Maldigestion Explained | Why Your Gut Can’t Absorb Nutrients Properly"

Maldigestion Explained | Why Your Gut Can’t Absorb Nutrients Properly


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by Arianne Missimer

Most people think digestion starts in the stomach. The truth? It actually starts in your brain. If you deal with bloating, gas, or nutrient deficiencies, chances are you’re not digesting food well, and you may be skipping the most important steps at the very beginning of digestion.

Let’s break down how the process really works, why maldigestion happens, and what you can do right away to improve it.

Rather watch or listen?

Youtube video

The Cephalic Phase: Digestion Starts in the Brain

When you see, smell, or even think about food, your brain kicks off digestion. This is called the cephalic phase, and it accounts for about 40% of your digestive secretions before you even take a bite.

Here’s where your cranial nerves step in:

  • Olfactory nerve (I): picks up smell.
  • Optic nerve (II): sees the food (yes, presentation matters).
  • Facial and glossopharyngeal nerves (VII & IX): trigger saliva and taste.
  • Trigeminal nerve (V): senses texture as you chew.
  • Vagus nerve (X): signals your stomach to release acid, your pancreas to send enzymes, and your gallbladder to release bile.

Action step: Pause before you eat. Smell your food. Take two or three deep breaths. Chew 20–30 times per bite. Eat in a calm state. Stress turns digestion off.

Saliva: Your First Digestive Juice

Saliva isn’t just spit; it’s packed with enzymes.

  • Amylase breaks down starches.
  • Lingual lipase begins fat digestion.
  • Lysozyme helps defend against bacteria.

Action step: Stay hydrated. Get enough zinc and B vitamins for healthy enzyme production. Keep your mouth closed and nasal breathe—even while you sleep—to support saliva flow and a healthy oral microbiome.

The Role of Stomach Acid

Hydrochloric acid (HCl) in your stomach:

  • Breaks down proteins.
  • Activates pepsin.
  • Helps absorb minerals like iron and magnesium.
  • Produces intrinsic factor, which is essential for vitamin B12 absorption.

Support stomach acid with:

  • Zinc (pumpkin seeds, meat, oysters).
  • Salt (for chloride).
  • B vitamins, especially thiamine.

Signs of low stomach acid: bloating after meals, reflux, or undigested food in your stool.

Small Intestine & Enzymes

Once food leaves the stomach, bile from the liver and gallbladder emulsifies fats. Pancreatic enzymes finish the breakdown:

  • Lipase digests fats.
  • Amylase digests carbs.
  • Proteases break down proteins.
  • Nucleases break down DNA/RNA.
  • Bicarbonate neutralizes stomach acid so enzymes can work.

Support this step with:

  • Choline (eggs or supplements).
  • Taurine and glycine for bile flow.
  • Magnesium, zinc, and amino acids for enzyme production.

If you’ve had your gallbladder removed, extra bile support may be necessary for proper fat digestion.

Aging and Digestion

Digestive strength naturally declines with age.

  • About 30% of adults over 60 have low stomach acid.
  • Pancreatic enzyme production drops by 20–40% by age 65.
  • Bile flow often slows due to gallbladder and liver changes.

Action step: If you’re over 50 and notice bloating, nutrient deficiencies, or fat in your stool, consider targeted support with enzymes or hydrochloric acid.

So, what can you do?

Here’s what you can start doing today:

  • Activate your cephalic phase: Smell your food, chew thoroughly, and relax before meals.
  • Support stomach acid and enzymes: Prioritize nutrients like zinc, B vitamins, and amino acids.
  • Be mindful of age-related changes: Pay attention to symptoms and don’t brush them off.

And remember—it’s not only what you eat, it’s how well you digest it. Comprehensive stool testing can also give insight into how your digestive system is working.

Next Steps

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