EPISODE 115: What body systems, aside from the gut-brain connection, does the microbiome influence?

We want to thank AFB International for sponsoring this podcast. AFB is the premier supplier of palatants to pet food companies worldwide, offering off-the-shelf and custom solutions and services that make pet food, treats and supplements taste great.

Lindsay Beaton, editor, Petfood Industry magazine and host, Trending: Pet Food podcast: Hello and welcome to Trending: Pet Food, the industry podcast where we cover all the latest hot topics and trends in pet food. I'm your host and editor of Petfood Industry magazine, Lindsay Beaton, and I'm here today with Dr. Bushra Schuitemaker, head of microbiology at Pooch & Mutt and head of science and research at Biome9. Hi, Bushra, and welcome.

Dr. Bushra Schuitemaker, head of microbiology at Pooch & Mutt and head of science and research at Biome9: Hi, thank you so much for having me.

Beaton: In case you're unfamiliar with Bushra, Pooch & Mutt or Biome9, here's what you need to know.

Dr. Schuitemaker is head of microbiology at Pooch & Mutt, where she leads microbiome science, research and innovation across canine gut health. With a Ph.D. in microbiology and expertise spanning zoology, molecular biology and microbiome analysis, Dr. Schuitemaker specializes in translating complex scientific data into practical insights for pet health and nutrition. Her work focuses on understanding how the gut microbiome influences digestion, immunity, inflammation and overall well-being in dogs, supporting the development of evidence-led products, testing and education for pet owners and veterinary professionals.

Pooch & Mutt is built for real life with dogs, from puppyhood to senior years — for all breeds and needs. Its refreshed, color-coded range makes it easy to shop by life stage, taste and functional need. With complete wet and dry foods plus treats, supplements and bone broths across Wellbeing, Fresh, Superfoods, Primal and Veterinary lines, the range is designed to mix and match as needs change, developed with input from vets, behaviorists and microbiologists. Pooch & Mutt offers an at-home gut health test that analyzes a dog's stool sample to deliver science-backed insights and tailored recommendations.

Biome9 is a microbiome analysis platform focused on canine health. Founded in 2023, Biome9 was created to address what it calls a silent canine microbiome crisis, developing gut health solutions meant to deliver measurable health benefits for dogs.

Dr. Schuitemaker's experience in microbiome research in both the human and pet spaces is why we brought her on to answer this question: What are some of the other body systems, aside from the gut-brain connection, that the microbiome influences?

I want to start by asking what may be an obvious question. Why has the gut-brain axis taken up so much space in the conversation about the microbiome? What put that first on the list?

Dr. Schuitemaker: The gut microbiome is the first and easiest microbial community to study at scale. Fecal samples are relatively easy to collect, especially in dogs, and as dog owners, it's something we have a close relationship and proximity with. Dog owners are constantly talking about their dogs' stool samples — when I first got my rescue dogs, it was the main topic of conversation in the household in terms of monitoring their health. We've always known, as dog owners, how important that is.

As humans, we know that when we're a little stressed, it can cause stomach upset, and we see a very similar pattern in dogs, because dogs and humans have co-evolved alongside each other for thousands of years. They've got very similar microbiomes, which makes canine microbiome research very accessible, because discoveries made in human microbiome research are often applicable to the canine population as well.

One of the big topics we look at with Biome9 in terms of the gut-brain axis is complex conditions like epilepsy. From human pediatric studies, we know that children with epilepsy can have the severity of their symptoms and seizures reduced through diet and probiotics — moving toward a more ketogenic diet and prioritizing targeted probiotics like lactobacillus and bifidobacterium had a positive effect. We took the same approach, working with specialist vets in the U.K., and saw similar results.

This first came up as a topic of interest when someone with an epileptic dog reached out to me. Their dog had fairly well-controlled epilepsy — maybe one seizure a month at most — and then the dog went on a course of antibiotics, and the seizure frequency rose to around four seizures a week. That was a clear indication that something was going on between the gut ecosystem and brain activity, and we've used that as a model to better understand the gut-brain axis in dogs.

One of the key things we look at are GABA-producing bacteria. This can be a bit controversial, because some studies have shown that the GABA and serotonin produced by gut bacteria can't necessarily cross the blood-brain barrier. But we still see a significant signature and association between these GABA-producing bacteria and the severity of epilepsy. Improving the gut microbiome also improves absorption, so if a dog is on epilepsy medication, that helps the medication become more effective. It's a complex system, and that's just one specific model and disease.

What we now want to do is better understand how those bacterial signatures relate to other behavioral issues, such as anxiety and aggression. Behavior is emotionally powerful, especially for dog owners, and in both humans and pets, anxiety, stress, cognition and behavior are areas people care deeply about. In dogs specifically, there's a lot of emerging evidence linking gut microbiome composition with behavioral and cognitive outcomes, including anxiety, stress responses and learning. Researchers looked at working dog populations and found that, especially in older working dogs, certain bacteria were associated with better performance and longer working lives.

There's a lot of opportunity here, but a lot left to learn, because dogs, like humans, are heterogeneous — diverse in breed, genetics, lifestyle and diet. Using large data sets like we have at Biome9 and Pooch & Mutt, we're able to apply tools like machine learning to find the signal within the noise. The idea that bacteria in the gut may influence the brain is easy to communicate, but we're careful not to oversimplify it to "one bacteria equals one behavior."

A 2025 study in companion dogs found that microbiome composition could predict anxiety and aggression groups using machine-learning modeling, with one group of bacteria, Blautia, repeatedly identified in relation to anxiety — though that doesn't mean we can use it to diagnose or treat behavior. I see the microbiome as an additional tool to support dogs, the same way training and diet are tools.

Gut-brain became a well-known topic because it connects two things owners notice every day: digestion and behavior. But the science is far more complex than "gut bacteria make dogs anxious." It's about communication between microbes, metabolites, the immune system, hormones and the nervous system. I also work closely with vets and behaviorists on identifying potential hidden pain, because that's a common reason dogs become anxious or aggressive — they're expressing behaviors tied to a pain symptom that hasn't been noticed. We see changes in the gut microbiome relating to many functions across the body, and the fact that we can see those changes in the gut environment first gives us a clear indication when something else is going on that isn't directly tied to the gut-brain axis — it could be joints or digestive function. Addressing that issue then addresses a behavior that was really a result of hidden pain.

Beaton: With all of that going on, it seems clear there are other body systems a microbiome influences. At what point did people start looking at those other systems? 

Gut health and the gut-brain axis were the first things to come out, and gut health has been around in the human space for quite a while — at the very least, everybody knew what a probiotic was by the time it hit the pet market. What are some of those other systems, and how are we finding that the microbiome influences them?

Dr. Schuitemaker: When I talk about the gut microbiome versus gut health, I use the metaphor of a football game, where the gut microbiome are the players, but there are also other important things, such as the rules and the playing field itself. When we talk about gut health, we're talking about all of those interconnected things together. Even without understanding the microbiome, there were plenty of examples before this research showing how those things connect. We knew that behavior, or even skin condition and allergies, could be influenced by diet — that's why a dog with skin issues might be put on a specific or exclusionary diet. We didn't always know the cause and effect until we could dig into what was going on with the players: the microbiome.

Skin is a strong example. Dogs have their own skin microbiome, and recent metagenomic work in healthy dogs found that skin site and breed influence microbial variation. Dogs lick themselves, so there's a lot of crossover between the skin microbiome and the gut microbiome. Skin also matters because it's not just a surface — it's an immune barrier, and when that barrier is disrupted, microbial communities can shift both externally and internally, which may be relevant to itching, allergies, atopic dermatitis and skin infections.

One breed we've researched extensively is French bulldogs. They're known for atopic dermatitis and other skin-related issues, and for a long time this was assumed to be tied to the breed's genetics. But because of their physiology — the size of their hips and head — many French bulldogs are delivered by cesarean section rather than naturally. Pediatric studies in humans show that babies born by cesarean are more likely to develop eczema, allergies and asthma as they age, so something similar could be happening with French bulldogs: cesarean delivery may put them at greater risk of atopic issues, atopic dermatitis or allergies. Cases of canine atopic dermatitis have reported dysbiosis — disruption of the natural ecosystem — in both the gut and the skin simultaneously, suggesting the skin disease may not be purely a skin issue but part of a wider immune and microbial picture.

Related to that, given how dogs lick themselves and the interaction between skin and gut, is the oral microbiome. This is a promising area, because periodontal disease is so common in dogs — a 2024 study noted that gingivitis and periodontitis are the most common oral diseases in dogs and can affect up to 70% of canine patients. Using saliva and dental plaque microbiome analysis to identify microbial and functional biomarkers of periodontal disease gives us a new way to target these issues and support dogs' long-term health.

Another area gaining attention is the respiratory tract microbiome — the gut-lung axis, in both dogs and cats. That research is still developing, but it's relevant to immune response and how local airways may interact with the gut and the wider environment.

I work with dogs now, but my Ph.D. and background were in poultry, and I've also worked extensively in human microbiome research, particularly pediatric microbiomes. What fascinates me is how conserved early microbial development is across species — looking across birds and mammals, including humans, in the first few weeks to the first year of life, and the importance of bacteria like lactobacillus and bifidobacterium for immune system development. When something in biology is that well conserved and shared across species, it shows how vital it is to development and immune function.

Another area I find interesting in dogs is the joint-mobility axis. In our data, dogs that get more than 60 minutes of exercise a day generally have really good microbial markers. Dogs with a good microbiome also tend to respond better to joint supplementation. At Pooch & Mutt, using the science of Biome9, we created a joint supplement that also contains probiotics, to help break down large molecules like glucosamine and chondroitin so they're more easily absorbed — improving both the gut microbiome and the efficacy of the supplement, supporting the joint-gut axis.

Other recent canine work has looked at microbiome variation in aging dogs. Puppies have a really diverse microbiome, which makes sense given how a puppy lives — exploring the world with its mouth, chewing on everything, with a lot of environmental exposure and enrichment. As dogs age and settle into a more routine lifestyle, we see a drop-off in diversity and richness starting around age 7. A loss of diversity and richness is associated with less energy, worse joint health and higher inflammation. One study on aging dogs with osteoarthritis found a stronger age-related microbiome change than a clear osteoarthritis-related clustering — a useful reminder that these relationships are rarely simple, since dogs are so heterogeneous and require large populations for this kind of analysis.

The microbiome touches almost every system, not always directly. Sometimes it's local, like the mouth and skin; sometimes it's more systemic, through immune signaling, inflammation, metabolites or barrier function.

Beaton: With all these different systems, and every dog — every human — having their own microbiome, how similar are dog microbiomes to each other? Can we take a one-size-fits-all approach to something like hip and joint health, or is there nuance and customization involved?

Dr. Schuitemaker: In the U.K. population — and it's important to look at this on a country-specific and regional basis — we see big differences, say, between a U.K. dog and a dog from Canada. That could partly come down to differences in food processing systems as well as environmental exposure. But around 75% of the canine microbiome shows the same species of bacteria fairly consistently. At Biome9 and Pooch & Mutt, we compare our data to published studies to better understand where our findings align or differ.

Dogs generally live a fairly consistent life — they typically live 12 to 15 years and don't move around too much. Humans eat a huge variety of food, live a long time and move around the world during our lives, whereas dogs have a more refined lifestyle, which gives us more consistency to work with. In our research, we recruit dogs considered healthy by a vet — ideal body scores, no illnesses, no symptoms, on a good diet — and use that as a healthy control population to understand what's considered normal. We see some variation based on factors like age, but we can control for that with statistical modeling.

We also see interesting breed-specific patterns. French bulldogs, for example, tend to have specific concerns around the gut-skin axis, and Spitz-type breeds — huskies, malamutes, Akitas — tend to do much better on very high-protein diets. Although we see variation with some specific breeds and groupings, when we take all of this data together, we can identify a clear, healthy microbiome profile, with specific markers — species within the microbiome and the levels at which they should sit — for what we'd consider a stable gut.

Because there isn't a one-size-fits-all approach to probiotics, supplements or diet, we tell people the best thing to do is stop guessing and use the science. Sending a fecal sample to our labs allows us to run a microbiome analysis and compare a dog to the healthy population relevant to it — toy breed, giant breed, puppy or senior — to determine what would be considered healthy for that dog, and then build recommendations from there.

Our recommendations run over six months. With dogs, changes — like a diet change — need to happen gradually, or you'll see adverse effects if things shift too quickly. We want to modulate the entire ecosystem, so we break the process into three phases. In the first two months, we prime the ecosystem using prebiotics — high fiber — to feed the beneficial bacteria already present. In the second phase, we introduce probiotics, which are able to establish because we've set up the environment for them. In the final phase, we reinforce that new ecosystem.

After six months, people retest, review their results, and typically don't need to move on to another supplement plan. Alongside that, we give dietary recommendations — increasing natural fiber, diversifying protein sources, introducing more lean, digestible protein, and increasing omegas and oils — all based on the bacteria profiles identified from the fecal sample.

Beaton: There's a lot going on here. How are you finding the reception from veterinarians and consumers? What kind of education has to happen so veterinarians can have this conversation? They're the first line of defense — something's wrong with your pet, you take it to the vet — but if they aren't aware of this, or don't have the knowledge, they might miss it entirely or not consider it. Where are we on the education spectrum right now?

Dr. Schuitemaker: Because the microbiome has been such a hot topic in humans for the past five to 10 years, we tend to see that when something is popular in humans, it moves over to pets as well. There was already interest and buzz before we started introducing this for dogs.

For education, we're certified trainers, so we go and train vets directly, or give them access to online seminars so they can learn the science. We don't expect them to become microbiologists overnight, so we're there to support them with these discoveries. That's also why, with our analysis, we've structured it around specific functions and how the microbiome can be summarized — for example, is the microbiome supporting coat and skin health? We use a traffic-light system, zero to 100, and behind that sits all of the complex science, but we try to simplify it into an easy readout for both vets and owners.

We also give guest lectures at universities for the next generation of vets and vet nurses. This ties into the canine microbiome crisis that got Biome9 started — there are so many dogs with repeat vet visits for digestive issues or non-responsive skin issues, where no matter what people try, it keeps flaring up again. Just when you think you've got on top of it, there's another flare-up. 

These cases often land with vet nurses, who are left doing a bit of trial and error — try eliminating chicken, try eliminating grains, see how that helps, maybe try this probiotic. We want to take away that guesswork. It's frustrating for veterinary professionals and dog owners alike, and it gets expensive when you're cycling through diets — you might end up on steroids or antibiotics. We want to reduce all of that and take a more holistic approach to overall dog well-being.

In the veterinary industry, probiotics are more routinely used now. It's been recommended for a long time in human medicine that if you're on a course of antibiotics, you should also take probiotics to help restore beneficial bacteria, and vets can recognize this in dogs' recovery after antibiotics as well.

Another topic becoming increasingly popular, and closely related to the microbiome, is fecal microbiome transplants. This is already used successfully in human medicine to treat recurrent gastrointestinal infections, and it's now being used to treat dogs with chronic enteropathies, with really positive results. 

It started being done without the same level of advanced microbiome analysis we have now, so there was a bit of "we know it's working, but why is it working?" Now, using large data sets, we're better able to understand what to look for in both donors and transplant recipients, to make sure the treatment succeeds.

In terms of communicating with dog owners, Biome9 is a scientific subsidiary of Pooch & Mutt. We focus on the science, working directly with vets, behaviorists and nutritionists, and publishing our research, while Pooch & Mutt focuses on dog owners across all breeds and needs and helps translate that complex science into something understandable and accessible. When we run a dog's gut health test through Pooch & Mutt, we provide scores and videos explaining everything we've found.

The key part is that we identify four priority areas — the four areas from a dog's gut ecosystem that scored lowest based on our internal signatures — and provide recommendations based on those areas, whether supplements, diet or lifestyle changes. Targeting those four key areas tends to boost some of the other scores as well. We want to focus on what's the priority for that dog right now.

Beaton: Are you finding pet owners are really interested in this topic — engaged and willing to be educated?

Dr. Schuitemaker: Definitely, because, as with the gut-brain axis, digestion and behavior are two things dog owners care deeply about. Some people getting the gut health test are being proactive — their dog doesn't currently have symptoms, but maybe it's getting a little older and they want to make sure it's on the right diet. More often, though, the people reaching out to us are at the end of their rope, having already tried a lot of things. 

If you have a dog with sensitive digestion or recurrent skin issues, you want something you can track and understand, follow advice on, get results from and monitor over time. People are often already fairly engaged coming into it, and because we work closely with vets, they're also able to provide this as a recommendation.

Beaton: As we wrap up, whenever I do an episode covering a lot of research, I want to know what's coming next. Since you're involved in the research, what are you most looking forward to? What's currently in progress or upcoming that has your attention right now?

Dr. Schuitemaker: So many things. One big one: the canine microbiome has really been our focus, but we're now expanding into the feline microbiome as well, because it's important for us to better understand the long-term gastrointestinal health of cats. We're still building that database so we can run the same kind of complex machine learning, but I'm excited to see how we can support cats the way we've supported dogs over the past three years.

Another area I'm excited about: we've learned a lot from human studies and human microbiome analysis, but there's a massive opportunity for humans to learn from dogs, too, especially as we branch further into anxiety and aggression. If we can better understand that in dog populations, there could be findings applicable to humans as well. When we share biology, we can share benefits and outcomes, and that makes it better for all of us.

Beaton: Do you think there will be major differences found in cats compared with dogs, or is it similar enough?

Dr. Schuitemaker: Cats will be very different. Dogs and humans are similar partly because of co-evolution, but also because both species are omnivorous, whereas cats are strict carnivores. They have a very different diet composition and a much simpler microbiome. Dogs have bacteria that support fiber digestion, protein digestion and carbohydrate digestion, while cats are more focused on protein digestion than those other components — which makes it trickier to identify the key bacteria involved, since cats tend to be fairly similar to one another to begin with.

Another challenge with cats is that some are outdoor and some are indoor, and that seems to drive a lot of differentiation in the data — not always in the direction you'd expect. Indoor cats actually seem to have more protein-degrading bacteria, while outdoor cats have more fiber-degrading bacteria, and in other species those bacteria are key to preventing pathogens and supporting the immune system. Part of that may be environmental exposure from being outside, including eating small animals that might carry fiber-degrading bacteria. We're trying to better understand what causes those differences, what's considered healthier, and how we can support both types of cats.

Beaton: Thank you for coming on today, Dr. Schuitemaker, to talk about one of the hottest topics in pet food right now, one that's covering more ground in so many different ways. We've been inundated with gut health and gut-brain axis messaging, and I'm starting to see dental health and overall wellness pop up here and there, too. It's been interesting to hear how far the research has come across these categories — it sounds like there's still a lot left to learn. Before we go, where can people find more information about you, Pooch & Mutt and Biome9?

Dr. Schuitemaker: You can find everything about me on LinkedIn — just search for Bushra Schuitemaker. You can check out the Biome9 website, biome9.com, and the Pooch & Mutt website, poochandmutt.com. You can also find Pooch & Mutt on Instagram, Facebook and LinkedIn. We have a lot of resources on YouTube and Instagram, so if you want to learn more about your dog's gut health, check out the blogs at Pooch & Mutt and Biome9.

Beaton: That's it for this episode of Trending: Pet Food. You can find us at petfoodindustry.com, SoundCloud or your favorite podcast platform. If you want to chat or share feedback, I'd love to hear from you — email me at [email protected]. 

And thanks again to our sponsor, AFB International, the premier supplier of palatants to pet food companies worldwide, offering off-the-shelf and custom solutions and services that make pet food, treats and supplements taste great. 

Once again, I'm Lindsay Beaton, editor of Petfood Industry magazine, and we'll talk to you next time. Thanks for tuning in!