Blog Post 1: Why Undigested Food is Making You Sick (And How to Stop the Rot)The Theory & Science: The Hidden Cause of Inflammation:
- Jaime Hernandez
- 3 hours ago
- 4 min read
By Jaime Hernandez LMT, MES, CPT
We often think of digestion as a simple "in and out" process. You eat, you get energy, and you eliminate the waste. But for many of my clients—whether you are recovering from an injury, managing stress, or simply trying to maintain independence in your later years—this process is broken.
When digestion fails, food doesn’t just "sit" there. It rots.
In my practice at Health and Exercise Prescriptions, I often see clients suffering from joint pain, brain fog, and chronic fatigue. They think it’s just aging or an old injury acting up. Often, however, the root cause is Gut Dysbiosis and Endotoxemia caused by undigested macronutrients.
Today, we are going to look at the science of "Gut Autointoxication," and I will introduce you to a clinical concept called "Enzymatic Intervention."
The Cycle of Toxicity
three red danger zones:
Undigested Protein → Putrefaction (Ammonia/Toxins)
Undigested Carbs → Fermentation (Gas/Bloat)
Undigested Fats → Rancidity (Inflammation) Center text: "The Root of Systemic Inflammation."
The Science of the "Rot": Why Digestion Matters for Rehab and Wellness
When we talk about "gut health," we aren't just talking about avoiding a stomachache. We are talking about preventing systemic poisoning.
Your stomach requires specific enzymes to break down the three major macronutrients: Proteins, Carbohydrates, and Fats. If your stomach acid is low (common in seniors) or your stress levels are high (common in busy professionals), your body fails to produce enough enzymes.
When this happens, the food moves into your intestines in large, solid chunks rather than a liquid nutrient soup. This is where the trouble begins.
1. Protein Putrefaction (The Inflammation Trigger)
For my clients focused on recovery and pain management, this is critical. If you eat chicken, steak, or eggs and don’t have enough Protease enzymes, that protein travels to the colon and undergoes putrefaction.
The bacteria there attack the protein, producing toxic byproducts like ammonia, amines, and hydrogen sulfide. These toxins can cross the gut lining (Leaky Gut) and enter the bloodstream, settling in your weakest points—often your joints and old injury sites—causing inflammation that no amount of physical therapy can fully fix.
2. Carbohydrate Fermentation (The Bloat)
For those seeking holistic balance, this is usually the culprit behind that heavy, sluggish feeling. If starches aren't broken down by Amylase, they sit in the small intestine and ferment. This feeds the wrong bacteria, creating gas, pressure, and brain fog (often diagnosed as SIBO).
3. Fat Rancidity (The Nutrient Block)
For my older clients, absorbing nutrients is key to bone density and brain health. If fats aren’t broken down by Lipase, they coat the digestive tract, becoming rancid and blocking the absorption of essential vitamins like A, D, E, and K.
The Enzyme Key
"Lock and Key" mechanism.
Lock = Protein Molecule. Key = Protease.
Lock = Starch Molecule. Key = Amylase.
Lock = Fat Molecule. Key = Lipase.
"Unlock Your Nutrition before it Becomes a Toxin."
The Solution: Strategic Enzymatic Intervention
The solution isn't just to "eat better." It is to ensure your body has the tools to process what you eat.
We need to utilize Enzymatic Pre-Strikes. Cooking food preserves nutrients, but it destroys enzymes. To fix this, we must introduce raw enzymatic foods with our cooked meals. This "pre-digests" the food in the stomach, ensuring it flows into the intestines as fuel, not poison.
For Protein: We need Proteases (found in Pineapple and Papaya) to act as natural tenderizers for your stomach.
For Carbs: We need Amylases (found in Mango and Raw Honey) to break down sugars before they ferment.
For Fats: We need Lipases (found in Avocado and Miso) to emulsify fats, ensuring they nourish your brain rather than inflaming your gut.
When Food Isn't Enough: Clinical Support
While I always advocate for food first, I know that life gets busy. Sometimes we can't source raw papaya, or our stomach acid is simply too low due to age or stress. For clients who need a guaranteed result—or those with compromised digestion who need a "jump start"—I recommend high-quality supplementation.
You need a broad-spectrum enzyme that covers all macronutrients, and a probiotic that is shelf-stable.
Through my partnership with Thorne, the gold standard in clinical supplementation, I have curated a specific protocol for digestive repair.
Bio-Gest: This provides HCL (stomach acid) and enzymes (pepsin, pancreatin) to ensure complete digestion. It mimics your body's natural gastric juices.
FloraMend Prime Probiotic: A proprietary blend designed to survive stomach acid and specifically target gut flora balance.
[Link: Shop My Curated Gut Health Protocol at the Thorne Dispensary](https://www.thorne.com/u/HealthAndExercisePrescriptions)
Note: By using my dispensary, you ensure you are getting authentic, temperature-controlled products.
Conclusion
By taking control of your digestion, you are taking control of your pain, your energy, and your future. In my next post, I will share a full 7-Day Meal Plan to put this science into action.
If you need help building a nutrition and movement plan that fits your specific medical needs, visit my website to learn more about my services.
Part two.
Disclaimer: This content is for educational purposes only and does not constitute medical or rehabilitation advice. Consult your physician or qualified healthcare provider before starting or changing an exercise program—especially if you have pain, injuries, cardiovascular, metabolic, or other medical conditions. Stop any activity that causes sharp pain, dizziness, chest discomfort, or unusual shortness of breath.
Author Jaime Hernandez LMT, MES, CPT.
Thank you for your time and energy...Be well.