All Disease Begins in the Gut

gut-healthIn the industrialized world, improved public health measures and various medical innovations over the last two centuries have helped us overcome many infectious diseases and rapidly decrease infant mortality rates, among other things. However, when it comes to effectively addressing chronic health conditions such as colon cancer, type-2 diabetes, irritable bowel syndrome, acne vulgaris, and cardiovascular disease, not a lot of progress has been made. That’s not to say that there hasn’t been developed a wide range of pharmaceutical drugs for these disorders, but the problem is that these medicinal products usually fail to address the underlying causes of the disease. Rather, they only help mask and control the symptoms.

Although the recent newspaper headline on medical research might claim otherwise, there are no “quick fixes” or rapid cures on the horizon for most of the chronic diseases that plague us in the modern world. Why? Because chronic health problems such as the ones mentioned in the beginning aren’t caused by a specific pathogen or one single factor that can be addressed with a drug or pill. Rather, there are several causes that underlie the so-called diseases of civilization; one of the most important being poor gut health.

Was Hippocrates right all along?

All disease begins in the gut

The importance of gut health has largely been neglected by mainstream medicine, something that has led to a lot of unnecessary suffering for millions of people worldwide. It’s only with the emerging focus on the human microbiome and the increased appreciation for the role gut health in human disease that have occurred very recently – about 2000 years after the father of medicine, Hippocrates, said the famous words above – that we’re starting to realise how right he was. Of course, saying that all disease begins in the gut is clearly stretching the truth. However, when it comes to the pathogenesis of the chronic diseases of civilization I talk so much about on this blog, it’s safe to say that gut health plays a key role.

Some key facts about the gut

  • The gut is an important interface between you and the outside world.
  • More than 70% of our immune system is located in and around the gastrointestinal tract, with gut-associated lymphoid tissue (GALT) being the prominent part of mucosal-associated lymphoid tissue (MALT) (1).
  • There are a lot more microbial than human cells in our body. Most of these critters are found in the GI tract, with the large intestine harboring the densest communities.
  • The gut microbiota regulates our immune system, plays an important role in our digestive processes, produces various neurotransmitters and other compounds that can enter systemic circulation and reach various bodily organs (e.g., the brain), and regulates intestinal barrier function.
  • Gut dysbiosis and increased intestinal permeability (AKA leaky gut) have been linked to a myriad of chronic health problems. E.g., acne vulgaris, type-2 diabetes, obesity, and irritable bowel syndrome.
  • There’s strong evidence to suggest that we’ve lost some “old microbial friends” that co-evolved with our ancestors for millions of years. The genes of some of these microorganisms may have been “written into” the human genome, which can help explain why a loss of old friends can set the stage for chronic diseases associated with poor immunoregulation.

How a modern lifestyle impairs gut health: 12 main problems

  1. Antibiotic use
    Antibiotics don’t just save life and help us combat infectious disease, they also damage our health by wiping out beneficial bacteria, altering the community structure of the gut microbiota, and leaving gut niches open for exploitation by pathogens (6).
  2. A high intake of acellular carbohydrates
    A high intake of refined grains, refined sugars, and other so-called acellular carbohydrates likely promote the growth of proinflammatory bacteria in the upper GI tract, which can set the stage for increased translocation of endotoxins from the gut, chronic low-grade inflammation, leptin resistance, and weight gain (2).
  3. A low intake of fermentable fibers
    A low intake of resistant starch, inulin, and other fermentable fibers sets the stage for poor colonic health.
  4. A very high fat intake
    As I explained in my comprehensive article on saturated fat, a high intake of butter, oils, cream, and other foods with a very high fat density alters the gut microbiota and may induce endotoxemia and chronic low-grade inflammation.
  5. A high intake of Neolithic foods
    As everyone who’s followed this blog knows; whole grains aren’t the ultimate health food some people make them out to be. Neolithic foods such as whole grains and certain dairy products contain potentially problematic compounds (e.g., antinutrients, bioactive compounds) that can increase intestinal peremability and/or enter into systemic circulation (3, 4, 5).
  6. Inadequate and altered microbial exposure
    Our primal ancestors ate foods with clinging soil bacteria, performed all of their activities in a microbe-rich, natural environment, and exchanged microbes with other healthy humans. This is in stark contrast to the modern, developed world, where we eat industrially produced, “clean” food, spend most of our time indoors, and live among people who carry unhealthy gut microbiotas. Our microbial environment has changed dramatically over the past millenia.
  7. C-sections and infant bottle feeding
    Caesarean births and bottle feeding in infancy are evolutionarily novel practises that negatively impact the development and gut health of a growing child (7, 8, 9).
  8. Insufficient and/or disordered sleep
    Yes, even sleep affects gut health. E.g., A recent study showed that circadian disorganization can impact the intestinal microbiota which may have implications for inflammatory diseases (10).
  9. Chronic stress
    Chronic stress can induce changes to the gut microbiome by altering the composition, diversity and number of microorganisms living in the gut (11, 12).
  10. Consumption of Western-style diets
    Besides being high in certain Neolithic foods, acellular carbohydrates, and very fatty foods and low in fermentable fibers, Western-style diets have several other unfavorable characteristics. E.g., they are composed of foods with an evolutionarily abnormal nutrient composition and are high in starch, omega-6, and trans-fats.
  11. Exposure to harmful substances
    In the modern world we’re exposed to a wide range of compounds that our primal ancestors never or rarely encountered. Some of these substances can enter into systemic circulation through the gut and/or may have a unforeseen impact on the gut microbiota or intestinal lining. For example, we’re regularly exposed to various pollutants, and many of us drink chlorinated, bottled water that contains compounds such as bisphenol-a (BPA). While it’s clearly impossible to completely avoid being exposed to many of the potentially problematic compounds found in our environment, it is certainly possible to take steps to reduce our exposure.
  12. Inadequate physical activity
    Physical activity, mostly performed at a low-moderate intensity, may have protective effects on the gastrointestinal tract (13). Recent research also suggests that exercise has an impact on the gut microbiota (14).

What can we extract from the two lists above?

The main takeaway from list 1 is that more and more research seems to support Hippocrates’ statement that “all disease begins in the gut”. As for list 2, the main point is that several factors associated with a “modern” diet and lifestyle negatively impact gut health. Put these two things together, and you can quickly understand why so many people in the modern world suffer from chronic health problems such as IBS, IBD, colon cancer, and acne vulgaris.

A poor gut feeling

Some people who have little knowledge about human health seem to believe that the gut is a stable machinery that isn’t really affected by what we do and eat. Basically, some people seem to be under the impression that all of the digestive and regulatory functions of the gastrointestinal tract are inherently written into the human genetic make-up. If they regularly get an upset tummy, they might just think that their digestive machinery is inherently flawed, and if they seem to be unable to propery digest a specific food, they may end up believing that they have a food intolerance that is going to be with them for life.

However, as anyone with some knowledge in these areas will tell you, adverse reactions to certain foods and/or gastrointestinal distress are typically not caused by a genetic predisposition or “permanent flaw” in the system, but rather by underlying problems associated with the gut microbiota (e.g., lack of biodiversity, leaky gut, pathogenic biofilms). As Dr. Art Ayers explains:

Food intolerance is based on missing bacteria in the the gut rather than inadequacy of human enzymes, e.g. lactase, or altered immune system (15).

Another common misconception is that eating a healthy diet is enough to achieve good gut health. While this is certainly a good starting point, it’s not enough; particularly for those who have a dysfunctional gut microbiota. Health depends on having a gut microbiome that is matched to the diet. In other words, if you don’t harbor a diverse gut microbiota that possesses the genetic capabilities that are needed to break down the nutrients that enter into the colon, symptoms of food intolerance occur. For many, it’s not enough to just eat a healthy diet, they also have to introduce missing species of bacteria.


Poor gut health is a common denominator of many, if not most, of the chronic health problems that plague us in the 21st century. Even if you don’t actually feel “sick”, I’ll argue that chances are that your gut health is less than optimal, as it’s simply very hard to maintain a perfectly healthy gut when you live in the modern environment we’ve created for ourselves. What we eat, how much we exercise, which drugs we take, and how much time we spend outdoors are just some of the many things that impact our gut health. That doesn’t mean we should be constantly worried about how our diet and lifestyle choices affect our gut health; it just means that most of us could benefit from paying a little more attention to what’s going on in the long tube inside us. All in all, it’s safe to say that paying attention to gut health should be a priority for everyone who’s looking to overcome chronic health problems and/or achieve good health. The old saying that “Good health starts in the gut” definitely holds a lot of truth. 

Do you take your microbial inhabitants into account when you make diet and lifestyle choices? Do you have any questions regarding how to improve your gut health? Let me know in the comment section below.


  1. Hi Eirik,
    I’ve struggled with gut problems most of my life, possibly due to periodic antibiotics. I’ve had frequent bouts with IBS (diarrhea, cramps, flatulence, food intolerances–the whole bit), Doctors I’ve seen only want to prescribe drugs. One even suggested eating a lot of whole grains to “bulk” up the stool. Sticking (for the most part) to a Paleo diet hasn’t helped much with the gut problem..

    I am beginning to think one of the results of a compromised GI tract has been chronic and inappropriate inflammation in my muscles and joints. I understand that inflammation is a normal part of the healing process, but if I get injured–tendonitis in my foot, for example–inflammation sets in and doesn’t go away within a normal period of time. With me it can hang on for months–eventually healing but taking forever to do so. Meanwhile, NSAID use is the only thing that gives me relief from swelling and pain. I am trying to get to the bottom of this problem and fix it. Doctors rattle on about “inflammation cascade” but they don’t offer any workable solution.

    After reading some of your articles and comments, and those of Dr. Ayers (thanks for the link, btw), I see a pressing need to incorporate fermented food into my diet–which it does lack. Can you recommend an adequate course of doing this? Which types of fermented foods do you consider best? You previously stated to start with a teaspoonful. Should I just gradually increase the amount daily, or weekly, according to body tolerance, or is there a better way? Does a diversity of fermented products make a difference, or can I just stick to a few that I like?

    • Hi Shary!

      Some comments from me:

      I am beginning to think one of the results of a compromised GI tract has been chronic and inappropriate inflammation in my muscles and joints.

      No doubt. Gut dysbiosis and leaky gut set the stage for translocation of endotoxins and chronic inflammation.

      After reading some of your articles and comments, and those of Dr. Ayers (thanks for the link, btw), I see a pressing need to incorporate fermented food into my diet–which it does lack. Can you recommend an adequate course of doing this? Which types of fermented foods do you consider best? You previously stated to start with a teaspoonful. Should I just gradually increase the amount daily, or weekly, according to body tolerance, or is there a better way? Does a diversity of fermented products make a difference, or can I just stick to a few that I like?

      Glad you mentioned Dr. Art Ayers. His blog is a favorite of mine. I highly recommend that you check out his articles. These two are probably particularly relevant to your situation:
      Gut Flora Risk and Repair
      Dr. Oz on Gut Flora Repair

      As for fermented foods, make your own at home or make sure you get a hold of high quality products.
      A lot of people start out with kefir, kimchi, and/or sauerkraut. Diversity does matter.
      How rapidly you increase the amount you’re eating depends on how your body is responding. Unless the adverse reactions get very bad, I wouldn’t be afraid to increase the amount on a daily basis. It’s just food 🙂

      Good luck!

      • Thanks for the tips. I’ll definitely try them. Also, I think miso is fermented (?). I love miso soup and make it often for myself. It doesn’t seem to affect me adversely when mixing a tablespoon or so with hot water. I like Marukome All Natural Miso & Easy for its convenience.

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