Digestion: How It Works, What Goes Wrong, and What to Do About It

Most people think digestion is a stomach thing. You eat, the stomach does something, and nutrients go in. That's about a third of the story.

The full picture starts in your brain and ends at your colon, with a series of critical handoffs in between. When any one of those handoffs breaks down, the effects ripple through your entire body — your energy, your immune system, your skin, your mood. Most of the symptoms people chalk up to aging or stress are downstream of a digestive system that isn't doing its job.

Here's the actual chain.

It starts before you take a bite

The smell of food, the sight of it, even just anticipating it — these trigger your brain to begin preparing your digestive system. Your salivary glands activate. Your stomach starts producing acid. This is called the cephalic phase of digestion (cephalic just means "relating to the head"), and most people skip it entirely.

Eating while distracted — phone in one hand, food in the other, TV on in the background — blunts this phase. Your body hasn't had time to prepare. You're asking your digestive system to do its job cold.

Slow down. Put the phone face down. Actually look at your food before you eat it. This sounds trivial. It isn't.

The mouth: the first real step

Saliva isn't just there to help you swallow. It contains amylase — an enzyme (a biological catalyst that speeds up chemical reactions) that begins breaking down carbohydrates before food even reaches your stomach. Chewing thoroughly increases surface area, giving enzymes more to work with and reducing the load on everything downstream.

Most people chew three or four times and swallow. The stomach has to compensate for what the mouth skipped. Do that at every meal for years and it adds up.

The stomach: where most people's digestion goes wrong

The stomach's job is to break food down into a liquid called chyme — essentially a thoroughly acidic slurry of partially digested food — using hydrochloric acid (HCl) and digestive enzymes.

HCl does several things that most people don't realize are connected:

• Activates pepsin, the enzyme that breaks down protein
• Denatures proteins — meaning it unfolds and dismantles their structure so enzymes can work on them
• Kills bacteria, parasites, and pathogens before they can set up shop further down
• Triggers the pyloric sphincter (the valve between your stomach and small intestine) to open — but only when the chyme is acidic enough

That last point is where most people get surprised. The valve to your small intestine only opens when your stomach acid is at the right level. If your stomach acid is too low — and this is the part that runs counter to everything you've seen advertised — food sits. It ferments. It putrefies. And then a small amount of that acid refluxes upward into the esophagus.

Most acid reflux is a symptom of too little stomach acid, not too much [1]. When chyme isn't acidic enough, the pyloric valve doesn't open properly, pressure builds, and what acid exists splashes up. The standard treatment — acid reducers, proton pump inhibitors — suppresses acid further and worsens the root problem. This is one of the clearest examples of conventional medicine treating a symptom in the wrong direction.

Low stomach acid is driven primarily by chronic stress, excess alcohol, and diets high in processed carbohydrates. If you eat and then feel a heavy, sitting-brick sensation in your chest, this is where I'd start looking.

The small intestine: the critical handoff

When properly acidic chyme enters the small intestine — specifically the first section, called the duodenum — it triggers a hormone cascade. Two hormones are released: secretin, which signals the pancreas to send enzymes and bicarbonate, and CCK (cholecystokinin — the name doesn't matter, the function does), which signals the gallbladder to release bile.

Bile is made by the liver and stored in the gallbladder. Its job is to emulsify fat — to break large fat globules into smaller ones so digestive enzymes can reach them. Think of it like dish soap cutting through grease. Without adequate bile, fat moves through poorly digested.

The pancreatic enzymes finish breaking down protein, fat, and carbohydrates. Bicarbonate neutralizes the acid in the chyme so the intestinal lining isn't damaged in the process.

When stomach acid is too low, this entire cascade is blunted. The chyme arrives at the wrong pH, the hormonal signals misfire, and fat and protein pass through only partially processed.

What happens to undigested food

Partially digested fat rancidifies in the intestine. Partially digested protein putrefies. Carbohydrates ferment. The bloating, gas, and discomfort most people experience after meals is this process — essentially, rot in a tube.

Over time, the chronic inflammation from undigested food and the bacterial overgrowth it feeds damages the intestinal wall. The wall becomes permeable — this is what's called leaky gut — and incompletely digested particles enter the bloodstream [2].

Your immune system treats those particles as foreign invaders and responds. The reaction can be subtle: fatigue, brain fog, joint aches, skin issues. Or it can be severe: food allergies, autoimmune flares. I found out I was reacting to bananas — something I never would have connected to my immune system without an IgG food intolerance test. Most people never make this connection because the reactions are delayed and diffuse, not immediate.

The long-term result is a chronically taxed immune system combined with whole-body nutrient deficiency. You're eating food, but the nutrients aren't being absorbed. Slowly starving while feeling full.

What to actually do about it

Digestion is one of the six foundational areas the NTA addresses first for a reason — most downstream health problems trace back to it. The interventions are straightforward.

Slow down and chew. Thirty chews per bite is the number used in nutritional therapy training. That sounds excessive until you try it and realize how different food tastes when you actually break it down. This single change improves digestion more than most supplements combined.

Eat without distraction. No phone at meals. No TV. Sit down, look at your food, and let the cephalic phase do its job before the first bite. This is not aesthetic advice — it's physiological.

Support stomach acid naturally. One tablespoon of raw apple cider vinegar in water before meals stimulates acid production. Digestive bitters work by the same mechanism. For more significant low-acid conditions, betaine HCl supplementation has clinical support — but dosing should be calibrated with a practitioner [3].

Cut what suppresses stomach acid. Chronic stress is the biggest driver. Processed food and excess alcohol follow closely. These aren't new recommendations, but most people don't connect them to their digestion specifically.

Eat real fat to support your gallbladder. Bile production depends on having adequate dietary fat to begin with. Low-fat diets impair bile flow. Eating enough animal fat — butter, tallow, fatty cuts — keeps the gallbladder working the way it's supposed to. Bile salt supplements are an option if the gallbladder is sluggish.

Bone broth and fermented foods. Bone broth provides gelatin and collagen that support intestinal wall integrity. Fermented foods — sauerkraut, kefir, quality yogurt — introduce beneficial bacteria and support gut lining recovery. Both are foundational for anyone dealing with leaky gut.

Digestion is a chain. Every link depends on the one before it. The place to start is always the top: slow down, chew, protect your stomach acid. Get those right and most of what follows corrects itself.

Sources

[1] Beasley, D.E. et al. (2015). The evolution of stomach acidity and its relevance to the human microbiome. PLOS ONE. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0134116. See also: Wright, J.V. & Lenard, L. (2001). Why Stomach Acid Is Good for You. M. Evans & Company.

[2] Fasano, A. (2012). Leaky gut and autoimmune diseases. Clinical Reviews in Allergy & Immunology, 42(1), 71–78. https://pubmed.ncbi.nlm.nih.gov/22109896/

[3] Guilliams, T.G. & Drake, L.E. (2020). Meal-time supplementation with betaine HCl for functional hypochlorhydria. Integrative Medicine: A Clinician's Journal, 19(1). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7238915/