The Origin of Illness (the Microbiome~)

My understanding of the microbiome is evolving.

New research is surfacing almost every day. Some of it I don’t fully comprehend.

Most recently, I’ve been reading David Perlmutter’s Brain Maker, which simplifies things enormously.

Here’s a step-by-step (with diagrams~) of my current understanding of the origin of illness. As ever, I welcome your thoughts.

The Origin of Illness

Both health and illness begin in the microbiome.

Here’s the basic idea:

Microbiome 1

My initial understanding involved a 3-step process:

  1. Inflammatory food upsets the balance of the bacteria in the gut, resulting in intestinal permeability.
  2. This allows foreign particles to leak into the body, causing systemic inflammation.
  3. Inflammation causes disease.

The connection between diet and gut health is the foundation of the nutritional elements of the Autoimmune Protocol as outlined in The Paleo Approach by Sarah Ballantyne, (as well as all other evidence-based healing protocols like the The Wahls Protocol and The Bulletproof Diet).

But not only autoimmune conditions are caused by an unhealthy imbalance in the microbiome: it seems that most illnesses are.

The notion that most chronic health conditions are at least partly caused by inflammation is, in itself, a radical departure from the previous, mechanistic understanding of health. But this story gets way more interesting:

Microbiome 2

Inflammation isn’t the only cause of health problems.

We also need to consider genes & environment. Which leads us to…


Epigenetics is the study of the interaction between genes & environment. It’s partly this interplay that determines whether or not a genetic predisposition to a particular disease gets activated in response to systemic inflammation.

And helps explain why one person might get Psoriasis while another one gets Multiple Sclerosis.

Here’s a cute overview on Epigenetics:

The Origin of Gut Dysbiosis

Gut dysbiosis is an unhealthy imbalance in the microbiome and as mentioned, it is this imbalance that is a primary culprit in illness.

What causes an imbalance?

In addition to an unhealthy diet, chemicals (like chlorine); environmental factors (like excessive hygiene); side effects from drugs (including antibiotics); Caesarean birth and formula or bottle feeding all contribute to dysbiosis.

Before we are born, we have a minimal microbiome. We begin to acquire a robust one at birth. A vaginal birth followed by breastfeeding is the best possible way to get a healthy and protective microbiome started.

Interestingly, Dr Natasha Campbell-McBride suggests that a newborn receives microbiota from both the mother and the father (or the mother’s other sexual partners) during vaginal delivery. Which gives a whole new meaning to the term ‘dirty sex’~!


Stress is a really big deal.

Not only does ongoing stress contribute to gut dysbiosis through elevated cortisol levels, but gut dysbiosis causes stress.

And because chronically elevated cortisol levels contribute directly to intestinal permeability and inflammation, stress creates a nasty reinforcing loop of disease-provoking conditions in the body.

What causes stress?

Modern life.

We just weren’t designed for living this way.

Microbiome 3

 Toxins in the Brain

We used to think that the blood-brain barrier protected the brain from toxins. According to David Perlmutter in Brain Maker, that isn’t so.

Intestinal permeability allows toxins into the body and some of these travel up to the brain.

This is one explanation for the mental health epidemic we are now experiencing, including widespread depression and anxiety.

Remarkably, toxins can stress the brain into perceiving threat, which automatically triggers a neurological takeover by the limbic system.

The limbic system does a great job of protecting us from old-school hazards like predators, but is incapable of higher reasoning or anything approaching enlightenment, and simply can’t navigate the complexity of modern life.

So these toxins not only provoke depression and anxiety, but can render us incapable of making good decisions.

The Collateral Damage of Chronic Health Conditions

Compounding the problem, people who end up with chronic health conditions end up dealing with a host of other factors that contribute to stress, including pain, financial impacts and negative effects on relationships, which add add to the stress fest that help create their illness in the first place.

Microbiome 4

Mental Health

Obviously, the presence of toxins in the brain isn’t the only cause of mental health issues. The whole point of creating a convoluted spaghetti diagram like this one is that the origin of illness is complex.

In addition to epigenetics (genes & environment), trauma & brain architecture are significant factors to consider when thinking about our mental health.

I haven’t seen any reference to the connection between microbiome research and neurological development research in the literature, but it’s highly relevant.

(Still with me? We’re almost done~!)

Toxic Stress & Brain Architecture

Neurological research over the past 20 years has demonstrated that toxic stress in childhood changes the architecture of the brain.

The Harvard Centre on the Developing Child is a wonderful repository for this research.

The basic idea is that all children experience stress, but prolonged stress without the support of a caring adult is toxic to early brain development and permanently impairs executive functioning.

The ability to handle stress, fascinatingly, is wired into the same part of the brain as executive function skills, so that reduced executive function capacity also results in reduced ability to handle stress throughout the lifespan.

Executive function skills are also exactly what become impaired in an adult who experiences brain fog as a symptom of systemic inflammation.

Trauma & Nervous System Dysregulation

Finally, trauma, whether it occurs during childhood or adulthood, can result in nervous system dysregulation, which also impairs the body’s ability to manage stress.

So there it is.

My current (& no doubt flawed & incomplete) understanding of the origin of illness.

Next up: what we can do about it~!

25 thoughts on “The Origin of Illness (the Microbiome~)

  1. That’s pretty much how I see it. Simple in some ways but incredibly complex in the sense that each person comes with their own unique terrain and history of stressors. That means no one size fits all but a unique size for every individual. This is where bio hacking comes in. No way to deal with this magnitude of investigation, trial and error etc. on a society wide basis. At least not any time soon.

  2. Petra – I think this is my most favourite of all your blog posts to date. I know – BIG call. I love your way of dissecting and collecting disparate pieces of information and reforming them in your unique Petra way. It’s both informative and engaging.

    The stress-factor is what I’m particularly interested in at the moment.

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