The D in DIGIN: Digestion Is the Foundation of Gut Health

When patients tell me they eat well but still feel bloated, exhausted, or somehow nutrient-deficient despite a healthy diet, I usually start by asking: Are you doing a good job in digesting the food? Because it doesn't matter how healthy your meals look if your body cannot break them down and absorb what it needs.

Digestion is not automatic

We often assume digestion just happens. You eat and your body takes care of the rest.

In reality, digestion is an energy-intensive, neurologically coordinated process. It requires:

• Thorough chewing to mechanically break food into small pieces

• Adequate stomach acid to denature proteins and activate enzymes

• Timely pancreatic enzyme release to continue breaking down fats, proteins, and carbohydrates

• Coordinated bile secretion to emulsify fats

• A calm enough nervous system to allow all of this to occur

The overlooked role of chewing and eating state

Chewing mechanically breaks food down, reducing the workload on everything downstream. But it also signals the brain to activate digestive secretions—salivary enzymes, gastric acid, pancreatic enzymes. This preparatory cascade depends on your nervous system state.

Eating while rushed, distracted, or stressed keeps you in sympathetic mode—the "fight or flight" state that actively diverts resources away from digestion. Blood flow shifts to muscles instead of the gut, and enzyme secretion and motility are affected as well.

Even slowing down for the first few bites, taking a breath and being mindful before meals, or eating away from screens can be enough to support your digestion.

Stomach acid: more often too low than too high

Heartburn and reflux are almost universally attributed to excess stomach acid. In practice, the opposite may be also be common, which is insufficient acid production, or hypochlorhydria.

Stomach acid does more than just break down food. It:

• Denatures proteins, preparing them for enzymatic digestion

• Activates pepsin, the primary protein-digesting enzyme in the stomach

• Creates an inhospitable environment for most ingested bacteria and parasites

• Facilitates absorption of iron, calcium, magnesium, and zinc

• Triggers release of intrinsic factor, essential for vitamin B12 absorption

When acid production is low, protein remains inadequately broken down. Larger polypeptide fragments advance into the small intestine, where they undergo bacterial fermentation. This fermentation produces gas and pressure. That pressure can push the lower esophageal sphincter open, allowing stomach contents to reflux upward—creating heartburn that paradoxically mimics too much acid.

When we develop reflux symptoms, proton pump inhibitors are prescribed to suppress acid. Symptoms may improve initially as acid drops below the threshold needed to irritate the esophagus, but the underlying digestive dysfunction are still present.

Pancreatic enzymes and bile: the silent workhorses

Once food leaves the stomach and enters the small intestine, digestion relies on pancreatic enzymes and bile to continue the breakdown process.

When pancreatic function is impaired, people often notice bloating after meals, particularly following fatty foods. Stools may appear pale, greasy, or float—signs of fat malabsorption called steatorrhea. Over time, deficiencies in fat-soluble vitamins (A, D, E, K) can develop.

A stool test measuring fecal pancreatic elastase can assess exocrine pancreatic function. Low levels indicate the pancreas is not producing adequate enzymes—pointing to a mechanical explanation for symptoms often dismissed as generic food intolerance.

Bile, produced by the liver and stored in the gallbladder, serves as an emulsifier. It breaks large fat globules into smaller droplets that digestive enzymes can access efficiently. Bile acids also help regulate gut microbial composition and facilitate absorption of fat-soluble vitamins and essential fatty acids.

When bile flow is sluggish—whether from gallbladder dysfunction, liver congestion, or bile acid insufficiency—there might be suboptimal fat digestion and the microbial ecosystem may shift unfavorably.

Why poor digestion creates downstream problems

When food is not fully broken down in the stomach and upper small intestine, several cascading problems emerge. Larger, partially digested food particles move through the GI tract. These become substrates for bacterial fermentation in areas where fermentation should be minimal, producing gas, bloating, and altered bowel patterns.

The immune system encounters incompletely digested proteins—larger peptide fragments more likely to be recognized as foreign. This can trigger immune reactions that would not occur if proteins had been properly reduced to amino acids.

Chronic exposure to partially digested food may contribute to intestinal permeability—the breakdown of the gut barrier's tight junctions we will explore in the next post. As the barrier becomes more porous, immune activation intensifies, which leads to inflammation and food reactivity.

Clinical patterns that suggest impaired digestion

In practice, digestive insufficiency shows up through these signs:

• Bloating that begins soon after eating, especially following protein or fat-rich meals

• Feeling full quickly or experiencing prolonged heaviness after moderate portions

• Fatigue or mental fog after meals

• Frequent belching or reflux

• Visible undigested food in stool

• Food intolerances

• Signs of nutrient deficiency—brittle nails, thinning hair, persistent fatigue—despite adequate dietary intake

Restoring the Foundation

Supporting the digestive foundation requires more than just replacing what is missing; it requires a shift in how we interact with food. We begin by removing barriers—addressing chronic stress and identifying medications that may impair secretions. We then move to the "Replace" phase of the 5R protocol, utilizing targeted supports such as Betaine Hydrochloride with pepsin, broad-spectrum digestive enzymes, or digestive bitters to stimulate the body's natural output.

Digestion is the gatekeeper of human biology. It is the process that converts the external world into the building blocks of your cells. When this foundation is secure, the rest of the gut can begin to heal. In our next post, we will move to the first "I" in DIGIN—Intestinal Permeability—to explore what happens when the gut barrier fails and the immune system goes on the offensive.

References:

• Age-Related Changes of the Gastrointestinal Tract. Pilotto A, Custodero C, Crudele L, et al. The Lancet. Gastroenterology & Hepatology. 2026;11(1):59-70. doi:10.1016/S2468-1253(25)00235-3.

• The Risks and Benefits of Long-Term Use of Proton Pump Inhibitors: Expert Review and Best Practice Advice From the American Gastroenterological Association. Freedberg DE, Kim LS, Yang YX. Gastroenterology. 2017;152(4):706-715. doi:10.1053/j.gastro.2017.01.031.

• AGA Clinical Practice Update on the Epidemiology, Evaluation, and Management of Exocrine Pancreatic Insufficiency: Expert Review. Whitcomb DC, Buchner AM, Forsmark CE. Gastroenterology. 2023;165(5):1292-1301. doi:10.1053/j.gastro.2023.07.007.

• ACG Clinical Guideline: Small Intestinal Bacterial Overgrowth. Pimentel M, Saad RJ, Long MD, Rao SSC. The American Journal of Gastroenterology. 2020;115(2):165-178. doi:10.14309/ajg.0000000000000501.