#159: Ben Lynch, ND- Genetic Testing, Methylation, MTHFR & SIBO

by Deanna Mutzel, DC


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Mike Mutzel Podcast High Intensity Health



About Dr. Ben Lynch

Dr. Ben Lynch is a naturopathic physician and methylation expert. In this episode, he discusses life beyond MTHFR genetic variants and common gene SNPs. It’s all about paying attention to your environment, he says. We also discuss ways to overcome exercised-induced asthma and seasickness, and how to handle over/under methylation.

Resources discussed in this podcast

StrataGene helps to simplify the 23andMe genetic data. Learn about the key factors that influence your genetic SNPs and potential health implications.

Genos Research

Related Recipe:

Chicken Bone Broth (low in histamine and glutamate)

Podcast Show Notes

01:55 Folic Acid: If that’s all you have, take it. In rat studies a small amount of the folic acid was able to be processed. The maximum that can be processed is much less than human bodies require.

03:52 Harms of Folic Acid: Folic acid blocks folate receptors. These receptors are designed to bind to methylfolate, but folic acid will bind preferentially over methylfolate. Folic acid will bind to transport proteins, again blocking the binding of methylfolate. Too much folic acid will downregulate the folate binding proteins. Try to limit intake of folic acid by avoiding enriched foods. Eat your leafy greens, which are part of a diet rich in natural folate and you can take methylfolate supplements rather than folic acid. Folic acid is prevalent in children’s multivitamins.

05:49 Folic Acid Link to ADD/ADHD: Folate makes neurotransmitters that help with focus and attention.  Consuming processed food is linked with ADD/ADHD and blood sugar crashes. There may be a link to the synthetic folate in the food, causing aberrations in methylation. The enzyme which was studied to see of folic acid could get through, DHFR, is slow in humans. DHFR can become preoccupied and overwhelmed with folic acid, rendering it unable to perform other tasks important to neurotransmitter function, like the recycling biopterin. Biopterin becomes oxidized and can be useful again. This reduced biopterin supports your dopamine, norepinephrine, serotonin, and nitric oxide for your cardiovascular system.  Supplementing with biopterin (as with nitroglycerin and arginine) is a crutch and dosage must be increased continually to get the same effectiveness.

10:46 Supplementation:  A supplement is to add or enhance. We think that we need to take them every day. Dr. Lynch strongly believes that a supplement should be to add or enhance. The majority of supplements should not be used every day.

11:45 Dirty Genes: Dr. Lynch has written a book about genes that are perceived to be bad. MTHFR is seen as negative, but it may help with DNA synthesis and possibly repair. For generations, polymorphisms have been passed down. Rather than doing genetic testing for “bad genes”, do it to see what genes you have and how they are functioning in order to modify your lifestyle to get the most out of them. Dr. Lynch no longer says that MTHFR is bad. MTHFR is the last step in the process to make methylfolate, only one type of folate.

13:44 Folinic Acid and MTHFR: Take folinic acid for hair growth. Methylfolate is for methylation. Folinic acid does DNA-based repair or DNA-based production and works with adenosine, which is used in ATP, energy. Dr. Lynch has a theory that environments that have a lot of sun exposure, have a lot of skin damage, which requires a lot of DNA repair, which requires a lot of DNA- based production, and that requires a lot of folinic acid. These populations may be higher in MTHFR to protect DNA-based production. In other environments where a lot of green leafy vegetables are consumed, people may be at more risk for the MTHFR 677T homozygous, the more common serious form of MTHFR. It represents a slowing of the enzyme by 80%. Twenty percent capacity is all you have left. The job of MTHFR is to make methylfolate. If you are eating lots of leafy green vegetables rich in methylfolate, it can make up the difference.

17:05 Genetic Polymorphisms: We all have genetic polymorphisms, about 1 ½ million of them. They are not bad. They are just different. They can cause negative things to happen. If we know what they can cause and we alter our diet, lifestyle, mindset and environment, those SNPs can be favorable for us.

17:45 Folate Needs during Pregnancy: Pregnant women need a combination of folinic acid and 5-MTHF. Creation and maintaining a placenta creates a great demand for folate. Prenatal vitamins should have folinic acid and methylfolate, as well as choline.

18:31 Choline in Pregnancy: Seventy percent of pregnant women are choline deficient. Choline, found in meat products, egg yolks and animal liver, is the primary methyl donor backup to folate. Perhaps our ancestors who did not have access to green leafy vegetables received methylation support indirectly through choline. Transmethylation goes from homocysteine to penthianine directly and choline feeds into this. Transmethylation is found primarily in the liver and the kidney, but not much in the brain. Eight-five percent of methylation reactions occur in the liver. Gallbladder dysfunction is a common condition in pregnancy. With the depletion of folate and choline from the liver during pregnancy, the liver struggles, causing gallbladder stasis and thus SIBO, constipation and other symptoms of gallbladder problems. Taking SAMe or phosphatidylcholine during pregnancy can reverse liver problems.

21:51 COMT Polymorphism: Women should have way more estrogen than men. Estrogen is demanding of liver function. It uses the liver for transformation. Estrogen, dopamine and norepinephrine comes through the COMT enzyme, which is hugely polymorphic. If a woman’s estrogen and dopamine sluggish, she will be quick to become irritable. Research shows that women who have the COMT polymorphism have a greater risk of estrogen based cancers and PMS. The co-factor for the COMT enzyme is SAMe, which also needs methylation, which needs folate, B12 and choline.

23:15 Liver Dysfunction: Non-alcoholic liver disease is pervasive and growing in prevalence. Carbohydrate intake is a heavy contributor to this. The fatty deposits in the liver from liver dysfunction impacts methylation. Liver function testing range is a sick person range. Studies show that on ALT and GDT, when your levels are above 28, you begin to see histological damage within the liver, cellular damage within the “normal” range. Indications of gallbladder problems can be: feeling heavy in your middle, getting more constipated, getting referred right shoulder tightness and pain, eating fatty foods and not feeling good from it, itchy skin, lethargy, and more irritability.

25:50 Fatty Liver: It may be an early sign that we are shifting metabolism from aerobic to anaerobic. Cancer cells love lactate from anaerobic metabolism.

26:32 SIBO: Papers coming out now show SIBO is a metabolic disorder, not a dysbiotic disorder. The trigger for SIBO could be dysbiosis, but the primary trigger could be metabolic. Bile acids are antimicrobial, keeping dysbiotic bacteria in check. If you have liver dysfunction, you will have insufficient bile acids which may trigger SIBO or dysbiosis. The bile dumps into the small intestine. Bile is 70% phosphatidylcholine. Phosphatidylcholine uses up about 70% of methylation.

29:07 Supporting the Bile: Ox bile supplements are useful for treating SIBO. When it causes fast major die off, it shows that you not only have SIBO, you probably have gallbladder stasis.

30:09 Ketogenic Diet: An improperly constructed ketogenic diet (no fiber, no phytonutrients) causes the absorption of bacterial endotoxin, which can cause fatty liver formation, effecting methylation.

30:47 Gene Testing: We all have the same core DNA, but there are polymorphisms, variances, in the alleles of that DNA.  The 23 and Me test identifies genetic polymorphisms in the genes. This test checks about 780,000 bases. Genos Research is developing a test that checks 50 million.

32:26 Addressing SNPs/Single Nucleotide Polymorphisms: The majority of SNPs are in regions of the gene that have no effect on your body or genetic function. It is important to assess the clinical relevance of the SNP and functionality of the gene. Your lifestyle impacts functionality of your genes. If you have a sluggish MTHFR and you are going out drinking, you should think about supplementing with B12 and folate. Sometimes supplements have side effects. The number one article read by far on the website is Methylfolate Side Effects.  As you improve your lifestyle and environment, you may not need as much methylfolate. There is a lot of misinformation on the internet about supplementation.

42:56 StrataGene Tool: Dr. Lynch’s StrataGene translation program only uses 23 and Me data, but will expand to include Genos. looks at ancestral DNA, not health related DNA. This means that some clinically relevant SNPs are not tracked. StrataGene reports 50 clinically relevant SNPs. SNPs cannot be viewed in isolation. StrataGene does not make supplement recommendations. It provides co-factors and genetic controls and places the SNPs in pathways so you can understand the bigger picture. It empowers root cause resolution.


Related Podcast

#96: Ben Lynch, ND– Histamine and MTHFR, Overmethylation and Asthma


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Join the conversation

  1. This video was amazing. Have a question about methyl B12, Hydroxy B12 or Adenostyl B12. What about the transdermal applications? Are these effective?

    • Thanks, Denise!

      I’m glad you found it helpful.

      Transdermal for certain autoimmune skin issues; but overall I think oral or injectable is preferred to raise systemic levels.

      I personally like to experiment with different forms of B12; 80% of clinicians like methyl and 20% prefer hydroxy.

      Check out Seeking Health’s blends, they have an array of B12 options for different people.



  2. Thank you for all the information Dr Ben and Mike for explaining it for us mere mortals. I’ve had gallbladder issues, Fatty Liver and SIBO … also A1298c MTHFR. I took 1mg of folic acid for 20 years because of a blood clotting disorder! I stopped as soon as I found out fromDr. Ben. That it was harming me. I see now that taking methylated folate and b12 is not helping with my energy ATP for fibromyalgia and Hashimotos. I am definitely getting the genetic testing and translation done. I’m so tired of taking so many supplements that only make other things out of balance!

    • Hi there Janis,

      It’s probably better to use 5-MTHF instead of folic acid, eh? Glad you caught that one.

      Have you looked into adenosyl B12? I mention that as you suggest mitochondrial function and ATP production, could be worth considering. Also, if you have methylation SNPs and energy issues, creatine could be an option to consider as well.

      But as you said, it’s probably best to run your genetics through the SteteGene and see what pathways need most support.

      Thanks so much,


  3. This video has opened up a window for me. I did not realize that some people are more susceptible to developing NAFLD. I have been working to heal my fatty liver and liver cysts with almost no success. I have changed my lifestyle dramatically and still have not found the key(s). Never knew the high bilirubin numbers can be a marker for low bile. Also, the methylfolate symptoms were great to hear again… I needed that. Thank you for all you do!

    • Hi there Tina,

      So glad this was of benefit to you. Not sure that we touched in bilirubin in the podcast; but high bilirubin may be suggestive of a sluggish UDP-glucuronosyltransferase enzyme.

      This is a critical enzyme involved in detoxification of various environmental chemicals. So if you’re bilirubin is high, you may wan to ramp up your intake of cruciferous vegetables or possibly add Sulforaphane caps to your supplement program as well.

      Hope that helps some,


  4. I just received my genos results two weeks ago so extremely interested in when StrataGene will be able to accept it.

    That or a suggestion to try until then knowing it would not be the same level as described during the podcast.

  5. Hi Mike,

    I wonder if Dr. Lynch would suggest to get the Genos testing done, even though its in its beta phase, over the 23andme testing at this point, knowing the huge increase is base pair testing.


  6. Thank you for the interview, it was very helpful. I wander if there’s any info on the over supplementation of 5-MTHF, can it cause tinnitus and vertigo?

  7. I am so interested in the science behind Methylation and learning about how everything works together, like what Dr. Lynch teaches, but I would like to learn more, and maybe even go into practice on a lower professional level. Do you have any suggestions on where I can start? I have been looking at Functional Medicine and Integrative Nutrition. Will that give me enough training to be able to understand the science behind what Dr. Lynch teaches without being a doctor? Thanks for any advice you can give me.

  8. This podcast came at exactly the right time for me. I had a blood test ordered from my holistic physician (Cockerell labs) and we found that I’m homozygous for the MTHFR gene as well as adrenal fatigue, too much iron and estrogen. I’ve practiced a very healthy lifestyle my entire life- paleo, lots of moving around, careful with diet. Currently though, I’m going through an immense amount of stress which at times was accompanied by a little more alcohol than I should have consumed.
    My physician communicated how serious these conditions were and that was so defeating. He ordered 7 supplements in addition to a candida program- one month totaling $1000.-. I am getting low on supplements and was wondering really how important are they? Will I have serious problems down the road if I miss a week, etc. It’s all become a bit complicated for me. This video was indeed an “aha” that I need to make more subtle lifestyle choices, life better stress reduction techniques- etc. Will stick with the core supplements that I took previously- Sam-e, tryptophan, 5-HTP.
    Will order StrateGene for sure as I believe it will help me muddle through all the information I had from my physician and to limit my supps.
    Thanks so much

  9. Hi,
    I have sibo and took ox bile which gave me diarrhea. I stopped it thinking at had some intolerance to it, but could it be a sign of “die off” like you mentionned ? A part from charcoal and vitamin c, what can I take to be sure that I can have the benefits of ox bile without side effects ? I also suffer from a strange pain in all my left side body which my acupuncturist said was gallbladder related, and great fatigue and muscle pain, histamine, oxalates and salicylates intolerance. I suffer from pancreatic insuffiency, too, and I take pancreatic enzymes. I am considering testing MTHFR, too, and I hope it will enlighten many of my unresolvable symptoms. D you know a good laboratory in Europe or France ?

    Thank you for this podcast

  10. wow, so many light bulb moments during this talk. I have SIBO and realised that I need to change my SIBO protocol. Not enough liver/gallbladder support!!! Thank you!!!!!!! Think I will order ox bile to see what happens 🙂 Got nothing to lose 🙂 Thank you again for inspirational talk.

  11. WOW! I must confess I’m blown away. In the recent past, one of my docs tested my MTHFR and COMT areas and I had “something” with those, I left her soon after for another doctor, so I have never found treatment for these possible deficiencies/polymorphisms. But what really blew my mind in your video was the connection of fat/bile issues and later develiopment of SIBO. I could be a posterchild to what you’ve said in your video here, it’s kinda crazy! I had my gallbladder removed 15 years ago. Within a year I could no longer eat wheat, after that it was dairy, then came corn and soy… and the list goes on. 7 years ago I started displaying symptoms of fibromyalgia and didn’t know about SIBO until 3 years ago. No wonder people don’t recover from it as they have not reached the root cause by any stretch, assuming everyhing you’ve shared is completely legit (awaiting studies). Sounds like the next step is ox bile along with the 23andm3, with your companies analysis and finally a doc who is trained and knows how to put it all together in a cohesive, supplement/lifestyle ready, package. I cannot express my delight sufficiencly to have stumbled upon this video golden nugget. I thank you kindly!!!

  12. Would you say the preferential binding of folic acid is due to a lack previously of it in the diet and therefore methylfolate could easily bind in the past without the inhibitor, or an adaptation to prevent excess of methylfolate entering cells?

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