Can Naturally Occurring Enzymes and Beneficial Microflora in Raw Pet Food Withstand Digestion?

Raw pet diets are often promoted as containing naturally occurring enzymes and beneficial microflora that may help pets digest food more efficiently and provide other health benefits. These enzymes include calpains and cathepsins, proteases which help turn freshly slaughtered muscle into meat, tyrosinase (an oxidase) which promotes browning in fruits and vegetables, elastase an enzyme made by common spoilage microorganisms that breaks down muscle fibers, and many others. 

But here’s the question:

Do these enzymes and microorganisms survive the harsh environment of a dog’s or cat’s stomach, travel intact to the small intestine, and remain active there?

Or, like most proteins, are the enzymes irreversibly inactivated by gastric acid and pepsin, becoming simply a source of amino acids rather than functioning as enzymes?

Are the microorganisms destroyed just like pathogenic and spoilage bacteria, yeasts and molds without conveying benefits to the gut microbiome.

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Why This Matters To Pet Parents 

Many raw feeding advocates posit that the functional enzymes in unprocessed meat and produce improve digestion, and that beneficial microorganisms survive digestion and interact with gut microbiota, producing beneficial compounds.  While this sounds appealing, whether these enzymes and microorganisms remain functional after ingestion has significant implications for understanding how raw diets work — and for decisions about enzyme and probiotic supplementation, and the types of foods fed to pets with pancreatic or digestive issues.

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The Gastric Environment: Designed to Breakdown Proteins

Gastric acid is a 400 million year old adaptation.  It keeps us alive.  Gastric juice is a unique combination of hydrochloric acid (HCl), lipase, and pepsin. Its main function is to inactivate swallowed microorganisms, thereby inhibiting infectious agents from reaching the intestine.

The stomach of both dogs and cats is highly acidic.

• Fasted gastric pH is typically between 1.5 and 2.5.
• When food enters, pH rises briefly but soon drops again as gastric acid is secreted.
• Pepsin, the major gastric enzyme, is activated at low pH and begins cleaving peptide bonds of unfolded dietary proteins.

This system exists to unfold, denature, and enzymatically break down proteins, including any enzymes present in the food itself, and the proteins within the cell walls of microorganisms. Essentially, the stomach is a “protein deactivation chamber.”

This disruption of protein molecules is one of the ways gastric acid destroys microorganisms (bacteria, yeasts, molds) as all cellular membranes contain protein molecules.  When these molecules are damaged, cells can die.  And if gastric acid is killing infectious microbes, then it is arguably equally effective with destroying friendly bacteria.        

Evidence from Pancreatic Enzyme Therapy Shows Enzymes are Inactivated by Gastric Acid 

The clearest real-world evidence for how fragile enzymes are in the stomach comes from decades of research on pancreatic enzyme replacement therapy (PERT) used to treat exocrine pancreatic insufficiency (EPI) in both humans and animals.

• Studies show that up to 85% of uncoated pancreatic enzyme activity is lost in the stomach due to low pH and pepsin activity.
• Because of this, enteric-coated enzyme microspheres were developed to protect enzymes until they reach the higher pH of the small intestine.
• Multiple clinical trials in dogs with EPI confirm that enteric-coated formulations outperform uncoated powders, leading to significantly improved digestion and clinical response.

If even pharmaceutical-grade enzymes can’t survive the stomach without protection, it is extremely unlikely that naturally occurring raw food enzymes would remain active after gastric exposure.

 A Closer Look at Protein Digestion Shows Light Cooking Improves Protein Digestibility and Bioavailability

Proteins are chains of peptides.  Peptides are chains of amino acids. Proteases are enzymes that break down proteins and their peptide chains.  In order for the intestinal mucosa to absorb dietary proteins, they must be digested into single amino acids or very short peptides of a length of not more than four amino acids. 

Science shows that several pancreatic proteases released into the intestinal tract (e.g. trypsin, chymotrypsin, and elastase) are remarkably inefficient in cleaving native folded proteins whereas pepsin, which acts at very low pH (pH 1.2) is much more efficient.  This efficiency is likely due to the denaturing conditions in the stomach whereby gastric acid causes the proteins to unfold exposing cleavage sites to the enzymatic action of pepsin.

Research has shown that heat treatment – but not acid treatment followed by return to neutral pH (as would be found in the intestinal tract) – can improve cleavage by the pancreatic enzymes in the intestinal tract considerably.   This aligns with other findings discussed below which show improved digestibility of lightly cooked meats over undercooked meats or over-processed meats. 

It appears that pepsin is the prime enzyme cleaving dietary proteins (including the enzymes in raw food) into small peptides (thereby irreversibly inactivating those food-based enzymes).  Once broken into small peptides and passed into the intestinal tract, pancreatic enzymes disassemble peptide chains into very short peptides or amino acids for uptake by intestinal mucosa.

Enzymes Cannot “Reactivate” in the Intestine Once They are Cleaved by Pepsin in the Stomach

Is it possible for enzymes denatured by gastric acid, to refold and become active again once they reach the more neutral pH of the small intestine?

From a biochemical standpoint, this is highly implausible:

• Denaturation typically involves irreversible structural collapse and peptide bond cleavage. Without cellular machinery (e.g., molecular chaperones), refolding into an active enzyme form is extremely unlikely.
• Hence, denatured dietary enzymes cannot regain their original 3D structure and catalytic function after gastric exposure.
• Key point: Reactivation of raw food enzymes in the intestine is not supported by physiological principles or evidence.

Why Enzyme and Probiotic Supplements Work

The main mechanism enabling ingested active enzymes and live probiotics to reach the small intestine involves specifically protecting them from stomach acid, as in:

• Enteric-coated pancreatic enzyme microspheres used to treat EPI in dogs and cats.
• Certain plant-derived enzymes (e.g., bromelain, papain) that are naturally more acid-tolerant, though they still experience some degradation.
• Fermented foods are made by treating them with probiotics like lactobacillus acidophilous that are acid-tolerant.  Full fat fermented dairy products also have the benefit of the food matrix which acts as a buffer temporarily raising stomach pH.

Even if Enzymes and Microflora Are "Decommissioned" In the Stomach They Still Have Nutritional Value

Even though the enzymes themselves do not survive intact, they still provide value as high-quality dietary proteins.

• Gastric digestion breaks them into amino acids and peptides, which are then absorbed and used by the pet’s body to build its own proteins — including its own digestive enzymes.

New research on parabiotics (“ghost” probiotics) shows that dead probiotics can be just as beneficial for the body as probiotics in addressing many GI, immune and metabolic disorders too.

So, while raw food enzymes aren’t acting directly in digestion, they still contribute to overall nutrition.

Cooked and Fermented Foods Are Helpful for Animals Who May Not Tolerate Raw Foods Well

There’s a progressive denaturation of proteins with light cooking and fermentation.  At low temperatures or with short-term fermentation, protein molecules unfold exposing cleavage sites in their peptide bonds.  When these foods are consumed, cleavage sites can be easily acted on by pepsin and proteases in the intestinal tract, improving digestibility. 

An interesting study footnoted below looked at the digestibility of meat cooked to 140°, 167° and 194° Fahrenheit and found that the best digestibility was at 167° F; the worst was at 194°.

So while food-based enzymes in the cooked meat would be irreversibly inactivated in the cooking process, the lightly cooked meat still delivered improved digestibility.

At high temperature cooking, with prolonged fermentation, or at high pressures seen in HPP (a pasteurization process used on some pet foods) denaturation progresses to the point of oxidation.  When protein molecules oxidize, they aggregate, hiding cleavage sites in peptide bonds from digestive enzymes.  This makes over-processed proteins less digestible and bioavailable, and would be the reason that protein digestion decreased when the meat in the aforementioned study was cooked to 194° F.

Practical Takeaways for Pet Parents and Veterinary Professionals

1. Most naturally occurring enzymes and microflora in raw meat are irreversibly inactivated in the stomach.
2. Light cooking and fermentation can be helpful for animals by making proteins in food more digestible.
3. For pets with digestive issues like EPI, veterinary-prescribed, enteric-coated enzyme supplements are necessary for therapeutic enzyme delivery.
4. The benefits of raw diets — when well-formulated and handled safely — likely stem from other factors, such unheated fats, high-quality proteins, antioxidants, polyphenols and other phytonutrients, nutrient bioavailability and balance, moisture content, and anti-inflammatory microbiome effects, not active food enzymes or microflora.

Conclusion

The science is clear: while raw diets contain naturally occurring enzymes, these enzymes generally do not survive the acidic, protease-rich environment of the stomach and cannot reactivate in the intestine. Their primary value lies in their role as high-quality proteins, not as active catalysts.

For pets with special digestive needs, lightly cooked and fermented foods and clinically proven, enteric-coated enzyme products remain the most reliable way to deliver highly digestible proteins and active enzymes to the small intestine. By understanding the true fate of food-borne enzymes, pet parents and veterinary professionals can make more informed decisions about diet, supplementation, and health.

References

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9. Parambeth JC, et al. Randomized placebo-controlled clinical trial of a new pancreatic enzyme formulation for canine exocrine pancreatic insufficiency. J Vet Intern Med. 2024;38(1):143-153.  https://pubmed.ncbi.nlm.nih.gov/30221800/
10. Hall EJ, et al. Exocrine pancreatic insufficiency in the dog: An update. Comp Cont Educ Vet. 2023;45(4):175-185.  https://www.researchgate.net/publication/328996196_Exocrine_pancreatic_insufficiency_in_canines_An_update
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