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News|Podcasts|May 12, 2026

The microbiome through the early life in puppies and kittens

This episode of The Vet Blast Podcast presented by dvm360 dives into practical, evidence-based strategies for supporting microbiome development in neonates.

On this week's episode of The Vet Blast Podcast presented by dvm360, host Adam Christman, DVM, MBA, and Emmanuel Fontaine, DVM, MSc, PhD, DECAR, discuss the importance of microbiome development in neonatal puppies and kittens. 

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Throughout the episode, Fontaine explains to Christman that the long‑held “sterile womb” hypothesis is no longer accurate. Instead, we now know that bacteria are present around the placenta and that microbial colonization begins before birth. As a result, newborn puppies and kittens don’t just inherit genes from their mothers, they also inherit aspects of their mothers’ microbiome, making maternal health and microbial balance crucial. And more!

Below is a partial transcript, edited lightly for clarity.

Adam Christman, DVM, MBA: So when we think of natural birth versus C-section, then, is there a difference with the mode of delivery? Does that alter microbial development?

Emmanuel Fontaine DVM, MSc, PhD, DECAR: Yes, yes, yes. And it's very important. When I worked in clinics at the vet school, we were doing a lot of C-sections because certain breeds are predisposed to have C-sections, and C-sections are great tools. I remember one paper we published many, many years ago on elective C-sections in dogs. And for me, the best finding was that we had a 0% neonatal mortality rate. When you think of it, that's awesome because that's what you want. You want to optimize the survival of those newborns. And sometimes when you're in-clinic, you think there is this female coming for dystocia, whether a dog or cat—‘Maybe I should just go straight to C-section.’

Actually, 80% of the dystocia cases we see in our clinics end up with a C-section. But in the end, we think, ‘Oh, we are optimizing neonatal survival—that's what we want.’

And that's true, but I keep telling my students these days that C-sections are tools, not shortcuts, and that's very important because it does have an impact on the microbiome development. When you look, there have been several studies that have been done in recent years showing that actually, when you have a puppy or a kitten that is born by C-section, its microbiome is less diverse than a puppy or kitten born by natural wellbeing.

And that makes sense, because it hasn't been in contact with all the bacteria in the vagina of their mother. It hasn't been in contact with all the maternal fluids and everything. But when it gets even more interesting, remember I told you about this elective sensation that I loved practicing because it was so much more convenient, because you have a team and everything, it was perfect. But they found that when you do an elective C-section, actually, the microbiome is even less diverse than when you do an emergency C-section compared to a natural birth.

So when you think of it, this tool, this elective C-section tool that we are using to optimize neonatal survival, actually comes with less microbial diversity in those newborns, and we know that this is correlated with their longtime health because those bacteria in the gut, they participate in many, many, many different mechanisms. They participate in immune development. They participate in brain development.

I have in one of my presentation, I have a little slide that shows how the gut microbiome is connected to all the different organs. And I think there's basically all of them. And by doing a C-section, actually, we can interfere with this normal development.

So don't get me wrong here. I don't want to demonize C-sections. As I said, C-sections are tools, not shortcuts, but we need to keep that in mind because when we do C-sections, we optimize neonatal survival. But there are some consequences. The trick today, and the goal today, is to find how to overcome those consequences.

Christman: Yeah, it's fascinating. I didn't know that actually, [and that] there even is a difference between emergency C-sections versus a planned or scheduled C-section.

Want to hear the rest of the conversation? Check out the audio at the top of this article, or wherever you listen to podcasts.


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