Diet and Microbiota: The Two Most Important Determinants of Your Health

plant-foodsWhat does it take to be healthy? If you ask a dozen people on the street this question, the majority of the ones you ask will probably say that adequate physical activity, a healthy diet, and sufficient sleep are the keys to achieving good health. Some may also mention that it’s important to prioritize stress management, spend time in nature, and get adequate sun exposure. Few, if any, of the people you meet will probably say anything about microbes.

This is not surprising, because as a society, we’ve been taught that it’s primarily the human part of our body that is important in the context of health and disease, not the microbial part. Over the past decade, the number of news stories covering topics related to the human microbiome has increased at a progressive pace, but there’s still a long way to go before the average Joe gives his microbiome the attention it deserves.

Some people are not even aware of the fact that their bodies are home to a teeming ecosystem of bacteria. And even those who are tend to underestimate the importance of the microbiome in health and disease. 

A healthy diet will only get you so far

I think few will disagree that all of the lifestyle factors that were mentioned in the beginning of the article are important in the context of health and disease. In order to be healthy, we need to exercise, get enough sleep, and eat a prudent diet. We should also spend as much time as we can in nature, take steps to manage our stress levels, and get some sunlight on our skin, among other things.

Adhering to these healthy lifestyle practises is not always enough though. You can eat a perfect, non-processed diet, spend hours at the gym every week, and sleep for eight straight hours every night, it’s not going to provide you with a healthy body and mind if you harbor an unhealthy microbiota. If your microbiota is in good shape, however, you will experience the full benefits of the aforementioned activities and probably feel pretty great.

There’s no doubt in my mind that a lot of people these days are unhealthy not because there’s anything wrong with their diet or exercise program, but rather because there’s something wrong with their microbiome. Since most doctors, nutritionists, and other health practitioners know little or nothing about the microbiome, the majority of these sick individuals are not made aware of the fact that fixing their microbiota may be the key to fixing their health problems. They may adopt the healthiest diet in the world, but still not get better, because their microbiota is in a compromised state.

An unhealthy diet will always produce an unhealthy microbiota, but that doesn’t mean that a healthy diet will always produce a healthy microbiota. If you already harbor a diverse mix of gut microbes and your gut microbiota is in pretty good shape, simply adhering to a prudent, species-appropriate diet may be suffient to make you healthy; however, if you harbor a degraded, dysfunctional microbiota, adopting a good diet is not going to be enough; you also need to take steps to repair your microbiome.    

All free-living macroscopic organisms (e.g., humans) carry a microbiome. The human microbiome acts as an extension of the human genome, in the sense that it provides important genetic capabilities that the human host lacks. When the microbiome is in bad shape, the human host is in bad shape.

The microbiota helps regulate our immune system, breaks down some of the food we eat, impacts our reproductive and sexual function, and produce a long list of hormones, neurotransmitters, and other compounds that affect various organs in our body. Moreover, the microbiota can exert control over our behavior and thoughts, and has been implicated in a long list of chronic health disorders, including mental conditions such as autism, ADHD, and depression.

Why it can be difficult to repair a damaged microbiota

Eating healthy, exercising, and sleeping are easy tasks when compared to the job of repairing a damaged microbiota. In the upper part of your gastrointestinal system, more specifically in your stomach, an acidic shield is blocking microbes from travelling down into the lower parts of your gut. Not all of the microbes you ingest are unable to pass through this acidic barrier, but many are.

The gastric acid is important, in the sense that it destroys potentially harmful microbes that may otherwise be allowed to cause havoc in your body. However, in doing so, it also wipes out many bacteria that have the potential to enhance your health. This is one of the reasons why a lot of people find it difficult to diversify their microbiome.

It takes time and persistence to boost the diversity of the gut microbiota, unless you take a microbiota pill that comes in an acid resistant capsule or perform a fecal microbiota transplant – a procedure in which bacteria are infused directly into the lower parts of the gut.

Key takeaways

In order to achieve good health, it’s not enough to lead a healthy lifestyle and eat a species-appropriate diet, you also need a well-functioning community of microbes in your gut.

  • A healthy diet plus a healthy microbiota equals good health.
  • A healthy diet plus an unhealthy microbiota equals disease.
  • An unhealthy diet plus an unhealthy microbiota equals disease.
  • It’s impossible to eat an unhealthy diet and have a healthy microbiota, because a bad diet will select for a microbiota that is mismatched with the human genome.

Other factors, such as physical activity, sleep, sun exposure, and genetics, are obviously also important determinants of human health, but they may not be as important as diet and microbiota.


  1. An interesting point to this is that fermented foods, vegetables or fruits drenched in brine and left to ferment over several days, thrives in a brine that is very similar to the sodium levels in regular sea water. This could point towards an ancestral which relied on multibacterial fermented food through the winter season which was stored in sea water brine.

    The fecal transplant or microbiota pill may not contain the balance seen in “naturally” fermented foods…

    • Interesting point.

      I have a couple of objections to your theory though.
      – The microbes that are transplanted via a FMT have already displayed an ability to grow in the human gut.
      – When compared with fermented veggies, a FMT delivers a broader range of bacteria, including bugs that are specialized at degrading various complex polysaccharides. Fermented foods contain primarily lactobacilli; they do not contain the broad range of microbial species that are needed to rebuild a damaged microbiota.
      – The weight of the evidence suggests that most (exceptions may exist) preagricultural humans did not consume fermented foods on a regular basis. (They may occassionally have eaten som berries and other plant foods that had started to ferment). The same can be said for modern day hunter-gatherers, who eat primarily fresh food.

      I agree that there are some potential downsides to FMTs. There are pros and cons with both fermented foods and FMTs.

      Thanks for the comment!

      • E de Boisgelin says:

        Quite a few primates and other mammals gorge on fermenting fruit, love the alcohol, I suspect hunters and gatherers do too. There are even suggestions that raising crops came about to produce food for fermenting. As far as I know FMT has been useful when the gut biome is in a very sorry state but has not been useful in increasing microbial diversity otherwise. I think the narrow view of what constitutes a healthy gut – no mention of fungus, helminths, viruses – is probably one reason why it is so hard to alter the proportions of bacteria. Additionally the reason why the microbiota is damaged should be addressed, also has irreparable damage been done to the environment of the bacteria ie the mucus of the intestines?

        • Hi Boisgelin,

          Yes, as you say, many primate species are known to consume fruits that have started to ferment. Our early primate ancestors probably did so as well, as supported by recent studies (e.g., this one). That said, I’m not aware of any evidence suggesting that Paleolithic hunter-gatherers regularly consumed signficant quantities of fermented foods. The same can be said for modern-day hunter-gatherers who live an an area of the world where our species originated. E.g., the Hadza consume primarily fresh food.

          I’m willing to change my opinion on this if you show me the evidence 🙂

        • Chimps and the other primates do have a fermentative gut because they use the short chain fatty acids as the primary fuel.
          Humans have a gut that is between them and carnivores…
          The fact that they may occasionally consume fermented stuff around is a farcry from claiming that they ate plenty of that, also because it was not so easy to find it…and agriculture was not meant to ferment anything…crops were conserved dried.

  2. You’re really right, I’ve seen cases of healthy diet and disrupted microbiome and the result is sickness.
    It’s also easily understandable, since health or disease start in the gut, everything impacting the gut has a key role in our health.
    When this happens, it may lead people to think that diet is not important to be healthy, instead of thinking that you have to take care of your health from multiple perspectives.
    One of my friends has tyroid issues and going on a paleo diet has not been enough for her.
    However, instead of following my advice to check if something is going on on her gut, she gave up and went to a conventional doctor who says that she has nothing wrong, “eat everything in moderation and go jogging”(this crap for 300 €!!, dumb guy burn in the hell)…the next day she was eating again her crackers…she’s doomed! My heart is full of pity and anger…
    There are many issues to target, and SIBO is a nasty stuff, to diagnose and to cure especially.
    A question: what do you think about soil based gastro resistant probiotics like prescript assist? Of course it has far less species compared to an healthy ecosystem, but maybe it is much better than lactic ones with just a couple of species…

    • I’m not a fan of Prescript-Assist or any of the other soil-based probiotics that are on the market today.

      Here’s what Dr. Art Ayers, a man I have great respect for, had to say about Prescript-Assist:

      “As far as I can see from the list of bacteria and fungi listed as ingredients, this “probiotic”, is a bunch of spore forming organisms mixed with Leonardite, a relative of coal that prevents compaction. The choice of organisms seems to be based on availability, because they are used commercially to produce ingredients for other industries. One of the fungi used, for example, is the source of the enzyme, cellobiose dehydrogenase, that I discovered in Stockholm. Most won’t grow in the gut, so they are transients, similar to dairy probiotics. They will not repair gut flora, but they may provide temporary benefits in cases of severe dysbiosis. Homemade fermented veggies are better. ” (

      I tried Prescript-Assist a couple of years back. My N=1 is that it didn’t do much.

  3. Oh furthermore, I forgot to say that the aforementioned genius MD told my friend that everything is in her head suggesting to take drugs for mental issues…
    When they don’t know and can’t help, they blame you…
    So sad and itching…

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