Mainstream Medicine Overlooks the Two Major Causes of Chronic Illness

woman-medicinesScientific research carried out over the past couple of decades has shown that dysbiosis (microbial imbalance) and inflammation are at the root of numerous diseases and health problems, including acne vulgaris, colon cancer, chronic depression, and autoimmune conditions such as type-1 diabetes (1, 2, 3, 4, 5, 6, 7, 8). Dysbiosis and inflammation can develop secondary to disease; however, it’s also well established that these conditions can drive the development of disease, both chronic and acute. 

Unfortunately, many doctors are unaware of these things, which isn’t really surprising, given that most medical students learn little about dysbiosis and chronic low-grade inflammation – the type of inflammation that goes hand in hand with chronic disease. Moreover, these two conditions aren’t picked up on the standard blood tests that general practitioners carry out on their patients. Most doctors conduct C-reactive protein tests, but unfortunately, these tests are rarely used in the context of the treatment of chronic disease. They are generally conducted to rule out severe inflammation. They are less frequently used to detect and correct low-level inflammation.

Instead of addressing the underlying factors that drive the progression of the aforementioned diseases, most mainstream health practitioners target the symptoms: they prescribe various antimicrobial creams to patients with acne; put people with diabetes on a lifelong supply of insulin, without considering the possibility that it could be possible to reverse the progression of the illness and perhaps even bring the pancreatic beta cells back to life; they largely overlook the vital importance of diet and gut microbiota composition in the pathogenesis of colon cancer; and they go the pharmaceutical route to treat chronic depression, rarely considering why depression develops in the first place.

I wish I was exaggerating here, but I’m actually not. This is very much the way mainstream medicine operates at the moment. I’m frequently contacted by people who’ve gotten no real help within the conventional medical system and are desperate to find solutions to the chronic ills that plague them.

Perhaps needless to say, not all mainstream health practitioners adhere to the aforementioned strategy – there are some good guys out there. However, as a whole, I think it’s safe to say that we have a long way to go before our health care system deserves its name. At present, we’re not taking good care of people’s health; we’re merely trapping them in a vicious cycle of drugs, illness, and despair. As someone who conveys health/medical information to the public and regularly works with people who suffer from a variety of different health disorders, I work tirelessly to turn this vicious cycle into a virtuous one.

I believe one of the first and most important steps we can take to bring about this change is to cool down the body of the modern man, bringing down the levels of inflammatory compounds in his bloodstream, and manipulate his microbiome in such a way that it reaches a state that matches better with his genetic make-up.

Dysbiosis + Inflammation –> Fatigue, gastrointestinal problems, low libido, low energy levels, impaired mental functioning, and chronic illness

A body that is chronically inflamed and harbors an imbalanced microbiota is a sick body!

Everything falls apart if the microbial ecosystem of the body is somehow messed up and an internal, inflammatory fire starts burning. The liver becomes overloaded with toxins; substances that shouldn’t be allowed to pass from the gut into systemic circulation are allowed to pass; the blood-brain barrier becomes compromised; and the whole hormonal system spins out of control. Together, these changes can cause a range of health problems, including insulin resistance, bloating, fatigue, food intolerance, sexual dysfunction, and depression (2, 5, 6, 7, 8, 9)

It’s all connected. No organ system, receptor, or hormone operates in isolation.

All of the above conditions have a somewhat similar etiology and are a part of a bigger cascade of problems. Hence, if a patient suffers from let’s say chronic fatigue, then chances are he also suffers from depression, irritable bowel syndrome, and/or other chronic health problems.

This is something that seems to elude mainstream medicine. Instead of viewing the human body for what it is – a complex biological system that has been shaped over eons of time by evolutionary forces – the conventional medical community has historically viewed the body as a machine. If one part of this machine is damaged, efforts are put into “repairing” that part. Little attention is typically paid to the rest of the machinery and how the various components interact.

For example, in the case of mental health problems such as autism and ADHD, virtually all of the attention has historically been on what goes on in the brain. This is unfortunate, because a solid body of evidence indicates that many mental health problems actually originate in the gut – not in the brain (9, 10, 11, 12, 13, 14). In my mind, there’s little doubt that gut dysfunction is at the root of a long list of mental health problems.

A multifaceted treatment approach is required to combat dysbiosis and chronic inflammation

The conventional, drug-based approach to treating the types of chronic health problems we’ve talked about so far has proven to be largely ineffective, which is not surprising, given that it’s impossible to resolve complex genome-environment conflicts with a pill or a cream.

I would argue that in order to effectively treat the chronic ills that plague the modern man, we have to acknowledge that virtually no disease or health problem develops in isolation. If one part of the human body exhibits signs of disease, then chances are something is wrong deeper down in the system and that many other parts of the body are also functioning at suboptimal capacity.

If this is the case, it will obviously be futile to try to treat only the part of the system that signals the presence of disease. To really make some headway, we have to dig a little deeper and try to find out where the problems we see originated.

Typically, if we dig in the right direction and go deep enough, we’ll find dysbiosis and inflammation. They may not be the only things we find, but they are typically dominating in their presence.

The dysbiosis/inflammation pandemic is largely caused by the hurricanes of evolutionary mismatches that have swept across the globe over the past 10.000 years. There are no simple solutions to this public health problem. We can’t simply give sick people some pills and expect their problems to go away. We have to get to the root of the problem, something that can only be done via the evolutionary route. We have to acknowledge that many, if not most, of the chronic ills that plague us in the 21st century don’t develop because the human body is inherently flawed, but rather because we expose our bodies to an environment for which they are poorly adapted (1, 3, 15, 16, 17). We bombard them with drugs, grains, processed foods, pollutants, and many other harmful agents. It’s a wonder some – not many – people seem to maintain okay health.

Here’s what a 2015 review paper had to say about this matter:

Chronic inflammatory diseases are a major cause of morbidity and impaired work and social functioning and are responsible for 35 million to 52 million annual deaths worldwide. A state of low-grade inflammation might be considered the “cause of causes” for these deadly and disparate conditions. In contrast to inflammatory patterns observed in hunter-gatherer groups living more in accord with lifestyles that were prototypical across human evolution and in which inflammatory responses are brisk and time-limited (i.e., resolving within a maximum of 42 days), in the modern world chronic proinflammatory activity can last for weeks, months, or even years. (18)

A Paleo-inspired lifestyle, coupled with microbiome restoration (e.g., via fermented foods or microbiota transplants), is the “medicine” of choice to treat chronic inflammation and dysbiosis. It’s the only medicine that effectively addresses the evolutionary mismatches that underlie these conditions. Not everyone will be able to overcome the chronic ills that plague them by adopting an evolutionary approach to health, but many probably will. At the very least, they will experience marked health improvements.


  1. I have Alpha-1 Antitrypsin Deficiency which appears to cause worse than normal inflammatory problems. My main problem is chronic and severe IBS issues so far, but switching to Paleo (and SCD) Diet, intermittent fasting, and fermented foods have helped a lot (though still not perfect).

    I am glad I found this and hope to delay COPD & Empysema onset caused by my genetic disorder.

  2. Microbiome restoration isn’t an easy thing to get… how do we get one? Is there a DIY version that’s safe? That we can do ourselves? How do we choose a donor? What could possibly go wrong? Any other ways to restore it? Can we eat dirt, for example? Can we live in a woodland for a month? I’m being serious… what can someone whose tried everything do? The probiotics and the fermented foods didnt work for me! I eat ‘clean’. I live ‘clean’ and I’m tired. I just want to eat without reactions ask the time and get rid of my food intolerances.

    • you may find many answers to your questions by researching Dr. Mercola, Dr. Axe, Chris Kresser, Dr. Alessio Fasano, orthomolecular medicine and intestinal hyperpermeability…also known as leaky gut. I have studied guys like these for the past 4 years, and was able to reverse 24 chronic conditions. People get confused on what “clean eating” actually is due to the biases of mainstream media. A good place to start would be an elimination diet (Tom Malterre has good info). Also, seriously reducing stress and getting at least seven hours of sleep a night is imperative for anything tried to work. Good luck to you.

      • Thanks Carol, I already follow most of them and have been researching extensively also. Healed my sibo (I believe) and did everything to heal leaky gut including fasting, whole 30 and elimination diet. Bone broth. Gelatine. L-glutamine. Colostrum. I eat gut bacteria friendly foods. Grapes. Sweet potatoes. Garlic. Onions… i make fermented foods. Took probiotics. De-stressed. Sleep in a dark room. Only drink water from glass bottles (no plastic). Get sun. Gentle exercise. Gave up cosmetics, body care, and house cleaning chemicals. Wear natural fabrics. Barefoot shoes. Squat. Everything… I even bought two hens for the organic eggs… and I still have food intolerances! The only thing left for me to try, I think, is either healing my emotions/ past trauma/negative thought (possible cause of disease according to Bruce lipton.) I don’t know… hormones? And fecal transplant.

        • What you are doing sounds very familiar to me, as I practice all of these lifestyle adjustments as well. Perhaps MMT may be the answer for you? Metabolic Mitochondrial Therapy, with the use of cronometer. It is described in Dr. Mercola’s new book, Fat for Fuel. Today is day 1 for me in doing it wholeheartedly, with intermittent fasting a key part of it, and he says it heals a lot. It is a more structured version of the keto diet. Very low in all sugars (carbs) and also low in protein, while being high in fat. Grapes are high in sugars. Cronometer is a great tool. Much more precise than is MyFitnessPal.

          • additionally, you do not mention grains. I found that the elimination of all grains and beans are integral to healing. Very limited nuts, due to the phytic acid wearing away at a weak gut lining, which is what you undoubtedly still have due to having food sensitivities. Nuts should be soaked and sprouted before consumption/

          • Carol, I’ll check it out. But in terms of diet I don’t believe keto is right for me… I’m very much in favour of feeding my microbiome so if I’m not avoiding my intolerances, I’m feeding my gut! Grapes may be high in sugars, but they are a favourite food of gut microbes! (And my focus right now is in feeding my critters!) I don’t eat any grains or beans (though I can tolerate lentils and chickpeas). I will take a look though! Thanks for the info!

  3. I’ve had emphysema for four years. I was taking Spiriva and Advair. I started with oxygen at night, and later all day long. Nothing seems to help. The minute I start to walk around the breathing gets bad. Even the oxygen doesn’t seem to help.I smoked for approximately four years, from age 18 to age 22. I am now age 66 plus. I had for some time now noticed having difficulty catching a deep breath. Never in my wildest dreams did it cross my mind that I may develop a serious lung disease, but here I was with a serious case of COPD. I am only writing this to inform others that nothing was really working to help my condition.I went off the Spiriva (with the doctor’s knowledge) and started on Emphysema herbal formula i ordered from Health Herbal Clinic, my symptoms totally declined over a 5 weeks use of the Emphysema disease natural herbal formula. i am now almost 68 and doing very well, my lungs are totally repaired!!


  1. […] my recent article entitled Mainstream Medicine Overlooks the Two Major Causes of Chronic Illness I made the case that dysbiosis and chronic low-grade inflammation are at the root of a long list of […]

  2. […] in human disease has the potential to completely revolutionize the field of medicine. Historically, mainstream medicine has paid very little attention to the trillions of microorganisms that colonize …. It’s long past time that this […]

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