To Achieve Good Health, Your Gut Microbiome Has to be Matched to Your Diet


A healthy diet will only get you so far…

Do you experience gastrointestinal issues, sugar cravings, fatigue, low libido, and/or other chronic health problems despite eating a very healthy diet? The reason is probably that you harbour a gut microbiota that is mismatched with the diet you’re eating. You can eat as much fiber-rich vegetables, grass-fed meat, fatty fish high in omega-3, and extra virgin coconut oil as you want, it’s not going to make you healthy if you don’t possess a diverse, resilient microbiota that is adapted to break down the indigestible (to the human host) compounds you get through your diet.

A healthy diet is just one part of the equation, the part everyone focuses on. The gut microbiota is the other part of the equation, the part everyone forgets.

Dr. Art Ayers, a former Harvard professor with a Ph.D. in Molecular, Cellular and Developmental Biology and one of my heroes in the world of health and medicine, has made the point above repeatedly on his blog. (I highly recommend that you read his articles if you want to learn more about the true causes and cures of chronic disease).

He makes the case that a healthy gut microbiota is a diverse community of microbes that is matched to the diet the person consumes. In other words, a healthy microbiota for a Hadza hunter-gatherer who consumes a fiber-rich diet will look very different from that of a Inuit eating an animal-based diet.

The important thing isn’t that you possess a specific set of beneficial microbial species, but that you harbour microbes that carry genes that code for enzymes that can break down the food you’re eating. It’s the genes that matter.

A healthy gut microbiota is an essential part of a well-functioning digestive system

At this point, you might be a little confused, so let me try to explain how I look at these concepts…

The human body was shaped over millions of years of evolution. We carry with us two major sets of genetic information: Our human genome, which we inherit from mum and dad, and the human microbiome, which is the collective genomes of all the microorganisms that live “in” and on our bodies. Compared to the human genome, the human microbiome is highly malleable, in the sense that what we eat, the types of drugs we take, how we exercise, and the type of environment we live in can have a profound impact on the composition of the microbiota (1, 2, 3).

The microbes that inhabit our body carry out essential functions that we haven’t evolved the genetic capability to perform ourselves. We have essentially outsourced certain parts of our immune function, metabolism, and digestion to these tiny critters. This is particularly important to keep in mind in the discussion of diet and gut microbiota adaptation.

The human body, excluding its associated microorganisms, possesses the genetic capability to break down mono- and disaccharides, starch, fats, and protein (of the major nutrients we get from our diet). Some exceptions do exist; for example, about 70% of the world’s population loses the ability to produce the enzyme lactase after infancy, and they therefore can’t break down the disaccharide lactose.

Non-starch polysaccharides, as well as certain other nutrients we get from our diet, are broken down by gut bacteria. That is, if we harbor microorganisms that are able to degrade these compounds. A lot of people don’t get the “promised” health benefits from eating a nutrient-dense, whole foods diet because they harbor a gut microbiome that is poorly matched with the diet they’re eating. In other words, you can eat as many prebiotic fibers as you want, but if you don’t possess a microbiota that is adapted to break down these substrates, you’re not going to experience the many positive effects associated with fiber consumption, but rather gastrointestinal distress and a leaky gut.

If nutrients pass into the colon that the microbiota is incapable of breaking down into end-products such as butyrate and acetate, food intolerance, gastrointestinal distress, and inflammation occur.

Why you shouldn’t follow the low FODMAP diet or other similar diets

A lot of people with a degraded gut microbiota experience health improvements when they adopt a low FODMAP diet, specific carbohydrate diet, or other similar diet, because these types of diets exclude certain indigestible (to the human host) carbohydrates that we depend on our gut bugs to break down.

The problem is that these types of diets only mask the problem, they do nothing to correct the underlying issue. Actually, they may exacerbate the underlying problem, due to the fact that many fermentable fibers are excluded from these diets; fibers that beneficial microbes in the colon depend on for growth and reproduction.

In other words, the long-term solution isn’t to adhere to a diet that restricts certain forms of carbohydrates, but rather to recruit new bacteria that are capable of breaking down the nutrients we get from our food that the human host is incapable of digesting without the help of the microbiome.

The microbiota plays a more important role in our digestion than previously thought

We now know that it’s not just the non-starch complex carbohydrates we get from our diet that are broken down by gut bacteria. For example: Some gut bacteria are able to degrade gluten, phytic acid, and lactose, meaning that if we have these gut bugs in our GI tract, many of the adverse effects associated with the consumption of these compounds could potentially be avoided (4, 5, 6, 7)

As for lactose, several studies have shown that consumption of yoghurt, kefir, and certain probiotics improves symptoms of lactose intolerance (5, 8, 9) This makes sense, because when we consume these products, we’re also eating bacteria that are able to break down lactose. These bugs can potentially colonize our gut or transfer genetic material to bacteria living in gut biofilms, meaning that we essentially add genes to our microbiome that are needed to break down lactose.

The human body is an environment for the microbiota. The microbes that live in our gut reside there because we we provide them with a habitat they can live in. If you suddenly shift your diet, your gut microbiota also changes, because different microorganisms specialize in degrading different nutrients. If you change what you eat repeatedly – e.g., jump from diet to diet every other week or consume different foods every day – the gut microbiome never gets a chance to properly adapt to the diet you’re eating. In other words, too much dietary variation is unhealthy.


If you experience gastrointestinal issues, sugar cravings, fatigue, low libido, and/or other chronic health problems despite eating a very healthy diet (e.g., a fiber-rich Paleo-style diet), the solution most likely isn’t to remove certain foods from your diet, try a new dietary pattern, or otherwise change what you eat. Rather, you have to acquire the bacteria that are missing from your gut and work on improving the health of your gut microbiota. Unfortunately, at the moment, you can’t simply go into the drug store and buy a pill that contains the microbes you need. However, as you know if you’ve been reading this blog, there are several other sources of bacteria out there, such as homemade fermented vegetables, raw, minimally cleaned plants from the garden or farmer’s market, healthy people and pets, and high-quality probiotic supplements.

P.S. If you want to read more about how to achieve a healthier gut microbiota, I recommend reading my previous articles on the topic and/or checking out some of the posts over at Cooling Inflammation (e.g., this one and this one).

Now I want to hear from you: Have you consumed a healthy diet for quite some time, but still feel sick, tired, and/or fatigued? After reading this post, do you suspect that your gut bugs may be to blame?


  1. Eirik, what you say about lactose intolerance makes sense, but I don’t know if it’s really that simple. I am somewhat lactose intolerant and have been for years. I can and do eat some yoghurt or kefir occasionally, or cottage cheese, but I can’t eat a lot of it and I can’t eat it every day. If I do it will cause GI tract problems. I can’t drink milk at all, and as I stated in another post, I can’t consume any kind of whey product without making myself sick. It seems to me that eating fermented dairy products now and then should have reduced my lactose intolerance by now, but if there has been any improvement at all, it has been so slight as to be virtually unnoticeable.

    • Shary, as I see it, there are two possible reasons why you still experience digestive distress from consuming yoghurt, kefir, and milk.

      1 (The most likely scenario): You haven’t been consistent enough. Simply eating some kefir or yoghurt occassionally (e.g., once a week) will not solve anything. You should eat kefir (it should be homemade) and/or yoghurt with live bacteria every day. Start with very small amounts (e.g., 1 or 2 teaspoons if you are very sensitive) and slowly work your way up. You also need to consume small amounts of lactose to promote the growth of lactose-digesting bacteria in the gut.
      Initially, this will cause some digestive distress, but as your gut biome adapts, the adverse reactions should subside.
      2) Studies consistently show that probiotic bacteria in fermented milk products improve lactose digestion. However, that doesn’t mean that everyone is able to completely overcome their lactose intolerance this way. One reason may be that they have a damaged microbiome (e.g., yeast overgrowth).

  2. I think you may be correct in saying – “In other words, you can eat as many prebiotic fibers as you want, but if you don’t possess a microbiota that is adapted to break down these substrates, you’re not going to experience the many positive effects associated with fiber consumption, but rather gastrointestinal distress and a leaky gut”
    However, I do believe that you can change the microbial activity by significant dietary changes. I introduced food source inulin into my diet (okra and jerusalem artichoke), but had GI distress. So I supped with inulin powder in slowly increasing amounts, and am now able to tolerate 1 Tbsp without adverse affect (did have trouble at first), as well as eating inulin rich foods without problems. The reason for the inulin specifically, is as an adjunct to potato starch, which feeds the proximal colon bugs primarily, but inulin moves to the distal colon so that your entire surface is bathed in SCFAs. I do believe that you can target small microbial changes with specific dietary manipulations. My point is that small steps may work, don’t just give up and say I don’t have those necessary bugs. You just have to know what you are trying to achieve.
    The other point of interest, is that if you don’t have any microbiota which can digest a particular fermentable fiber(ie prebiotic), you will be asymptomatic on it’s consumption, since there will be no organism that can digest it and make gas and discomfort. It will simply pass into your stool, untouched.

    • Absolutely, most everyone will experience some initial discomfort if they suddenly increase their consumption of a fermentable fiber like inulin. Usually, the gut microbiota will adapt and the adverse symptoms will gradually disappear.

      My point is that some people lack the microbial species (and their genes/enzymes) that are needed to break down the food component in question. For these people, simply continuing to eat the problematic food will not solve anything, they also need to acquire the missing bacteria.

      I find your last statement to be incorrect. If you have a gut microbiota that is mismatched with the diet you’re eating you will experience gastrointestinal discomfort. Fermentable fibers will not simply “pass through” completely undigested. Rather, a mismatch between flora and food generally results in symptoms of food intolerance.

      Thanks for your comments!

      • I am trying to think this one through Erik.
        By what mechanism would a nonutilized dietary fiber cause gas and cramps? These symptoms result from either the fermentation products and/or the consequent gas production? For the fiber to have an effect on the organism, there must be some interaction with the human or bacterial component – if the food is not fermented and if it cannot pass the gut barrier (for size – eg inulin), then it must go through unaffected.

        FROM – ….
        “RS1 is the physically inaccessible starch that is locked within cell walls such as nuts shells, seed coatings and hulls, and other food matrixes. Milling and chewing can make these starches more accessible and less resistant. While eating whole seeds is very healthy for our digestive systems, RS1 is not an important food source for gut microbes since many of these protective structures cannot be breached and they pass through the body completely undigested. When the coating is breached, RS1 becomes RS2.”
        My take on this, with regards to something like inulin, is that if it reaches the large intestine whole, and then you lack the bugs to cut it up and use the bits for their fermentation, then it will just go through you.
        Your thoughts?

        By the way, this cited post is also where I got the idea to combine PS and inulin….
        “For instance, a fiber found in inulin-rich foods, fructoologosaccharide (FOS) acts synergystically with RS. The combination increases populations of beneficial microbes more than either alone. FOS ferments very fast while RS takes a bit longer to degrade through microbial actions, this factor makes a combination of these fibers more desirable than the fibers administered alone. Inulin acts much like RS3 as a slowly degraded fiber, and when combined with RS and FOS can create an accurate tool for targeted applications of prebiotics to certain areas of the colon. These factors can be exploited easily by the adventurous dieter by eating a well-balanced, fiber-filled meal paying attention to get all the different fermentable fibers together. In an experiment with 32 rats divided into 4 teams, the group fed a combination of RS and inulin for 21 days showed a greater diversity of gut flora, better colon health markers, and improved absorption of dietary calcium and magnesium.”
        I wanted to share this with your readers, I think it is an important concept when we are on the topic of microbial diversity.

        I apologize for the length of this comment.

        • Some insoluble fibers pass through the GI tract mostly undigested. However, the fibers that are classified as fermentable (e.g., inulin-type fructans) will generally not be left untouched by the microbiota, regardless of whether the microbiome is adapted to “properly” break down these compounds or not.

          Let’s take lactose for example:
          If the body produces the enzyme lactase (lactase sufficiency) or bacteria with lactose-digesting enzymes are established in the gut, lactose should be digested without problem. In the latter case, lactose acts as a soluble fiber that is fermented by gut bacteria that produce lactic acid.

          If the person is lactose intolerant and doesn’t harbour a microbiome that is well-adapted to metabolize lactose, lactose will not simply pass through completely undigested. Rather, some types if bacteria in the colon will act on the milk sugar. This fermentation process produces copious amounts of gas (a mixture of hydrogen, carbon dioxide, and methane) that causes the various abdominal symptoms that are typically seen in lactose intolerant individuals who consume dairy. According to Wikipedia, the unabsorbed sugars and fermentation products also raise the osmotic pressure of the colon, causing an increased flow of water into the bowels (diarrhea).

          Other similar reactions (food intolerance) can occur for other indigestible (to the human host) compounds we get through our diet.

          • Yes, you are definitely correct in your statement that “the unabsorbed sugars and fermentation products also raise the osmotic pressure of the colon”, inert molecules can also cause an osmotic laxative effect – eg Mg (in old fashioned Milk of Magnesia)
            However,if a polysaccharide is neither digestible by humans nor is it a MAC (eg. methylcellulose), then that polysaccharide shouldn’t cause any symptoms beyond a mild osmotic laxative effect. For example, according to the makers of Citrucel ( a laxative), it contains only 100% non-fermentable soluble fiber, so none of it ferments to cause excess gas like the fermentable fiber in Metamucil (psyllium).
            Lactose is a different case because the colonic bacteria do exist to digest it, even if the human host is lactase deficient, thus creating fermentation products.

          • Now you’re just confusing the issue. Of course there are some carbohydrates (e.g., indigestible cellulose) that aren’t fermented by gut bacteria (just like I said previously).

            That’s not what’s relevant to this post. I’m merely stating the fact that a lot of people experience gastrointesinal problems because they lack the necessary gut bacteria to break down the food they’re eating. I don’t know why you’re bringing up laxatives all of a sudden, as they are obviously in a different category than the non-starch polysaccharides we get from the fruits and vegetables foods we eat.

            Anyways, I think we’re mostly in agreement, so let’s just end the discussion there.

            Thanks for the comments/discussion.

  3. Very interesting article!
    Yep, I really do everything right 99% of the time and have been for over a year. I’ve noticed a tremendous difference. A few months ago I added more handfuls of leafy greens just for more health phyto-nutrient benefits. I actually do prefer to eat very similarly every day. I get GI issues sometimes and I relate it to stress. I’m trying to start an evening herbal tea ritual and see if that helps.
    Thanks for the info & link to other articles.
    Have an awesome weekend!


  1. […] aren’t enough to curb their undesirable food cravings. Oftentimes, the problem is that their gut biome is mismatched with their diet, and hence, they also have to implement additional steps – such as consuming beneficial […]

  2. […] While it’s a good thing to include several types of fiber-rich plants in your diet, as opposed to just a few species, you should make sure that your diet stays fairly similar from day-to-day, because if you’re jumping from diet to diet or constantly changing what types of foods you eat, your gut microbiome will never have time to adapt to your diet […]

  3. […] not enough to eat a nutrient-dense, healthy diet. To achieve good health, you also need a gut microbiome that is adapted to this diet. In other words, the consumption of a healthy diet doesn’t produce health if the gut […]

  4. […] A fecal microbiota analysis will provide you with information about biodiversity, pathogenic overgrowth, etc., but it will not tell you whether or not you harbour a gut microbiome that supports healthy digestion and immune function when matched with your diet/lifestyle. As I’ve pointed out many times on the blog, to achieve good health, you need to eat a healthy diet AND have a gut microbiota that is adapted to that diet. […]

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