Posted by Paula Vandervoort on 4/3/2026 to
Neonatal Care
A breeder’s perspective supported by current microbiome science.
For years I’ve listened to claims that puppies — and senior dogs — “don’t have the microbiome” to handle raw food, and therefore must be weaned onto cooked or processed diets. To me, this argument ignores both the laws of nature and the science of early life microbial development. Puppies are not designed to transition from milk to baked pellets or cooked starch or even cooked meat. Puppies are not born with fragile guts that can only tolerate cooked or processed food. Their entire biological design — from gastric pH to maternal microbial transfer is built for raw, species appropriate animal tissue — exactly what their mothers would provide in nature.
Nature’s Weaning Pattern: Raw, Predigested, Microbially Rich
In wild canids, weaning is not a mystery. Mothers regurgitate partially digested raw prey for their young, and they offer small raw parts long before the pups are hunting on their own.
This is not optional behavior — it is a biological strategy for transferring enzymes, microbes, and predigested nutrients to shape the developing gut.
This natural pattern directly contradicts the idea that puppies “can’t handle raw.”
If anything, nature shows us that raw is the only thing they are built to handle.
What the Science Says About Puppy Microbiome Development
Modern research confirms what breeders have observed for generations:
the mother’s microbiome and diet are the primary architects of the puppies’ gut ecosystem.
A 2023 review in Animals found that microbial colonization begins before birth, continues through colostrum and milk, and is heavily shaped by maternal microbiota and maternal diet from birth to weaning.¹
AnimalBiome’s ongoing “State of the Gut” analyses echo this: puppies acquire their microbiome through maternal grooming, milk, saliva, fecal exposure, and early diet, and this early window is the most important period for shaping lifelong digestive and immune health.²
In other words, puppies are not fragile blank slates. They are primed to be colonized — and the substrate they are colonized on matters.
Raw vs. Kibble: The Gut Responds Very Differently
We now have controlled studies comparing raw meat–based diets (RMBDs) and kibble in dogs. One study found that raw fed dogs had:
• Distinct gut microbiota compared with kibble fed dogs
• Higher fecal IgA and IgG, markers of mucosal immune activity
• Higher intestinal alkaline phosphatase (IAP), associated with gut homeostasis
— without increases in systemic inflammation³
This tells us two things:
1. Raw diets are not inherently dangerous to the gut.
2. Raw diets actively support mucosal immunity and microbial diversity.
These studies are in adults, but the principle applies across life stages:
diet composition — especially raw vs. ultra processed — profoundly shapes the gut ecosystem.
What those immune markers really mean: IgA and IgG are the body’s “front-line antibodies.” They live in the gut wall and act like sentinels—catching pathogens before they ever reach the bloodstream. When these levels are higher, it means the gut lining is strong, selective, and doing its job. A healthy gut doesn’t just digest food—it trains the immune system, building memory and tolerance that protect the dog for life.
Interestingly, studies show that raw-fed dogs don’t have higher inflammation markers—things like C-reactive protein (CRP), erythrocyte-sedimentation rate (ESR), or total immunoglobulin levels stay the same. What changes is where the immune system is active: in the gut wall, not the bloodstream. That’s a sign of balance, not stress.
This reassures readers that “higher IgA/IgG” isn’t inflammation—it’s resilience.
What About Cooked Diets?
Cooked diets fall somewhere between raw and kibble. While they may preserve more nutrients than kibble, cooking still denatures enzymes, alters fats, and destroys many heat sensitive bioactive compounds that naturally support microbial colonization.
AnimalBiome’s analyses repeatedly show that dogs on cooked or processed diets often have:
• Lower microbial diversity
• Higher levels of dysbiosis
• Reduced populations of beneficial carnivore adapted bacteria²
Cooked diets may be digestible, but they do not replicate the microbial, enzymatic, or nutrient profile of raw animal tissue — the substrate puppies’ guts evolved to expect.
Maternal Regurgitation: A Natural Microbiome Transfer System
My observations — which match those measured in science— are consistent with ethological literature:
raw fed dams regurgitate; kibble fed dams rarely do.
Why?
Two biologically grounded explanations:
1. Sensory mismatch:
Kibble does not resemble prey in smell, texture, or gastric behavior. It is unsurprising that it fails to trigger regurgitative behavior that evolved around carcass feeding.
2. Nutrient density and “shareability”:
Raw diets are nutrient dense and biologically appropriate. Kibble is often bulked with starches and fillers. A dam’s body may simply be less inclined to “spend” low value food by bringing it back up for her pups.
We do not yet have a study titled “kibble prevents regurgitation,” but the pattern is consistent across breeders and aligns with what we know about maternal diet shaping maternal behavior and maternal microbiome transfer.
AnimalBiome’s work reinforces this: maternal microbial transfer — whether through milk, saliva, fecal exposure, or regurgitated food — is a full spectrum inoculation that puppies are biologically adapted to receive.²
Why I Wean to Raw
When I wean puppies, I am not trying to reinvent nature. I am trying to follow it.
Photo used with permission of 4 week old Boston Terriers in Oui Boston nursery by Maxine Uzoff
A raw, species appropriate weaning diet:
- Mirrors the natural transition from milk, predigested raw, and raw parts
- Provides enzymes, microbes, and nutrients that support early immune development
- Aligns with the maternal microbiome, which puppies are genetically adapted to
- Produces higher fecal IgA/IgG (mucosal immune markers) and intestinal alkaline phosphatase (IAP)³, meaning that they have a responsive, well regulated gut, not a stressed one
- Avoids the ultra processed, high starch substrate that drives dysbiosis in many dogs
- Supports a healthier, more resilient gut ecosystem from the very first bites
Think of the gut wall as the body’s security gate. A raw diet strengthens that gate—more IgA and IgG guards on duty, fewer intruders slipping through. The result is a calmer, smarter immune system that remembers threats instead of overreacting to them.
For my litters, this includes my Immunity Formula and Immunity Blend, which are designed to mimic the nutrient dense, enzyme rich, microbially supportive foods that raw fed dams naturally provide.
Conclusion
The idea that puppies or seniors “can’t handle raw” is not supported by nature, by ethology, or by the growing body of microbiome science. If anything, the evidence points in the opposite direction:
raw, species appropriate diets are what their bodies — and their microbiomes — are built for.
References
¹ Balouei F, et al. Factors Affecting Gut Microbiota of Puppies from Birth to Weaning. Animals. 2023.
https://www.mdpi.com/2076-2615/13/4/578
² AnimalBiome. State of the Gut articles and microbiome resources.
https://animalbiome.com/blogs/news
³ Sandri M, et al. Raw Meat–Based Diet Influences Fecal Microbiome and Immune Markers in Dogs. Frontiers in Veterinary Science.
https://www.frontiersin.org/articles/10.3389/fvets.2021.644836/full
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