All Disease Begins in the Gut: Why Your Microbiome Matters More Than You Think

“All disease begins in the gut.”

The ancient Greek physician Hippocrates’ words are as true today as they were 2,000 years ago.

Long before we had microscopes or microbiome maps, Hippocrates knew that the gut is more than a digestive organ — it’s a command center for the entire body, influencing immunity, inflammation, mood regulation, hormone balance, and more.

If it’s not functioning well, chances are high that the other systems in your body aren’t either. And reciprocally, if you’re experiencing an imbalance in another area of your health, the first thing to do is to look back to the gut.

The Gut: Your Body’s Ecosystem in Action

Inside your intestines live trillions of microorganisms — collectively called your gut microbiome. We could not function without it; these bacteria, fungi, and viruses work with your body to digest food, absorb nutrients, regulate inflammation, and maintain your immune defenses.

A healthy microbiome is diverse in its microorganisms, balanced in its composition, and resilient in its function. And one of its key functions is to produce a mucus layer that coats and protects the gut wall. 

If the microbiome is disrupted, this mucus layer is damaged, leaving the gut wall vulnerable. This disruption can be caused by many aggressors: an inflammatory diet, frequent or long-term antibiotic use, acute GI illnesses or infections, food sensitivities, or allergies, to name a few. 

And like a broken pipe, a compromised gut wall leaks — quite literally. 

When this happens (a condition often called “leaky gut” or intestinal permeability), toxins and undigested food particles can pass through the gut wall and leak out into the body,  triggering systemic inflammation.

That inflammation becomes the fuel for other diseases and symptoms.

Sarah Bird, DNP, nurse practitioner at PALM Health, breaks down the top four pathways through which gut imbalances can affect other areas of your health and why that is.

1. Gut Health to Hormone Balance

Your microbiome plays a key role in regulating estrogen, cortisol, insulin, and thyroid hormones. If you have a disrupted or “leaky” gut, a few things can happen:

• Estrogen overload. There is a subset of gut bacteria called “estrobolome” that help metabolize and excrete excess estrogen. “If the gut is imbalanced, estrogen is not excreted efficiently and can recirculate, fueling symptoms like painful periods, PMS, hormonal headaches, bloating, and even increased risk for hormone-sensitive cancers,” says Sarah. This estrogen dominance is also the foundational imbalance for conditions like endometriosis.
• An overactive stress response. A disrupted gut sends distress signals to the brain, leading to a constant release of cortisol (the key stress hormone) and keeping your body in a fight-or-flight state. Long-term, this can disrupt sleep and lead to adrenal fatigue, not to mention heightened feelings of stress and anxiety (more on this later). 
• Insulin resistance. Chronic inflammatory responses from poor gut health can affect your blood sugar and metabolic health over time. The insulin hormone acts as a “key”; when you eat and your blood sugar rises, insulin unlocks your cells to allow the glucose to leave the bloodstream and enter the cells, giving them energy to function.

The leaky gut-induced inflammatory response tampers with the “lock” (also known as the insulin receptor), so the cells don’t respond to the insulin. So, what does the body do? It becomes confused, and produces even more insulin to try to get that lock open. 

The result: Elevated insulin, which can lead to weight gain, chronic blood sugar swings, and metabolic disorders.

The thing about insulin resistance, too, is that it’s a self-perpetuating cycle that can also influence other hormones. Think of it as a leaky gut → insulin resistance → hormone dysfunction triangle. Once insulin is elevated, it can also drive androgen production and disrupt ovulation, becoming a foundation for both PCOS and endometriosis patterns.

When your gut is balanced, your hormones follow suit. When it’s not, everything from your cycle to your sleep to your resilience can fall out of sync.

2. Gut Health to Immunity and Autoimmunity

Did you know that over 70% of your immune system lives in your gut?

That’s no coincidence. “Your microbiome is your first line of defense,” says Sarah. “It trains immune cells to distinguish friend from foe, produces antimicrobial compounds, and fights viruses.

An unhealthy gut, however, can go rogue. When the gut lining is compromised, the ensuing inflammation triggers a constant immune response, and over time, the immune system goes into overdrive. It struggles to differentiate helpful molecules from aggressors and reacts to everything, including our own tissues.

This is what we call autoimmunity.

Autoimmune conditions like rheumatoid arthritis, lupus, Hashimoto’s thyroiditis, and inflammatory bowel disease stem from a dysfunctional immune system that attacks itself. This is also the case for individuals who frequently get sick with viral infections.

And, they all have root-cause links to gut dysbiosis. So, while certain medications and multi-factorial treatments may be necessary to manage and heal autoimmune conditions, the gut cannot be overlooked as a key piece of this puzzle.

3. Gut Health to Mental Health

Your microbiome doesn’t only connect to your physical health. Colloquially named the “second brain,” the gut also directly influences your emotional well-being.

Your gut and brain are in constant conversation via the gut-brain axis, a kind of highway system running between the two. This system encompasses the well-known vagus nerve, the remote control for your parasympathetic, “rest-and-digest” response.

All of this matters because if the gut is leaky and dysfunctional, its communication with the brain will be leaky and dysfunctional.

In fact, your gut makes about 90% of your body’s serotonin (the “feel-good” neurotransmitter) and sends it to the brain. Imagine how this process may be disrupted if the gut isn’t properly functioning: the result looks like mood swings, brain fog, anxiety, and even depression.

And on the other side: a balanced, diverse microbiome can help your mood and cognitive function stay regulated and stable. Happy gut, happy mind!

Start in the Microbiome

Each person’s gut microbiome will have different needs, which is why proper testing and personalization are key to approaching gut healing. But we do know that there are some helpful key guidelines that may benefit everyone as a starting point.

Here’s what Sarah recommends:

• Eat fiber-rich, whole foods to feed your beneficial bacteria.
• Diversify your diet. More diversity in the foods you eat = a more robust, healthy microbiome.
• Add fermented foods like kimchi, yogurt, and sauerkraut to your diet to repopulate the types and quantities of healthy bacteria.
• Cut down on processed foods and artificial ingredients like gums and sweeteners, which are known aggressors of inflammation.
• Test for food sensitivities and allergies to determine any triggers specific to you.
• Work directly with a functional medicine provider to get personalized and detailed recommendations.

One of the most common misconceptions about the microbiome is that poor gut health necessarily means you must have digestion-related symptoms: stomach pain, constipation, et cetera.

This isn’t strictly true. While some may have these in their symptom repertoire, many don’t — and this is why gut imbalances remain underdiagnosed and untreated.

Remember: clues that point to a struggling microbiome can be anything from hormone imbalances and PMS to weight gain to anxiety. So, in functional medicine, we follow Hippocrates’s guidance. We always start with the gut.

And, if you’re someone who feels like you’ve tried everything for your symptoms and found no answers, this information may give you some hope — there are more solutions to explore if you know where to look.