Every cell in your body depends on what happens in your gut. If your digestion isn’t working properly, no amount of clean eating, supplements, or willpower can make up for it.
Everything Starts in the Gut!
One of the most eye-opening lessons I discovered at the beginning of my journey in natural medicine was why gut health is so important in functional medicine.
It quickly became clear that digestive health was a central focus—something my primary care doctor had never once asked me about.
Walk through any modern pharmacy or supermarket today and you’ll see an entire aisle devoted to digestion—antacids, laxatives, probiotics, fiber powders, gas relief, digestive enzymes, and more.
The sheer volume of these products tells a simple yet sobering truth: our digestive health is suffering. Long before the age of pharmaceuticals and diagnostic machines, healers across cultures understood that the gut is the foundation of wellness.
The ancient Greek physician Hippocrates declared, “All disease begins in the gut.”
In Traditional Chinese Medicine, the stomach and spleen are known as the body’s “center burner,” where nourishment and energy are created.
Ayurveda describes Agni—the digestive fire—as the source of both vitality and disease.
James Sensenig, ND, the founding president of the American Association of Naturopathic Physicians and a dear friend, beautifully expressed how natural medicine approaches the root causes of illness through his classic naturopathic principles.
He often said, “All disease is caused by the breakdown of normal function within the body in one of three areas: the body is not getting what it needs, the body is not eliminating what it cannot use, or the vitality is low.”
When you think about it, the first of these—“the body is not getting what it needs”—isn’t just about eating healthy foods. It also depends on how well we digest and absorb them.
Digestion Was a Principal Focus as I Began My Path
In the mid-1990s, as I began my journey in natural medicine, I noticed an intense focus on digestive function as the cornerstone of a healthy body.
I attended countless lectures on dysbiosis—an imbalance between harmful and beneficial bacteria in the digestive system that can quietly undermine well-being.
Another frequent topic was leaky gut, a condition in which partially digested food particles pass through an inflamed intestinal lining and enter the bloodstream. This process can trigger the immune system to react as though those particles were foreign invaders.
We also discussed malabsorption, a related issue where the body fails to fully digest and absorb vital nutrients. These nutrients, instead of being used for repair and energy, are lost through the stool.
At the time, there was particular attention on protein malabsorption, which can deeply affect energy, immunity, and tissue health.
It became clear to me that natural and functional medicine recognized digestion as the foundation of good health—and poor digestion as the starting point of disease.
The Microbiome: The Missing Organ
One of the greatest rediscoveries in modern biology is the human microbiome—the vast community of bacteria, fungi, and viruses that live within our intestines.
Together, these trillions of microbes outnumber our own cells by roughly ten to one and carry more than 150 times the number of genes found in the human genome.
These microbes are far from passive passengers; they are active collaborators that:
- Digest fiber and produce short-chain fatty acids to nourish intestinal cells and calm inflammation.
- Synthesize essential vitamins, including B12 and K2.
- Regulate the immune system, teaching it to distinguish friend from foe.
- Communicate with the brain through the vagus nerve and neurotransmitters such as serotonin and GABA.
When the microbiome is diverse and balanced, it maintains a peaceful partnership with its host—you. But when it becomes disrupted by antibiotics, processed food, excess sugar, or chronic stress, harmful species can take over.
The result is inflammation, a “leaky gut,” and immune dysfunction.
These ideas circulated within the natural and functional medicine community long before the term microbiome was officially coined in 2001.
Elizabeth Lipski, PhD, CCN, was among the first clinical nutritionists to weave together functional medicine, naturopathic principles, and nutritional biochemistry into a unified model of gut-centered wellness.
When her book Digestive Wellness was first published in 1995, terms like microbiome and gut-brain axis were not yet part of mainstream medicine—but Lipski was already describing their concepts in clear, practical ways.
I still remember hearing Dr. Lipski speak at an Institute for Functional Medicine conference in the 1990s, along with other pioneers who were expanding our understanding of gut health.
Since then, the study of the microbiome and its influence on human health has grown tremendously in both natural and conventional medicine. I’ll be sharing a follow-up post soon, exploring this fascinating subject in more depth.
From Digestion to Disease: The Research Is Clear
Modern research is finally catching up. Over the past two decades, hundreds of studies have revealed strong links between poor digestive health and a wide range of chronic conditions.
What was once dismissed as “alternative speculation” has now become a leading frontier in mainstream science.
- Autoimmune Disease: Research published in journals such as Nature Reviews Immunology shows that intestinal permeability and dysbiosis can trigger autoimmune reactions.
When bacterial fragments cross a leaky gut barrier, the immune system becomes confused and begins attacking the body’s own tissues. - Metabolic Disorders: Studies in Cell and Science have found clear associations between gut microbial patterns and obesity, insulin resistance, and type 2 diabetes.
The gut bacteria of obese individuals differ markedly from those of lean individuals, influencing how calories and nutrients are absorbed and stored. - Mental Health: The emerging field of psychobiotics explores how gut microbes create neurotransmitters that affect mood and cognition.
Altered microbiota have been linked to anxiety, depression, autism, and even age-related cognitive decline. - Cardiovascular Disease: Certain gut microbes metabolize dietary compounds like choline into TMAO—a molecule associated with atherosclerosis.
In contrast, fiber-fermenting bacteria produce anti-inflammatory metabolites that protect cardiovascular health. - Sarcopenia and Aging: New research shows that older adults with lower microbial diversity absorb protein less efficiently, leading to muscle loss, weakness, and frailty.
These findings are not fringe correlations; they represent causal mechanisms being uncovered through genomic sequencing, metabolomics, and rigorous clinical trials.
How Conventional Medicine Approaches Digestive Health
If digestion is so foundational, why isn’t it treated that way in conventional medicine? The answer lies in the system itself—its training and structure.
Primary care physicians are taught to manage disease through standardized algorithms: matching symptoms to diagnoses, and diagnoses to medications.
Unless digestive issues become severe enough to require a gastroenterology referral, most physicians tend to:
- Prescribe proton pump inhibitors (PPIs) for reflux.
- Suggest fiber supplements or laxatives for constipation.
- Recommend antibiotics for suspected infections or small intestinal bacterial overgrowth.
- Refer patients for colonoscopy when red flags appear.
This approach excels in acute care—managing ulcers, infections, and inflammatory bowel disease—but it often falls short when dealing with chronic, functional imbalances.
Why the Primary Care Approach Falls Short
- Reductionism: Conventional medical education often treats digestion as a simple, mechanical process that takes care of itself unless something is visibly wrong.
Subtle dysfunctions—such as low stomach acid, pancreatic enzyme deficiency, or bile stasis—are typically overlooked. - Pharmaceutical Bias: The go-to solution is to suppress symptoms rather than restore normal function.
For instance, PPIs reduce stomach acid and provide short-term relief, but over time they can impair protein digestion and hinder mineral absorption, worsening the root issue. - Time and Reimbursement: Insurance-based appointments usually last just 10 to 15 minutes—barely enough time to write a prescription, let alone explore diet, stress, or lifestyle factors that influence digestion.
- Fragmented Specialization: Gastroenterologists focus on what can be seen through scopes or imaging, while nutritionists (if consulted) concentrate on food choices.
True collaboration between the two is rare, leaving many gaps in care.
For patients with chronic bloating, reflux, or fatigue, this fragmented system often ends with a few prescriptions and the reassurance that “your labs look normal.”
Yet the deeper question remains unasked: why isn’t your body processing nourishment properly?
The Functional Medicine Approach: Restoring the Root
Functional medicine begins from a very different premise: the body functions as an interconnected network, not a collection of separate parts.
In this model, the digestive tract is more than a single “system.” It’s the hub through which nearly every other system—immune, endocrine, neurological, and detoxification—interacts. The goal isn’t to silence symptoms but to restore normal function and balance.
1. Understanding the Terrain
Instead of asking, “What disease does this patient have?” the functional practitioner asks,“What internal environment allowed imbalance to take root?”
To find that answer, they explore how food, microbes, stress, toxins, and genetics interact within the individual. Testing may include:
- Comprehensive stool panels to assess microbiome diversity, enzyme output, and inflammation.
- Breath tests to detect bacterial overgrowth or fermentation patterns.
- Food sensitivity and antibody profiles to identify immune reactivity.
- Nutrient and amino acid panels to evaluate absorption efficiency.
These are not exotic tests—they’re functional measurements that reveal how the body is operating in real time.
2. Rebalancing the System
Once the weak links are identified, treatment focuses on rebuilding a healthy terrain rather than medicating symptoms.
A functional medicine plan may include:
- Dietary repair: Removing inflammatory foods—such as sugar, gluten, and processed oils—and emphasizing whole, nutrient-rich foods high in fiber and phytonutrients.
- Restoring digestive chemistry: Supporting stomach acid (with betaine HCl), pancreatic enzymes, or bile when deficient.
- Microbiome modulation: Using targeted probiotics, prebiotics, or short herbal antimicrobial protocols to rebalance gut flora.
- Healing the mucosal barrier: Nutrients such as L-glutamine, zinc carnosine, food-based peptides, and omega-3s help regenerate the intestinal lining.
- Lifestyle and stress care: Because the vagus nerve links the gut and brain, practices like meditation, breathwork, and restorative sleep are essential for digestive rhythm.
This approach may appear slower and more detailed, but it treats the cause rather than the consequence.
When the digestive system returns to balance, many seemingly unrelated symptoms—fatigue, joint pain, anxiety, even autoimmune flares—often begin to resolve.
Comparing the Two Paths
In short, primary care excels at crisis management, while functional medicine shines in cultivating long-term balance.
If you have an ulcer or active inflammatory bowel disease, conventional medicine can be truly lifesaving.
But if you struggle with chronic indigestion, bloating, fatigue, or unexplained inflammation, a functional approach is far more likely to uncover—and correct—the underlying cause.
The Cost of Ignoring Digestion
When we dismiss digestive distress as a minor inconvenience rather than a meaningful warning sign, the body eventually pays the price. Poor digestion often becomes the silent background noise of modern life—quietly influencing every system in the body.
Here’s what happens when it’s left unchecked:
- Chronic Inflammation: Undigested proteins, toxins, and bacterial fragments seep through a compromised gut lining (“leaky gut”), triggering widespread immune activation.
- Nutrient Deficiency: Even the healthiest diet can’t nourish you if stomach acid, enzymes, or bile aren’t doing their job. Over time, the body runs low on zinc, magnesium, B vitamins, and amino acids—nutrients essential for energy, repair, and vitality.
- Neurochemical Imbalance: Because about 90% of serotonin and a large portion of dopamine are produced in the gut, an imbalanced microbiome can deeply affect mood, cognition, and motivation.
- Metabolic Slowdown: Impaired fat digestion and microbial imbalance disrupt insulin sensitivity, thyroid function, and mitochondrial energy production—contributing to fatigue and weight gain.
- Immune Dysregulation: A distressed gut keeps the immune system in overdrive, paving the way for autoimmunity and allergic responses.
This is why so many chronic conditions—arthritis, depression, diabetes, even dementia—are now being reexamined through the lens of the gut-immune-brain axis.
A Personal Reflection
I once asked a leading researcher in muscle loss (sarcopenia) how he evaluated digestive efficiency in his subjects. His answer was simple: “Digestion takes care of itself.”
That response—offered without irony—perfectly illustrates one of medicine’s enduring blind spots. In truth, nothing in the human body “takes care of itself” in isolation.
Digestion is a living conversation between chemistry, microbes, and the nervous system. It depends on harmony, not assumption.
If that researcher’s patients were struggling to absorb protein—a likely factor in muscle decline—how would he ever know?
The tools of conventional research rarely ask that question, because digestion is still viewed as a mechanical process rather than a dynamic ecosystem.
And this oversight matters deeply. The human body is not a machine that simply breaks down fuel; it is an ecosystem that transforms energy.
When that ecosystem loses balance, no supplement or medication can restore vitality until the gut—the body’s living soil—is healed.
Reclaiming the Forgotten Foundation
To truly restore health, medicine must move beyond the notion that digestion “takes care of itself.” It must return to what traditional systems of healing have always known: the power to heal arises from coherence—and that coherence begins in the gut.
So the next time fatigue, anxiety, or inflammation appear, the most important questions aren’t “What pill do I need?” or “What organ is failing?” but rather:
Am I truly nourishing myself?
Is my digestion clear, strong, and balanced?
These questions reach deeper than any lab test, because they invite us to examine the most fundamental relationship of all—the one between our body and the environment that sustains it. When that relationship is in harmony, vitality naturally follows.
Closing Thought
Over the years, I’ve often been struck by how profoundly different modern medicine and natural or functional medicine truly are. The contrast is so clear, yet so often overlooked.
I chose to write this piece because it’s difficult to understand why modern, pharmaceutical-based medicine continues to dominate our healthcare system—especially when it comes to treating chronic disease.
Digestive function and gut health lie at the very center of human physiology. Natural medicine recognizes this truth and places digestion at the heart of every patient’s care.
Pharmaceutical medicine, on the other hand, often says, “Take this pill,” focusing on symptom suppression without addressing what those symptoms are trying to reveal.
My goal is to help you see this difference as clearly as I do. I deeply respect and applaud modern medicine for its precision and effectiveness in trauma care and infectious disease.
But it’s time for medical education to include the principles of functional and natural medicine if we are to overcome the epidemic of chronic illness.
And if you’re living with a chronic condition, I encourage you to take the next step. Seek out a naturopath, chiropractor, or functional medicine practitioner—someone trained to assess and repair digestive function.
You may find that healing your gut is the key to restoring your energy, clarity, and overall well-being.
