Dear Mark: Homocysteine, Some Kefir Questions, and the Stress of Worrying

For today’s edition of Dear Mark, I’m answering a bunch of questions from readers. The first one concerns another inflammatory marker, homocysteine. How could CRP be low but homocysteine be high? What could cause that? Next, I answer a barrage of kefir questions, including ones on kefir carb counts, pasteurized kefir, and water and coconut kefir. Finally, I address the elephant in the room: stressing out about your diet.

Let’s go:

How do Homocysteine levels figure in this equation? I have C-reactive protein under 1, but Homocysteine levels of 15, slightly high. Seems odd one so low and one a bit high.

Both indicate elevated inflammation, but they can have different causes. There are many nutrient deficiencies and interactions that go into elevated homocysteine levels—that’s why they indicate inflammation. What are they?

It all comes down to methionine. That’s the essential amino acid most abundant in muscle meats, the one most of you are getting a ton of if you’re eating a standard Primal, keto, or carnivore diet. We use it to perform cellular communication, regulate gene expression, repair cells, and build new tissue. It does some really important stuff, but it needs several different co-factors to work properly.

B12 and Folate—Vitamin B12 is a major one. So is folate. In fact, I lumped them together in one section because they are co-dependents. Vitamin B12 requires folate to do its job. Folate requires vitamin B12 to do its job. Both vitamins are necessary co-factors for methionine to do its important cellular work. Without either one, methionine builds up and contributes to homocysteine.

They even tested this in a controlled human trial. Giving a big dose of methionine without increasing B12 or folate increased homocysteine levels. Supplementing with B12 and folate protected against the methionine-induced increase in homocysteine.

Riboflavin—Some groups may need extra riboflavin to deal with homocysteine levels.

Glycine—After teaming up with the B-vitamins to do the gene expression and cellular repair/buildup, any excess methionine combines with glycine to form glutathione. That’s the body’s main antioxidant, and it’s very helpful to have. If you have low glycine levels/intake, then any leftover methionine goes into the homocysteine cycle.

B6—Vitamin B6 is also used to mop up and convert into glutathione any excess methionine after methylation.

Betaine—Similar to glycine, betaine acts as a buffer for excess methionine. In fact, high intakes of methionine deplete the body of betaine, while supplementing with betaine reduces homocysteine levels.

Choline—Choline is another methionine buffer. High methionine increases the need for choline, while adequate choline or supplementation reduces homocysteine.

If you’re missing those co-factors, methionine fails to assist with cellular communication, gene expression, cellular repair, or new tissue formation. Instead, it generates homocysteine.

For a primer on obtaining adequate B-vitamins, read this post. Meat of all kinds, eggs, organ meats, seafood, dairy, green vegetables, and even legumes are ways to obtain them.

For a primer on obtaining adequate glycine, read this post. You can get it through collagen, gelatin, bone broth, or bone-in, skin-on meats with a lot of gelatinous connective tissue.

To get enough betaine, include some beets and/or spinach in your diet. Wheat germ is the best source, but most of you aren’t eating wheat germ (nor would I recommend you start).

To get choline, eat egg yolks. That’s the single best source. If you’re not going to eat betaine-rich foods (beets, spinach, wheat), eat extra choline; you can make betaine from choline.

Isn’t there a relatively large amount of carbs in kefir, when consumed in quantity?

The fermentation process digests most of the lactose present in milk. The sourer the product, the lower the residual lactose. The sweeter the product (or even just less sour), the higher the residual lactose. At any rate, I wouldn’t worry too much about the carb content of kefir. It’s assuredly lower than advertised, and probably low enough for even keto eaters to incorporate at least a little.

There are even lactose-free kefirs that will be definitely near-zero in carbs. If that’s the case, it will be prominently displayed on the label.

Mark, don’t they at least partially”clean up” kefir? Does it really contain all that good stuff, or is pasteurized?

Commercial kefir uses pasteurized dairy, but the fermentation takes places after pasteurization. This means the finished product is fermented with living bacteria (and yeast, in the case of kefir).

I’ve never seen a commercial kefir that pasteurized after fermentation. If you’re worried, you can always get your own kefir grains and make your own kefir. It’s pretty easy and delicious.

Kefir – I just did a test of dairy and it definitely gives me a reaction. I’d love to read your take on water kefir though I’m not pleased that the recipes use sugar. What about coconut milk kefir?

Don’t worry about water kefir that uses sugar. All the sugar gets consumed by the kefir grains, leaving little to no residual sugar for you. You can tell by the taste (and I admit I’m no fan/expert of water kefir, only because I can tolerate dairy kefir). If it’s sweet, it contains sugar. If not, it doesn’t. Even if it has some sugar left, it’ll be far less than indicated on the label.

Coconut milk kefir is a good option too. Again, I prefer the dairy kefir, but I see nothing wrong with coconut milk kefir. I even put up a coconut milk kefir recipe some time ago.

Funny you mentioned to drink bone broth (for the glycine) to help with sleep. I have been keto-carnivore for 9 months and recently realized that the high level of histamines in bone broth was giving me insomnia. I can eat most foods that contain a moderate level of histamines, but canned fish and long-cooked bone broth have derailed my sleep on carnivore.

If that’s the case, straight glycine can work. That’s what several studies actually used to improve sleep in humans—isolated glycine.

Collagen may also work for you.

Could all this be too much worry from being obsessed with checking if they are doing the keto diet “right” ?

Ha! Yeah. That’s the issue with a certain subset of the Primal/keto crowd. Worrying about every little thing until it becomes a stressor. Ketone numbers running through the head as you lie awake. Waking up at 2 AM to test your urine. “Did I remember to Amazon Prime the MCT oil?” Wondering “Is the olive oil in my canned sardines truly the highest quality olive oil?”

Then there’s the true classic: stressing out about the stress you’re inducing from worrying about your diet. Educate yourself, but don’t forget to enjoy life. There’s only so much diligence we can orchestrate without losing the forest through the trees.

That’s it for today, everyone. Take care and be well, and make sure to leave any comments or questions down below.

About the Author

Mark Sisson is the founder of Mark’s Daily Apple, godfather to the Primal food and lifestyle movement, and the New York Times bestselling author of The Keto Reset Diet. His latest book is Keto for Life, where he discusses how he combines the keto diet with a Primal lifestyle for optimal health and longevity. Mark is the author of numerous other books as well, including The Primal Blueprint, which was credited with turbocharging the growth of the primal/paleo movement back in 2009. After spending three decades researching and educating folks on why food is the key component to achieving and maintaining optimal wellness, Mark launched Primal Kitchen, a real-food company that creates Primal/paleo, keto, and Whole30-friendly kitchen staples.

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14 thoughts on “Dear Mark: Homocysteine, Some Kefir Questions, and the Stress of Worrying”

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  1. Mark, I would love if you did a write-up on BPC-157 and LL-37 with regards to gut health. I’m surprised with all your articles on collagen peptides you haven’t written once about “synthetic” peptides. Thanks!

  2. The Beyond Meat people are in for some competition with “Air Protein” now. Using microbes in the air combined with minerals to produce an alternative protein. Sounds like science fiction for sure, but are we far from the meal pill?? Either way, I’ll take a hard pass.

  3. I read that fermentation removes between 20 and 30 % of sugars in kefir. (Journal of DairyScience 65, 1982) My full fat sour milk in my fridge has 4 % carbs. And is milk free of lactose free of sugar? Well, the full fat sweet milk, free if lactose, im my fridge, has 3 % sugar. How come? Probably because the enzyme lactase splits lactose into two sugars, glucose and galactose, and they are still sugars.

  4. “Educate yourself, but don’t forget to enjoy life. There’s only so much diligence we can orchestrate without losing the forest through the trees.”

    AMEN, Mark. I swear, Mark, you are one of a very, very rapidly disappearing kind of human: sane, rational, understanding, empathetic, and just plain NOT CRAZY. Please never change.

    1. Agreed 100%. Best takeaway from the post for me personally. Thank you Mark!

  5. This sorta brings up a question I’ve been meaning to ask. I’m sensitive to dairy (tested allergic as a kid) and it can’t be just lactose because even if very fermented it
    affects me. I’m fine with aged cheese though (Swiss, cheddar, parmesan, etc). Does the ageing process change the protein structure somehow (or do the constipatory effects counteract what dairy usually does to me).

    1. I have the same problem but it didn’t start to occur until after my third pregnancy. (I used to drink milk shakes during my third pregnancy so I wouldn’t lose weight) I can’t eat fermented dairy but aged cheeses are just fine.
      I think its a fodmap issue.

      I know where I can get raw dairy and plan to eventually try it to see if I don’t get my usual problems. (Its too far out of the way and expensive for a regular thing….but its jersey milk omg)

    2. Fermenting does not remove 100% of the lactose. Could be the difference between A1 and A2 casein.

  6. Hi Mark, have you heard of the protein leverage hypothesis? I’d love to hear your thoughts on it.

    Also, any thoughts on dry lips? I would say it could just be because I’m Canadian, but even during the summer mine are super dry and no amount of lip balm or coconut oil seems to do anything beyond cover the dry skin temporarily. It seems like a problem Grok probably wouldn’t have had way back when, so I’m hoping there’s a root cause or Primal fix.

    Thanks so much for all that you do!

  7. Mark, in regards to the query on bone broth causing insomnia, there are a number of studies that indicate that for some people collagen and/or bone broth can increase anxiety thus the insomnia. That hyper alert, heart pounding, stomach churning feeling can be a sensitivity and a reaction to both bone broth and collagen. The result can be tossing and turning all night.

    Re: the obsessing with diet, this is the main reason I won’t label myself paleo/keto/ vegetarian or omnivor etc.. I eat healthy whole foods period. When I travel and experience different cultures, I eat local fare. When I am visiting and am served a meal, I eat what is served. I find the obsessions with diet/food and health/wellbeing to be adding to the unhelpful narrative that there is something inherently wrong with us that the next magic diet/health breakthrough will cure. Life is up and down, we do well at times and not so well at other times. We have and then sometimes we have not. Being able to navigate the ups and downs, the good and bad, the ebbs and flows is far more important than strictly adhering to a particular ideology. Mark’s daily apple offers great advice and ideas with a good dose of reality and more importantly with enough humour and insight to remind us not to take it all too seriously. Sometimes life just is and we don’t need to put on a label or find a fix.

    Just my two cents. Thanks for your insights, always food for thought.

  8. I enjoy and miss Kombucha and Kefir very much since trying to eat keto.
    Are there particular brands or available instructions for making your own that you recommend.

  9. Home cultured kefir, made with grass fed milk or any organic milk at least: is not only a satisfying thing to do, a calming procedure but also is very calming spiritually, and the physical body welcomes it. I hope everyone commenting on kefir understands it is not to be compared with store bought except unfavorably. Grains are easily available and multiply if they are happy. is an excellent site for all kinds of learning, answers to questions, etc. about home cultured kefir. That’s not a typo; it’s their name by choice and they explain what it is. The moos is not a moo from a cow.