Yogurt Won’t Fix Your Gut Microbiome

yoghurtYogurt is the stereotypical probiotic food. It’s mentioned in virtually all newspaper articles and blog posts that talk about probiotics and gut health, and is available to consumers all over the world. When the average Joe feels that his gut isn’t working properly, he goes to the store to buy some of this milk product – or another similar fermented dairy food that contains live bacteria. This isn’t surprising, as the media, many health bloggers, and the dairy industry have promoted yogurt as a healthy food that has the ability to heal a gut that isn’t working properly.  

What these yogurt-lovers fail to recognize is that yogurt doesn’t provide the broad range of microorganisms needed to rebuild a damaged gut microbiota; it only contains a limited number of lactic acid bacteria, most of which are unable to colonize the human gut. Actually, some “dairy probiotics” may do more harm than good, in the sense that they could hinder the growth and survival of beneficial bacteria in the gut.

You can’t fix a damaged gut microbiota with a couple of strains of lactic acid bacteria

The human colon is home to a complex ecosystem of microorganisms. Just like all other organisms, these bugs need energy to survive and reproduce. Without energy, they wither and die.

They get this energy from us, the human hosts…

Most of the food you eat during a typical day are digested and absorbed in your small intestine. The rest passes into the large intestine, AKA the colon, where it either gets digested by bacteria or excreted.

The quantity of nutrients that escape digestion in your small intestine and is subjected to colonic fermentation depends on the composition of your diet. If you eat a lot of fibrous plants, the colonic microbiota gets to have a huge dinner, whereas if you eat an animal-based diet, low in fruits and vegetables, or a western-style, processed diet, the bugs deep in your gut don’t get to fully satisfy their appetite.

It’s important to remember these basic facts in the discussion of probiotics and gut microbiome repair, because they help guide our understanding of how the bacteria in the human gut operate.

There are several inherent problems with using fermented dairy foods (e.g., yogurt) and supplements containing “dairy probiotics” to repair an unhealthy gut microbiome.

First of all, these products only contain a handful of strains of lactobacillus and/or bifidobacterium. So, not surprisingly, they are incapable of installing a healthy ecosystem of hundreds of species of microorganisms in your gut. Second, most of the bacteria found in these products are incapable of colonizing the human large intestine. Rather than getting a green card and becoming permanent residents of the gut, these critters tend to be transient bypassers. Some probiotics may positively modulate the microbiota in various ways, but the effects tend to be temporary, rather than permanent.

Yogurt bacteria may be useful for treating lactose intolerance

To understand why yogurt bacteria come up short, we have to consider the issue from the perspective of an evolutionary biologist. The bacteria that live in yogurt are adapted to live in yogurt. They evolved to live in this fermented milk food; they didn’t evolve to live in the human colon. Yogurt bacteria possess the genetic and enzymatic machinery needed to utilize lactose, the primary sugar found in milk, as their primary energy source. They don’t produce the enzymes that are needed to break down the many complex polysaccharides and oligosaccharides that pass into the human large intestine.

In the guts of lactose tolerant individuals, lactose is digested by the brush-border enzyme lactase, produced in the small intestine. Lactose never reaches the large intestine, which is where the main microbial hub in the human body is found. In other words, the bacteria found in yogurt won’t have access to their regular staple food –lactose – in the colon of a lactose tolerant individual.

In the case of a lactose intolerant individual, however, the situation is somewhat different. Since the human host in this case is unable to break down lactose through the use of its own enzymes, the lactose that is consumed through the diet may become available to the colonic microbiota. What this means is that the bacteria found in yogurt and other fermented dairy foods can help the human host break down lactose, and hence, help alleviate symptoms of lactose intolerance (1, 2). Here, lactose acts as a prebiotic that fuels the growth of bacteria that grow on lactose.

Some probiotic supplements and industrially produced probiotic foods may do more harm than good

Microorganisms evolve at a rapid pace and are able to swap genetic material between themselves. The problem with the bacteria found in yogurt is that they don’t possess the genes/traits that people with a dysbiotic microbiota are lacking from their gut. They can contribute some genes that make the host better able to digest lactose, but they don’t do much in terms of repairing the ecosystem.

The fact that some studies indicate that “dairy probiotics” may be useful in the treatment of certain gastrointestinal diseases, depression, and other health disorders probably has more to do with the ability of these bugs to modulate the human immune system, carry out some of the same functions as a healthy gut microbiota as they pass through the system, and protect the human host against pathogens, than it has to do with their ability to repair the microbiota.

As I’ve discussed before here on the blog, there’s even evidence to suggest that some probiotic supplements (in particular high-potency, medical grade probiotics) and industrially produced fermented foods could undermine the health of the microbiota, in the sense that these products contain high numbers of just one or a couple of microbes, some of which produce bacteriocins (microbe-produced toxins) that inhibit the survival and growth of other microbes that are already present in the gut. Homemade, traditionally fermented foods can certainly be beneficial, but when it comes to most of the mass-produced probiotic foods and supplements you can find at the grocery store, I’m a lot more skeptical.

Key takeaways

  • Yogurt doesn’t provide the range of microorganisms needed to repair a damaged gut microbiota.
  • The bacteria found in yogurt are adapted to utilize lactose and its constituent monomers, glucose and galactose, as their primary fuel source. They don’t produce the enzymes needed to facilitate the breakdown of the wide diversity of polysaccharides and oligosaccharides that pass into the large bowel of a human being.
  • Some probiotic supplements and industrially produced, fermented dairy foods may do more harm than good, in the sense that they could block the development of a healthy gut microbiota.
  • The bacteria found in yogurt can help speed up the recovery from acute gastrointestinal problems (e.g., diarrhea) and may act as a band-aid that covers up some of the symptoms of a damaged gut microbiota.


  1. What are your recommendations for supplementing?

  2. I get all the reasons why this should be true, and in fact I am a believer that wheat and dairy should be avoided because I think most humans, in the developed world anyway, don’t tolerate them well for a variety of reasons. I do however have an anecdote to the contrary that confuses even me. A couple of years ago I was suffering an immune breakdown, and I had developed several food intolerances, including gluten and dairy. I had been in a long-term period of constant, intense emotional and physical stress, and my immune system was in a funk. Aside from all the auto-immune issues, I was also having low immune response and getting sick with everything all the time. I even had Thrush. I set out to learn about the GAPS and SCD diets, and came to a point where I was supposed to introduce the 24 hour cultured yogurt. I hesitated, but heard so many good things about great healing taking place when the yogurt was added. Well, it was true. I made and began eating the yogurt, and from that point forward I started feeling normal again. Stomach issues cleared up, my bowels normalized, my skin cleared up, thrush disappeared, and I stopped getting sick. I also began to feel less emotionally drained and depressed. Eating the yogurt was very calming to my system.

    That was short-term, maybe six months, of about 1/4 cup of the homemade, 24 hour cultured yogurt three times per day, but boy did that turn my healing around for me. Many, many others doing GAPS or similar healing diets report the same results.

    The science shows that actual fermented foods contain way more live probiotic bacteria than any pill ever has. I think for many who are dramatically ill, the yogurt is a good alternative because so many of the fermented vegetables can be hard to digest in the early stages of gut healing, whereas the yogurt seems to just soothe.

    • Thanks for sharing your experience, Ann.

      Here’s what I think happened: The probiotic bacteria in yogurt gave your immune system a sorely needed boost and enhanced your protection against gut pathogens. Rather than repairing your gut microbiota, the bacteria in yogurt covered up some of the symptoms of gut dysbiosis.

      The message I’m trying to get across with this article is not that yogurt is bad, but rather that people shouldn’t expect yogurt to fix their gut.

      • Yes, life is good, thanks. Always good to read your posts.

        Forwarding this link, may interest you/readers. Chris Masterjohn is one of my favourite PhD biochemists _ I am sending the link in reference to fermented veggies, not to try to persuade you about dairy!! His own blog is very instructive (very basic science oriented), in this link he is being interviewed.

        ” Why adding fermented foods is the optimal strategy for properly managing vitamin K2 intake (52:50)

        Vitamin K: The general population obtains Vitamin K primarily via cheese and egg yolk consumption. Vitamin K2 is a sub-type of vit K found in animal products and fermented foods. Vitamin K1 is found in green-leafy plant foods. Vitamin K2 is more effective at activating your body’s vitamin K-dependent protective system. The richest source of vitamin K2 is natto, a fermented soy food popular in east Japan. You can use the natto bacteria to prepare homemade fermented vegetables as a good source of vitamin K2 ”

        Best wishes as always.

  3. Also, I’ve read speculation that although soil-based probiotics don’t colonize, their job may be to have enough presence in the gut to allow better bugs an easier foothold. That seems to be one of the selling points to a lot of transient bacteria, and what is described as the job of bacteria we would have gotten from eating dirty food and the like. I know they certainly have a place in some healing protocols.

    Perhaps restrictive healing diets like GAPS and SCD provide enough fast, early healing of the gut, which might allow a bit of wiggle room in the digestion of dairy proteins, that the benefits outweigh the negatives. Yogurt is never introduced early on – it’s usually several months after starting the diets for most people.

  4. alec trivass says:

    hi eric
    very informative article that leaves me wanting more. i know you believe in organic produce that is consumed raw, having been minimally washed, in the hopes of ingesting some beneficial bacteria. what other reputable sources are there which will contribute to the beneficial gut biome, short of fecal matter transfer from another healthy individual?

    • Hi Alec!

      Do you make fermented vegetables at home? If not, then I highly recommend doing so.

      Some quick tips for optimal results:
      – Make several batches with different veggies. This can help increase the diversity of microbes you’re eating, because each batch has a somewhat different microbial make-up.
      – Take it easy on the salt. Use a little less than most recipes recommend.
      – Use a fermentation crock. Using a crock makes the whole process a lot easier.

      Let me know how the process goes.

  5. Hi Eirik, so do you give homemade kefir a pass?

    Here, by the way, are the bugs cultured from kefir – source – http://users.sa.chariot.net.au/~dna/kefirpage.html#composition-of-KG

    Microorganisms Found in Different Batches of Milk Kefir-Grains and Kefir

    Divided into Four Genus Groups [with revised nomenclature]


    Bifidobacterium psychraerophilum
    Lactobacillus acidophilus
    Lb. brevis [Possibly now Lb. kefiri]
    Lb. casei subsp. casei
    Lb. casei subsp. rhamnosus
    Lb. paracasei subsp. paracasei
    Lb. fermentum
    Lb. cellobiosus
    Lb. delbrueckii subsp. bulgaricus
    Lb. delbrueckii subsp. lactis
    Lb. fructivorans
    Lb. helveticus subsp. lactis
    Lb. hilgardii
    Lb. helveticus
    Lb. kefiri
    Lb. kefiranofaciens subsp. kefirgranum
    Lb. kefiranofaciens subsp. kefiranofaciens
    Lb. parakefiri
    Lb. plantarum


    Streptococcus thermophilus
    St. paracitrovorus ^
    Lactococcus lactis subsp. lactis
    Lc. lactissubsp.lactisbiovar.diacetylactis
    Lc. lactis subsp. cremoris
    Enterococcus durans
    Leuconostoc mesenteroides subsp. cremoris
    Leuc. mesenteroides subsp. mesenteroides
    Leuc. dextranicum ^


    Dekkera anomala t/ Brettanomyces anomalus a
    Kluyveromyces marxianus t/ Candida kefyr a#
    Pichia fermentans t/ C. firmetaria a
    Yarrowia lipolytica t/ C. lipolytica a
    Debaryomyces hansenii t/ C. famata a#
    Deb. [Schwanniomyces] occidentalis
    Issatchenkia orientalis t/ C.krusei a
    Galactomyces geotrichum t/ Geotrichum candidum a
    C. friedrichii
    C. rancens
    C. tenuis
    C. humilis
    C. inconspicua
    C. maris
    Cryptococcus humicolus
    Kluyveromyces lactis var. lactis #
    Kluyv. bulgaricus
    Kluyv. lodderae
    Saccharomyces cerevisiae #
    Sacc. subsp. torulopsis holmii
    Sacc. pastorianus
    Sacc. humaticus
    Sacc. unisporus
    Sacc. exiguus
    Sacc. turicensis sp. nov
    Torulaspora delbrueckii t
    * Zygosaccharomyces rouxii


    Acetobacter aceti
    Acetobacter rasens

    • Hey newbie,

      Hope you’re doing well.

      As I’ve said before, I think homemade kefir is the best fermented milk product out there, because it contains a much broader range of bacteria and yeasts than yogurt, acidophilus milk, etc. That said, it suffer from the same limitations as other dairy foods. The microbes that make up milk kefir grains evolved to live in milk. Some of these bugs may be able to colonize the human gut and/or positively modulate the composition of the microbiota, but kefir is certainly not going to fix a very damaged gut.

      I think homemade fermented vegetables are superior to kefir for a number of reasons. Among other things, fermented vegetables have better nutritional characteristics and may expose you to a greater diversity of microbes. This is particularly true if you make many different batches and use minimal amounts of salt.

  6. “don’t tolerate them well for a variety of reasons.”
    The main reason is because they are not species appropriate food for human beings.
    We have to get rid of the tolerance concept as seen in black and white, while it has many shades of gray that go from bad aging to cancer, diabetes, schizofrenia, autoimmune disease, chronic fatigue, etc..
    The concept of tolerance itself is a signal that they are not appropriate, you don’t wish to “tolerate” your partner, but you should love him/her.

    • I agree, Alessio.

      I talked about this issue in yesterday’s post on milk. The fact that someone who is lactose tolerant is able to digest milk and other lactose-containing foods without experiencing any acute problems (e.g., gastrointestinal distress) doesn’t necessarily mean that drinking milk is healthy for that person.

  7. I have suffered from chronic diarrhea all my life – and I am now 86. About six months ago I had a very severe prolonged bout which drove my wife to make a medical appointment for me. I had tried a small amount of probiotic yogurt with only a minimal response. However on this occasion I trebled the amount of the yogurt and the result was absolutely remarkable. My stool went from water to a relatively firm consistency – overnight.
    Since then I have found that by maintaining a regular ration of the probiotic yogurts I have essentially conquered my diarrhea problem.

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