In Part 1 of this series, we explored why digestion doesn’t begin with the gut—it begins in the mouth and continues through the stomach, where proper chewing and sufficient stomach acid set the stage for healthy downstream digestion.

Now in Part 2, we move deeper along the digestive tract to explore the next three critical stages: pancreatic enzymes, bile flow, and intestinal motility. These mid-phases are often overlooked, yet they are essential for nutrient absorption, microbial balance, and maintaining the integrity of the gut lining.

If you have addressed chewing and stomach acid, you are ready to optimize the next phases: enzyme production, bile function, and motility.

Step 3: Pancreatic Enzymes—Unlocking Nutrients for Absorption

Once your food leaves the stomach, it enters the small intestine as chyme—a semi-liquid mix of partially digested food and acid. Here, the pancreas steps in, releasing a blend of digestive enzymes that break down macronutrients into absorbable forms:

• Proteases (such as trypsin and chymotrypsin) digest proteins into smaller peptides and amino acids, crucial for muscle repair, immune function, neurotransmitter production, and metabolic health.

• Lipase breaks down dietary fats into fatty acids and glycerol, essential for energy production, hormone synthesis, and healthy cell membranes.

• Amylase, first released by the salivary glands and later by the pancreas, continues breaking down complex carbohydrates into simpler sugars like glucose—providing the body with a fast, accessible source of energy.

🧠 Did you know? Without adequate enzyme production, food isn’t properly broken down, allowing larger particles to ferment in the gut—feeding imbalanced bacteria, producing gas and bloating, and inflaming the gut lining.

Signs of Enzyme Deficiency

• Bloating or gas 1–3 hours after meals

• Floating, greasy, or foul-smelling stools

• Visible food particles in stool

• Fullness or discomfort after eating

• Nutrient deficiencies, especially in fat-soluble vitamins (A, D, E, K)

How to Support Enzyme Function

• Eat meals in a relaxed, parasympathetic state (stress reduces enzyme output)

• Consider a broad-spectrum digestive enzyme supplement (with practitioner guidance)

• Reduce inflammatory foods and high sugar intake, which can burden the pancreas

• Test pancreatic elastase-1 levels via stool testing if issues persist

Step 4: Bile Flow—The Missing Link in Fat Digestion and Detoxification

Bile is a digestive fluid produced by the liver, stored in the gallbladder, and released into the small intestine in response to fat consumption. It plays several vital roles:

• Emulsifying dietary fats: Bile breaks large fat globules into smaller droplets, increasing the surface area available for enzymes like lipase to act, enabling efficient fat digestion.

• Absorbing fat-soluble nutrients: Vitamins A, D, E, and K require healthy bile flow for absorption. These nutrients are critical for vision, bone density, immune resilience, and antioxidant defense.

• Eliminating toxins and hormones: Bile binds waste products—such as used hormones like estrogen, heavy metals, and excess cholesterol—and escorts them out of the body via stool.

⚡ When bile flow is sluggish, fat digestion suffers and toxins may recirculate instead of being cleared—burdening both the liver and the gut.

Signs of Sluggish Bile Flow

• Nausea or discomfort after fatty meals

• Light-colored or clay-like stools

• Hormonal imbalances, such as estrogen dominance

• Dry skin, acne, or itchy rashes

• Right upper quadrant tenderness under the ribcage

How to Improve Bile Flow

• Add bitter foods to meals (arugula, dandelion greens, lemon, ginger)

• Use digestive bitters or phosphatidylcholine to support bile secretion

• Stay hydrated and include moderate healthy fats in your diet

• Consider targeted supplements (like ox bile, taurine, artichoke extract) under practitioner supervision

Step 5: Intestinal Motility—Keeping Digestion Moving Smoothly

Motility refers to the wave-like contractions that move food through the intestines. When motility slows or becomes irregular, food can stagnate, leading to fermentation, microbial overgrowth (like SIBO), gas, and inflammation.

Signs of Poor Motility

• Progressive bloating throughout the day

• Constipation or incomplete bowel movements

• Recurrent SIBO or gut infections

• Brain fog or fatigue after meals

• Feeling full after small meals

How to Support Healthy Motility

• Stimulate the vagus nerve (gargling, humming, deep belly breathing)

• Take a walk after meals to encourage natural movement

• Consider practitioner-guided use of natural prokinetics (ginger, Iberogast, or 5-HTP blends)

• Ensure adequate magnesium intake:

  • Magnesium citrate and magnesium oxide promote bowel movements and are helpful for occasional constipation.

  • Magnesium glycinate is gentler on digestion, ideal for sensitive systems.
    Choosing the right form depends on your individual tolerance and digestive needs.

Why These Mid-Digestive Phases Matter

While most conversations about gut health focus on the gut lining, what happens upstream—with enzymes, bile, and motility—is just as important. Many people experience lasting relief from digestive distress simply by addressing these overlooked phases.

Before jumping to gut repair protocols, ask yourself:

• Is my food being fully broken down?

• Am I absorbing fats and key nutrients?

• Is my digestive system moving at a healthy pace?

Optimizing these steps can often resolve symptoms labeled as “leaky gut” by removing the root causes of intestinal stress.

What’s Coming Next: Gut Lining Repair and Microbiome Balance

In Part 3 of this series, we will explore how the gut microbiome, the mucosal immune system, and the intestinal barrier interact—and how to actually restore them once digestion is properly functioning.

Ready to Strengthen Your Digestion at the Source?

Book a personalized consultation with Dr. Mary Clark, DACM, LAc, and get to the root of your digestive symptoms—step by step.

📞 Call (919) 909-5736 or visit Raleigh Health & Wellness Center
📍 8358 Six Forks Road, Suite 204, Raleigh, NC 27615