and any doctor that doesn’t understand that then shame on them. With a chronic UTI you also should look into D-mannose as a tool in addition to the 10-day 4R program. Contact my office at and 208-322-7755 if you would like to speak to myself or Dr. McQueen for a more personalized treatment program. – In Health, Dr. Rostenberg

  • November 16, 2015 Reply


    I am confused on your reply that one must fix the gut before the methylation pathway but I am c677t +/+ and was only out of range by 1 for hydrogen but my ND thought this could be the missing link as I have loose stools every morning and go 4-5 times – I have had ibs-d for over 20 years but only got spasms with rich food! In sept 2012 I had a hysterectomy cervix and uterus abdominal and was given antibiotics intervenusly. Dec 2012 my dog died and I went Downhill. About 3 mos after I craved pototoe chips like never before and they were never something I liked. Eating a bag a day!! Aug 2013 all of a sudden anything I ate even water came out of me like water !! Tests were performed for every parasite but negative gluten free did nothing colonoscopy showed mild lymphocytic colitis. SCd diet to help caused major hives major flu symptoms I was sooo sick and I am sure it’s cause I don’t detox well. Entocort helped the hives and have been on mg until 2 months ago as weaning off and now at 6mg. Got on ketotifen as discovers histamine intolerance and had fat malabsorption so pancreatic enzymes helped immensely! Have had scans ultrasounds etc and nothing found – I have been hypo thyroid since 2nd child in 1996. So started candibactin br and all my old symptoms started coming back – allergies flushing severe diarrhea nauseas with food etc so wouldn’t this be because I don’t detox well?? So wouldn’t it be wise to fix the pathways first?? I take yaskos all in one and this last 2 months they don’t bother me and I can Finally eat bone broth soup! But after starting the sibo protocol I went backwards!!! Can you explain ?? Or help me?

  • November 16, 2015 Reply

    Analiz Flores

    Pariente has Allgrove Addisionismo Disease

    Leaving with infections in hospitals since 2014 Abril

  • November 16, 2015 Reply

    Lynn Fetters

    I have Lyme Diesease i eat no gluten dairy or sugar i take Ortho Digestzyme before every meal but it’s been 1 1/2 treating the Lyme Diesease not getting better i also have had my gallbladder out and have hormal problems any suggestions Thanks!

  • November 19, 2015 Reply


    You mention phneols, aromatic amino acids and aldehydes as toxins. What about d-lacate and ammonia coming from gut microbes? How do these affect the methylation cycle?

    • November 22, 2015 Reply


      Hi Troy,

      Thanks for your comment! Yes, in addition to phenolic compounds, aldehydes, alcohols, etc., we also get exposed to ammonia and d-lactate. Ammonia doesn’t have a direct impact on the methylation cycle, but it does consume resources and lowers arginine precursors as well as glutamine levels. The main problem with ammonia is that is combines with alpha-keto glutarate in the mitochondria to form Glutamate (neurotoxic) while depriving the citric acid cycle. So ammonia hurts our brain this way. Lactate creates acidosis in the body also, and tends to encourage fermentation instead of oxidative phosphorylation in the mitochondria. Both ammonia and lactate hurt the cells ability to breath and produce energy. But this is distinct and different than inhibiting enzymes in the methylation cycle. Hope that helps. – Dr. Rostenberg

  • December 19, 2015 Reply

    Rebecca Hill

    Hi Dr. Rosenberg.
    And if the 10 day diet program causes problems as it did for me, you may remember, then what? I am not feeling better at all after so long. Most feel better after working with their practitioners for 5-6 months. I have talked to so many people that are going through the same exact thing as me and most are now feeling much better. I’m in dire need of help so I can at least not feel so sick and hurt so much I want to die daily. Please help me. I’m begging you. Thanks.

  • January 11, 2016 Reply

    Darrin Smith

    Hi Dr. Rostenburg,

    How can this all effect managing conditions such as lyme and thyroid issues? I’ve been told by my physician that I need methylation support but when I take it, I get really nasty mood swings. B-vitamin supplements do this to me as well. I’m on a gut healing protocol right now. I don’t know where to begin with all this, but realize cleaning up my gut is a priority along with optimizing my methylation. HELP!

    Darrin & Karin Smith

    • January 18, 2016 Reply


      Hi Darrin and Karin,

      Thanks for your comment! I think you’ve already mentioned the answer – its a gut health problem. When people react negatively to methylation support and B-vitamins the first place we must look is at a dysbiosis in the gut. Methylation support and vitamins in general can act like fertilizer for our cells, but also fertilizer for bugs and parasites. We help many patients from all over the world figure out how to cleanse their body of these problems. Once the gut is enhanced with the correct protocol for the individual, treating thyroid and lyme issues becomes easier and more successful. How can we expect to treat lyme and thyroid issues if our gut cannot function correctly?

      The body has a lot of tools to kill lyme and balance our hormones, but that is nearly impossible with an ongoing gut infection. It sounds like you are already working on a gut healing protocol. Just realize there are very many kinds of gut protocols available, and many of them aren’t specific to what the patient needs. If you would like help please reach out and contact my office 208-322-7755 and Another good option is to perform the 10-day 4R program in the Protocols section. We routinely see great results with that program.

      Yours in Health,

      Dr. Rostenberg

  • March 12, 2016 Reply

    Lisa Larche

    Dr. Rostenberg,

    I have many issues, celiacs, hashimotos, sjogrens, mcs and the latest dx mast cell activation syndrome. I know I have mythelation issues, but I have a added complication with type IV allergies to cobalt, which is in the make up all B12. This allergy to cobalt causes debilitating rashes and is metal/ mineral, and is in everything. I was told by doctors not to take B-12. I did in the past and I get the rashes. It is the same type of reaction as to poison ivy, the type IV allergy. I have reached out to several through e-mail tha is suppose to be experts on methylation, but I never got a response. Thank you.

    • March 14, 2016 Reply


      Hi Lisa,

      Thanks for your comment! You clearly have a complicated health history and are dealing with several issues at once. In cases like yours we always have a foundational problem with gut function. Not only do autoimmune diseases begin and progress from a leaky gut, so too do histamine and mast cell issues. Most of the body’s histamine is the immune system lining the gut. What you are really describing is that your body is a chronic state of autoimmune inflammation. It has progressed to the point where your system is even rejecting vitamins. Likely what is occurring is the cobalt is going into your body and then being transported to your skin where the allergic dermatitis Type IV occurs. Methylation is a key process for any healthy person and it has a big influence on all body systems. The immune system and gut are no exceptions. I would be happy to discuss this more with you during a consultation. Please contact my office 208-322-7755 or By working together we can develop a personal treatment plan that takes into account your individual needs, genetics, history, etc.

      In Health,

      Dr. Rostenberg

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