The Root Cause: Rethinking Health Through the Microbiome

The human intestinal microbiome is fascinating, and it goes far beyond taking a probiotic supplement and hoping your digestion improves.

Your gut microbiome refers to the microbes living throughout your digestive tract, not just your stomach. The more we learn about it, the clearer it becomes that these microbes are involved in much more than breaking down food. They play a role in digestion, immune function, inflammation, metabolism, the strength of the gut barrier, and communication with the brain through what is known as the gut brain axis.

That gut brain connection is one of the most interesting parts of the conversation to me. It is wild to think that the microbial environment in your gut may influence how you feel, how you think, and even the kinds of foods you tend to reach for. I would be careful about saying a single bacterial species is directly telling your brain what to put in your mouth, but the microbiome clearly affects appetite, cravings, mood, and behavior through nervous system signaling, inflammation, and the compounds these microbes produce. Your brain is not operating separately from the rest of you, and your gut is part of that conversation whether people realize it or not.

This is one reason I think the microbiome deserves more respect than it gets. Gut health often gets reduced to digestion, bloating, and what supplement to buy next, but a disrupted microbiome can affect far more than what happens after a meal. Poor microbial diversity and dysbiosis have been linked to a long list of chronic health issues, including inflammatory bowel conditions, obesity, insulin resistance, type 2 diabetes, autoimmune issues, mood disorders, and other inflammatory problems. That does not mean the microbiome is the only cause, but it does mean it is a major player.

What I find especially interesting is the comparison between modern industrialized populations and people living much closer to how humans lived for most of history. Studies looking at hunter gatherer tribes and other non industrialized populations in different parts of the world have found a level of microbial diversity that tends to be much richer than what is seen in the average urban westerner. These groups often look surprisingly similar to each other in terms of diversity, while the average American microbiome falls short by comparison.

If people living in very different environments still share some common features in their microbiome, and those features look very different from what we see in modern industrialized life, then it is worth asking what we have changed. I think the answer is pretty obvious. We have changed the food, the water, the environment, the amount of time we spend outdoors, the amount of stress we live under, the products we put on our bodies, the medications we use, and the amount of processed junk the average person eats in a week.

That is also where the idea of keystone species gets interesting. Certain microbes seem to play an outsized role in keeping the ecosystem balanced. Dr. William Davis talks about examples like Lactobacillus reuteri and Bifidobacterium infantis, microbes that may be far less common in modern humans than they once were. Whether his exact list is the final word is not really the point. The bigger point is that the modern gut appears to be missing important players that may have been much more common in our ancestors and in people still living closer to traditional lifestyles.

To me, that changes the gut health conversation. Instead of only asking what supplement to add, I think we need to start asking what daily inputs may be disrupting the terrain in the first place. If the microbiome is connected to digestion, inflammation, immune function, metabolism, and the brain, then cleaning up the inputs matters a lot more than chasing the next powder or pill.

That is a big part of what I help coach people through. I help them step back, look at the bigger picture, identify the gut disruptors that may be getting overlooked, and build a more practical way of eating and living that supports the body instead of constantly working against it.