The Western Microbiome: How Our Modern Guts Make Us Sick, Fat, and Unhappy

gut-anatomyThe next time you’re out on the street, take a look at the people around you: The suit-wearing, busy office worker on his way to work, the female shopper carrying huge bags of newly bought clothes, the homeless guy living on the street corner, and the athlete on his way back from the gym. These people may all look and seem very different; however, they also have some things in common, one of which being that they all most likely suffer from some type of evolutionary mismatch disorder, whether it’s myopia, lower crossed syndrome, acne vulgaris, asthma, or more serious conditions such as type-2 diabetes or cardiovascular disease.

These and other so-called diseases of civilization, which were rare or nonexistent among our hunter-gatherer forebears, are highly prevalent in contemporary, industrialized societies. This doesn’t really come as a surprise when we consider the fact that we now live in a milieu that is completely different from the ancestral environments for which most of our genes were selected.

We’ve known for a long time that a western lifestyle adversely affects the expression of the human genes we carry with us throughout life. What we’re now learning is that the impact on the second genome in our body – the human microbiome – may in some ways be even more severe.

Microbiome depletion

When researchers first set out to map the microorganisms that live in and on the human body about a decade ago, they focused their attention on modern, industrialized people. The comprehensive research efforts that followed over the proceeding years gave us invaluable knowledge about our microbial inhabitants and their relationship with the human host. However, this initial approach to microbiome science also had its limitations, one of which being that it’s difficult – if not impossible – to establish what a healthy human microbiota may look like by studying industrialized populations.

In the western world, we’ve all been compromised in some way. Among other things, we drink chlorinated water, take antibiotics, eat processed food, and give babies infant formula that lacks the complex mix of microbes and prebiotics that are found in real breast milk. Over generations – as the damage has accumulated and microbes have been passed on from mothers to offsprings – there have been marked changes to our microbiomes.

In other words, to be able to establish what a complete, “unadulterated” human microbiome may look like, we have to turn our attention away from our own homelands and towards non-westernized, traditional societies. This fact hasn’t been missed by the scientific community, and over the last several years, studies with the purpose of mapping “the non-westernized microbiome” have been carried out among traditional populations such as the Hadza, a group of hunter-gatherers in Tanzania, Africa; the Tunapuco, a traditional agricultural community from the Andean highland; and the BaAka, a group of rainforest hunter-gatherers (1, 2, 3, 4).

One of the most important takeaways from these studies is that individuals who lead traditional lifestyles house a much greater diversity of microbes than westerners, including species that are never found in the guts of modern, industrialized people.

Examinations of ancient coprolites and analyses of the microbiomes of many different primate species further support the idea that human microbiomes have deviated from the ancestral state at an accelerated rate (5, 6). Here’s what a 2012 paper had to say about the matter:

Overall these studies reveal that human microbiome data has been preserved in some coprolites, and these preserved human microbiomes match more closely to those from the rural communities than to those from cosmopolitan communities. These results suggest that the modern cosmopolitan lifestyle resulted in a dramatic change to the human gut microbiome. (5)

Since we live in an environment that is very different from the ones hunter-gatherers occupy, we’re not necessarily best off harbouring the same mix of microbes as they do. As I’ve pointed out many times on the blog, the microbiota can adapt rapidly to environmental changes, meaning that what constitutes a well-functioning microbiome must be viewed in light of what kind of diet and lifestyle the human host adheres to. That said, there’s no doubt in my mind that we can learn a lot about how to shape a healthy microbiome by studying indigenous, non-westernized people.

Our modern way of life is putting the man-microbe relationship to the ultimate test

A modern lifestyle – with its chronic inactivity, processed foods, antibiotics, c-sections, and antibacterial lotions – is putting the man-microbe relationship that was forged over eons of time to the ultimate test. By designing and moving into closed buildings, adopting evolutionarily novel lifestyle habits, spraying our crops with man-made pesticides, and distancing ourselves from nature we’ve unknowingly disrupted the microbial ecosystems that not only live around us, but also in and on us.

The human body is not adapted to harbour the type of microbiome you get from eating highly processed food, taking broad-spectrum antibiotics, and living in closed-off, poorly ventilated buildings. In other words, the modern lifestyle selects for a microbiome that is mismatched with the human genome.

There’s little doubt that gut dysbiosis, which is defined as an unhealthy change in the normal bacterial ecology of the gut, is now an epidemic. Irritable bowel syndrome, insulin resistance, the metabolic syndrome, gallstones, type-2 diabetes, food intolerance, inflammatory bowel disease, and chronic depression are just some of the numerous health conditions that we now know are associated with a microbial imbalance in the gut (7, 8, 9, 10, 11). More readily apparent signs and symptoms of dysbiosis – whether it be in the oral cavity, gut, or any other location on the human body – include things like poor breath, a white coating on the tongue, obesity, and acne vulgaris.

Recent research has made it clear that gut dysbiosis and other disorders of the microbiome aren’t just benign conditions that occur secondary to chronic disease, but rather important underlying factors that are driving the development and progression of some health disorders (7, 11, 12). Here’s what a recent review paper had to say about the role of biome depletion in modern diseases associated with abnormal immune responses:

Evolutionary mismatches have left the typical immune system of industrialized humans prone to a wide range of allergic, autoimmune and inflammatory disease.

The primary factor associated with allergic and autoimmune disease is apparently loss of species diversity from the ecosystem of the human body, the human biome. Species depleted or even eliminated from the human biome include a wide range of pathogens, commensals and mutualists whose reproductive cycle is greatly diminished or even eliminated by modern sanitation, water treatment and medical practices. Importantly, the human biome, as with other biomes, not only includes species that are permanent residents of the ecosystem but also species that interact transiently with the ecosystem. The absence of species from the human biome leaves the immune system in a hypersensitive state that, when combined with environmental triggers and genetic predisposition, leads to allergic and autoimmune disease. (12)

The human superorganism

The human body is best viewed as a superorganism that is composed of trillions of microorganisms that co-exist side-by-side with the human host. We’re not separated from the environment around us; we are a part of it – connected to everything else through our invisible microbial inhabitants.

The air we breathe, the soil we touch, the plants we eat, and the family dog we take for a walk every morning all have their own microbiota, which interact with the one we carry with us. When we design homes and office buildings that are poorly ventilated and susceptible to mold growth, disrupt the microbial ecosystems in the soil with pesticides, or give the family dog cheap, nutrient-poor dog food from the grocery store, we’re messing with the balance of microbes in the environment that surrounds us, something that can have ripple effects down to the microbial reactor found in the tube that runs through our own body.

The microbes that call our body home regulate our intestinal barrier function, control our immune system, and produce a wide-range of enzymes, hormones, and neurotransmitters that play a role in our digestion, metabolism, and brain chemistry. When we put together what we know about the impact our lifestyle has on the microbiome and the role microbes play in shaping our health, it shouldn’t really come as a surprise that diseases associated with perturbations of the microbiota are now a huge problem in our modern society.

A dysfunctional microbiome can negatively impact our health through several different pathways, with perhaps the most well-known being that a microbial imbalance in the gut leads to increased translocation of bacterial endotoxins (“leaky gut”), activation of toll-like receptor 4, and chronic low-grade inflammation. It’s this inflammatory tone that’s problematic, as there are solid data to show that inflammation is at the root of many, if not most, of the chronic health disorders that plague us in contemporary societies.

The hidden epidemic

Microbial dysbiosis and other disorders of the microbiome are – or at least have been – hidden epidemics in the sense that we can’t see the trillions of critters that inhabit our body with the naked eye. It’s only very recently that scientists started mapping the human microbiome and we began to understand how complex the microbial rainforest that is found in our gut really is.

A mere 5-7 years ago, gut dysbiosis and leaky gut were considered by many to be “bogus diagnoses”, and health practitioners and scientists who claimed that microbial imbalances and candida overgrowth could lead to health problems such as irritable bowel syndrome, colon cancer, and autism were often ridiculed or labeled as quacks.

In the years that have passed, things have certainly changed a lot. No one who has bothered to keep up with the news coverage on gut bacteria or done a quick search for “microbiome” at PubMed doubts that gut dysbiosis is a real problem that afflicts millions of people worldwide.

Unfortunately, most people out there still know very little about the microbes they carry with them throughout life – and much less about the microbial environment around them. They may be completely unaware of the fact that their lifestyle has a profound impact on the composition of their microbiota or that their nagging headache, constant sugar cravings, disturbed sleep, and digestive issues are directly linked to a microbial imbalance deep down in their gut.

A lot of people have spent thousands of dollars on visits to various doctors and health practitioners and tried numerous diets, supplements, and drugs in order to overcome their health issues, but their health complaints remain as pervasive as ever. A large part of the problem is that the human microbiome hasn’t fully made its way from scientific journals into the offices of general health practitioners or the curriculum of medical schools.

Manipulation of the microbiome: The future of medicine?

Diet and lifestyle changes, and in some cases, remediation of poor indoor air quality, play a key role in repairing a dysfunctional microbiota. Unfortunately, most doctors know very little about nutrition, ancestral health, indoor mold toxicity, and the sick building syndrome, and they therefore have scant good advice to offer patients who suffer from health problems that are associated with a degraded, poorly functioning microbiota. Some medical professionals even believe that diet and microbial exposure have little, if any, impact on our health, a belief that may have been imprinted in their minds throughout a medical education that neglects the importance of these factors.

Another major issue at the moment is that there are no pills or drugs on the market that are specifically designed to repair a damaged microbiota. Most of the probiotic supplements on the market today only provide limited benefits, and some may even do us more harm than good. Fecal microbiota transplants have been shown to be very effective for some health disorders, but they are restricted by the medical industry, quite invasive, and expensive (at least those performed in a clinic). Not to mention the fact that many patients are grossed out by the whole procedure.

So, where does that leave us? We have to take responsibility for our own health and do the best we can with what we’ve got available to us. A lot of people can resolve their health issues “simply” by adopting a fiber-rich, whole foods diet and an ancestral lifestyle. However, for those with a severely damaged gut microbiota, this may not be sufficient to remedy the problem, meaning that to really be able to overcome – or at least slow down – the current epidemic of damaged gut microbiota, readily available and cheap solutions for repairing a dysfunctional microbiome may be required.

Final words

I think the overarching message from all of this is that we should all pay a little more attention to the invisible organisms that live on this planet alongside us. Not just the ones that inhabit our own body, but also the ones that live in our homes, in our soil, and in the guts of our pets; because in the end, it is all connected.


  1. But what is one to do once all the damage has been done – either by ignorance or by accidental disease (strep infection, trauma, etc)? How can beneficial bacteria be replaced once it’s been lost?

    • Hi Dana!

      This is something I’ve covered in-depth in many of my previous articles. If you browse through the posts on the human microbiome here on the site you’ll find many actionable tips.

      • I think if I had written this article I would have included a paragraph reminding everyone that the ‘western lifestyle’ that is in many ways responsible for the ‘evolutionary mismatch disorders’ is also responsible for more than doubling the Life Expectancy of those who live within that lifestyle….. I’ve met far too many people who want to use these issues as an excuse to tear down the agricultural infrastructure…. a swell idea if you are lucky enough to be one of those with enough wealth to afford the limited amount of food that could be produced if we eliminated all ‘non-natural’ processes from the farming/harvesting/food processing industries…

        • Hi dougwhite659!

          Welcome to the blog.

          I’ve discussed this issue/topic many times before on the site. I don’t want to have to bring it up in every post that covers something related to evolution, evolutionary mismatches, etc.

          The average life expectancy of industrialized people is much higher than among hunter-gatherers and traditional people, but that’s not because we today adhere to healthier diets and lifestyles, but rather because modern medicine (among other things) has helped us combat many acute illnesses (e.g., those caused by infections), decrease infant mortality, and prolong the lives of old, sick people. Basically, we’ve partly eliminated many of the selective forces that sculpted the human genome over millions of years. Improvements related to sanitation, hygiene, etc. also play a role, particularly when it comes to the increases in life expectancy that have occured over the last coupe of centuries in many developed countries.

          Modal (most common) age of adult death – which in contrast to average life expectancy is not affected by infant mortality rates – among hunter-gatherers is actually quite high.

          Here are two articles that cover this topic more in-depth:

          Thanks for your comment!

      • Michael Troy says:

        In Australia I have seen some remarkable turnarounds for people with severe mental illnesses like depression and Bipolar. I simply take them out for several sails on my yacht, often bring along my dog and feed them prebiotic feasts. They then have to come up with their own recipes and I make them all go for a swim and sip some clean seawater. I also advise them well everything you have outlined in this excellent article and all of them make immediate and lasting improvements. Pity they have to undergo years of torment dosed up with chemicals and confined to bed.

  2. I have a dear friend that I wish would read these articles. She’s been in the hospital several times recently, takes way too many prescription drugs, spends all her time running from one doctor appointment to another, and lives on processed junk food. Once I asked her if she ever cooks real food. She thought the idea was hilarious. She’s an educated person but doesn’t make the connection between what she puts in her mouth and the miserable state of her health. There are numerous other factors that could be improved upon, of course, but she isn’t open to suggestions, so I don’t say much.

    So thanks, Eirik, for all that you do for those of us who do care about our health.

    • I think you touch on one of the biggest problems with the general public’s perception of health, nutrition, and medicine here, Shary!

      Mainstream medicine and convenvential wisdom are built on the premise that prescription drugs, medicial procedures, etc. are the solution when it comes to preventing and treating disease. It’s often forgotten that many, if not most, of the chronic ills that plague us in modern societies are manifestations of an evolutionary mismatch. These disorders can’t be fixed with a botttle of pills from the pharmacy (This is not to say that prescription meds are never useful).

  3. Hi Eirik,
    I think you have to keep writing these type of blog posts, but I have to tell you that people like/enjoy the Western lifestyle, and the vast majority are unwilling to change, despite significant (and might I even say life-threatening) consequences. Having said that, even if you change only a handful of people, you will still have improved some lives, and that is always worthwhile. As well, your writing reinforces the attitudes of those who are already actively changing their life patterns.
    It makes for a good read, quite impassioned. You care. It shows. Bravo!

    • True!

      But I think it’s important to note that the message I want to get across with these types of articles isn’t that we should all go back to living as foragers in the wild (Something you, a regular reader of the site, of course are well aware of).

      We don’t have to give up all our modern comforts to achieve better health. It’s perfectly possible to adopt habits that positively affect gene expression (e.g., healthy diet, exercise) without giving up our iPhones and moving into the wild.

      It may be difficult – if not impossible – to attain “optimal” health in the evolutionarily novel environment we currently live in… But I would argue that’s not the goal either. Rather, I would argue that the goal has to be to find a balance between doing what is optimal in terms of health and longevity and what is enjoyable/pleasurable (Often these things interchange).

  4. Eirik, I never thought of miss matches between our inner and outer environment as the cause of allergies. It makes complete sense to me now. Excellent and well written article mate, well done.

    On a side note I played in the dirt yesterday and I loved it 🙂

  5. I have been suffering so long but the last 4 months have been hell and I’m not even living life just barely hanging on. Every specialist focuses on their area and will not even discuss other symptoms and how they might relate. They get angry that I refuse to take meds (other than thyroid) to mask my symptoms. My symptoms exploded in my second pregnancy with Hashimoto but also symptoms of Graves (7 years ago). Yesterday, after getting a thrush diagnosis, I decided to research further. I have learned that Candida can infiltrate every organ including the brain, especially people with autoimmunity.

    I have suffered unmanageable stress, my mothers and best friends deaths each in a pregnancy of mine, an incompetent endocrinologist and 4 miscarriages (one leading to sepsis), an ovarian dermiod cyst, endless ibuprofen and antibiotics, severe vitamin deficiencies, and through all of this I was a mom of two, waitressed, and completed up to my Masters.

    Last year I developed a thyroid nodule and a 6 month stretch of a sinus infection. Then pain in my knee, lymphadenopathy, 20 pound weight loss(I am 5 ft 5 and now weigh 98lbs) lymph nodes to swell. Candida in the stomach, indigestion, vomiting and malabsorption leading to rapid weight loss, despite eating and breakdown of natural enzymes and stomach acids(I also have very low stomach acids but diagnosed with Gerd?) The intestines, constipation, bloating, and cramping. The esophagus and throat, burning (mimics Gerd) swelling, difficulty swallowing and dryness (allergies I was told) hoarseness, and choking (nodule I was told) In the bones arthritis and muscles pain causing spasms, and numbness( knees and hips usually first site followed by spine and neck. My lymph nodes have grown into my hips)In the mouth thrush and ulcers. The sinuses, chronic sinusitis and burning. In the eyes, pressure, burning, gritty, light floaters (have seen my ophthalmologist who gave me drops). In the brain an abscess or multiple form (usually in the base, an MRI without contrast revealed an arachnoid cyst and I am wondering if it was misdiagnosed ) ringing in ears, headache, dizziness, vertigo, sweating, brain fog, cognitive and psychological decline, seizures, severe insomnia. So much pressure in my head that my neck wobbles and pain shoots down my spine. It can also infect the lungs and blood(thromboembolism? I have also got this diagnosis).

    Did I mention I am 36? My 10 year relationship has ended cause I never feel well and he cannot understand, amongst other reasons I chose to drop the stress. I have dropped from 6 shifts down to 3 and sometimes call out even then. I’ve put my PhD off because I can’t think about anything other than am I going to die before anyone figures it out. Other than the MRI no imaging has been done. No biopsies, other than thyroid, have been done. As my thyroid meds are dropped my TSH further suppressed and my t4 is dropping as well. I am told my blood count is normal and I have no fever or signs of infection. Yet, I had a piece of tissue left I my uterus after my first d&c and when I became ill, I was told the same thing and to take more ibuprofen. When I violently began vomiting I went to Er and my uterus was swollen and infected causing sepsis. I don’t run a fever, ever.

    I have the most amazing support system who tell me to keep searching and not to give up, even when I ask if I’m just crazy, they answer no. Sometimes, I’m not sure but I had never been sick before my son. Every doctor I see gives me a different diagnosis or answer. There are emergency protocols put in place because my loved ones are sure that I am having seizures while I am awake. The next time my head feels like it’s gonna explode (goes from pain level of 4-10 with no relief but that burning is always there and gets intense before an episode), I’m going to the ER before I end up in a coma. Sad that at this point I’m hoping its Candida because no one has ruled out cancer but it isn’t HIV, STDs, Mono, Lymes Disease, strep, or infection.

    • Hi Jamie!

      I’m sorry to hear about your situation.

      Let me know if you have any questions regarding how to get your microbiome/health back on track.

    • Jamie, I’m so sorry you’re having so many health issues. Please don’t give up looking for answers. I learned a long time ago that, contrary to popular belief, allopathic medicine doesn’t have all the answers, or even very many answers. An experienced naturopathic doctor might be able to help you resolve at least some of your issues. It’s worth a try.


  1. […] The next time you’re out on the street, take a look at the people around you: The suit-wearing, busy office worker on his way to work, the female shopper carrying huge bags of newly bought cl……  […]

  2. […] The Western Microbiome: How Our Modern Guts Make Us Sick, Fat, and Unhappy […]

  3. […] recent loss of microbial diversity from the human microbiota has largely been attributed to an overuse of broad-spectrum antibiotics […]

  4. […] can have widespread effects on our health and well-being. A Western diet and lifestyle selects for a microbiota that is very different from the ones our primal ancestors co-evolved with. Broad-spectrum antibiotics, caesarean sections, […]

  5. […] hygiene, c-sections, and a myriad of other factors have shaped modern microbiotas that are very different from those of our ancient ancestors. We’ve not only lost many microbial old friends, but also altered the overall community […]

  6. […] Our microbiota can also affect our survival and reproduction in other, more subtle ways. Microbes have far-ranging effects on our immunity, metabolism, brain function, and hormonal system. It has become increasingly clear to me over the years that the microbes associated with a human host can affect the host’s reproductive fitness through its impact on these components of our biology. Infertility, depression, impotence, and miscarriage are just some of the many conditions and events that are associated with chronic low-grade inflammation, which is tightly interlinked with dysbiosis and lack of microbiota diversity. […]

  7. […] but rather from a combination of factors that induce hormonal dysregulation, gut leakiness, loss of microbiota diversity, and abnormal gene expression patterns. In the modern world, most of us subject our bodies to […]

  8. […] (1, 2, 3). Moreover, it has become clear that a lot of people in contemporary, westernized nations carry a dysfunctional microbiota, lacking in diversity and stability, and that this is one of the reasons why chronic health […]

  9. […] novel foods, mold-contaminated buildings, and many other factors have produced microbiomes that are markedly different from those our primal ancestors […]

  10. […] that the human body’s ability to defend itself is compromised. Most people in the world today house a degraded microbiota and have a slightly compromised immune system; hence, they are prone to attacks by […]

  11. […] The microbiome of the modern man is in a sorry state. Unless microbiome restoration becomes a prioritized part of health-care, the prevalence of inflammatory bowel disease, type-1 diabetes, food allergies, irritable bowel syndrome, and many other chronic diseases and health problems will continue to increase. A Government-led effort to develop and mass-produce microbiota capsules containing broad spectrums of microbes that are adapted to live in the environment of the human body could dramatically improve public health and reduce health-care spending. […]

  12. […] temperature as well. They may even be the chief regulators of the thermostat. People who harbor an imbalanced, degraded gut microbiota are probably less tolerant to cold than healthy folks, due to the fact that their microbiota […]

  13. […] temperature as well. They may even be the chief regulators of the thermostat. People who harbor an imbalanced, degraded gut microbiota are probably less tolerant to cold than healthy folks, due to the fact that their microbiota […]

  14. […] temperature as well. They may even be the chief regulators of the thermostat. People who harbor an imbalanced, degraded gut microbiota are probably less tolerant to cold than healthy folks, due to the fact that their microbiota […]

  15. […] Combine that with the fact that we’ve become increasingly disconnected from the natural world and that it’s become very common to deliver babies via c-section and feed them formula, as opposed to breast milk, and you can quickly understand why the microbiome of the modern man is in such a sorry state. […]

  16. […] our modern lifestyle, saturated with antibiotics, processed foods, and other microbiota-disruptors, we’ve changed the microbial communities that colonize our bodies. These changes have made us sick and fragile. We’re at an increasing rate becoming allergic to […]

  17. […] for quite a while (1, 2, 3, 4). Not only have we, via our modern diet and lifestyle behaviours, altered the configuration of our microbiotas, but we’ve also caused a loss of biodiversity from the human superorganism. These changes have […]

  18. […] and lifestyle habits, have altered our microbiotas and that the microbiota of the western man is markedly less biodiverse than the microbiota of the typical hunter-gatherer. It’s also true that people who live or lived in non-industrialized environments often harbor […]

  19. […] vegetables, are great in that they contain a lot of live bacteria that can help us rebuild our damaged microbiotas; however, I think it’s very important not to go overboard with respects to the consumption of […]

  20. […] environment we currently find ourselves in, we’ve not only altered our living conditions, but we’ve also altered the microbial communities that our bodies interact with. There hasn’t been sufficient time or selection pressure for natural selection to adapt our […]

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