Feline Microbiome: What We Know (and Why It Matters)

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The feline microbiome includes a stable ‘core’ community of microbes most cats share after weaning, and a dynamic portion that shifts with diet, health, environment, and other factors. This illustration offers a creative peek into that microscopic world (definitely not to scale). Beneath the fur is a bustling ecosystem: the cat microbiome. It plays a huge role in digestion, immunity, even behaviour and stink-control.

https://video.wixstatic.com/video/57d70a_795d8ae1f4884af2aa026ce719017781/1080p/mp4/file.mp4

Cats groom to share and balance their microbiome. Jaspurr takes this job seriously. Purrl enjoys the spa treatment.

My cat Jaspurr has been sick, and after ruling out the usual Bengal issues—pancreatitis, allergies, infection, obstruction—the vet suspects Inflammatory Bowel Disease (IBD). So as a microbiologist (and a worried cat mom), I did what I do best: I dove into the scientific literature to understand what’s happening in his little plumbing system—and how the microbiome might be involved.

We often think of our cats—especially rulers of the roost like Purrl and mischievous Jaspurr—as fluffy bundles of attitude, biscuits, and occasional chaos. But beneath the fur and whiskers lies a bustling ecosystem: the microbiome.

Purrl, my iron-stomached queen, handles everything like a champ. Jaspurr, my discounted designer chaos gremlin, has a digestive system that rivals his personality in drama. And much of that difference comes down to their microbiomes.

If your cat has tummy troubles too, welcome — you’re in good company. We’re officially starting the IBD Cat Mom Support Group.

01

Microbes, Microbiota, Microbiome?

Microorganisms, microbiota, and microbiome in cats. A visual overview to clarify the terminology (not to scale).

Microbiology jargon can sound intimidating, but it doesn’t have to be. Let’s quickly unpack what “microorganisms,” “microbiota,” and “microbiome” really mean before we dive into the tiny world living beneath the fur.

Microorganisms

Microbes (short for microorganisms) are tiny living things you can’t see without a microscope. They include viruses, bacteria, fungi, and protozoa. Individually they differ, but together they shape many aspects of health — including your cat’s.

Microbiota

The microbiota refers to the community of microbes living in a specific place on or inside the cat’s body — such as the gut, skin, mouth, or lungs.

It includes:

• The helpful microbes (often called “normal biota”)

• Opportunistic or harmful microbes (pathogens, parasites, infectious agents)

The term has been used since the early 1900s, when scientists first realized that animals — cats included — host complex microscopic communities.

Microbiome

The microbiome is a broader concept. It includes:

• The microbiota (micro- "small" + bio- "life = all the microbes)

• Their genes

• Their proteins and enzymes

• Their metabolites (the substances they produce)

• The surrounding environment (diet, health, stress, indoor vs. outdoor life, etc.)

When the microbiome is disrupted (by diet, antibiotics, stress, or other factors), it can lead to dysbiosis, an imbalance in the body’s microbes. Dysbiosis may involve losing beneficial bacteria, gaining harmful ones, or reducing microbial diversity, and it’s linked to issues such as IBS and inflammatory conditions.

As the proud human of a chaos gremlin named Jaspurr, I can confirm: dysbiosis always picks the worst possible location.

02

The Feline Microbiome

Comparison of the dominant bacterial families across body sites in dogs and cats. Many taxa are shared between both species, highlighting how similar their microbiomes really are. Adapted from: https://doi.org/10.3390/ijms26167717.

Cats, dogs, and humans all host complex microbiomes—and despite our obvious differences, we share more microbial similarities than you might expect. A recent comparative review notes that the dominant bacterial groups across all three species include Firmicutes, Proteobacteria, and Bacteroidetes. The real distinctions lie in which microbial species are present and their relative abundance, reflecting each host’s physiology, evolutionary history, and dietary needs.

As obligate carnivores, cats have microbial communities adapted to a high-protein, meat-based diet, and they rely far less on fermenting carbohydrates and fiber than dogs or humans. Dogs and humans, both omnivores, display microbiomes that shift more readily with mixed diets—including those containing plant-derived nutrients.

In cats, the body site (gut, skin, or oral cavity) plays the biggest role in shaping the microbiome. In dogs, however, individual variation has a stronger influence —meaning dog microbiomes differ more from dog to dog than from body site to body site.

Because cats and dogs share so many microbial communities with each other —and sometimes with us— microbes can transfer easily through close contact.

03

What Influence the Cat's Gut Microbiome?

The less processed the diet (dry → wet → raw), the more the gut microbiome shifts away from the shared core and toward unique diet-specific bacteria. Based on data from: https://doi.org/10.3390/vetsci9110635

The gut microbiome is the most studied of all feline microbiomes because it plays essential roles in digestion, immunity, and overall health. Cats have a gut microbiome that leans more toward handling protein and fat. Many studies show that gastrointestinal conditions —especially IBD and chronic enteropathies— are linked to measurable shifts in both small-intestinal and fecal microbial communities.

So yes... let's dive into the litter box.

The Kitty Microbiome Project and related work highlight several patterns:

Diet matters (a lot).

• About 30 bacterial genera appear consistently across healthy cats—these form the “core microbiome.”

• Cats fed kibble-only diets show the highest proportion of core bacteria (about 70%) and the lowest diversity.

• Raw-fed cats show the greatest divergence, with most of their gut community composed of unique, diet-associated bacteria.

• Wet-fed cats fall somewhere in between.

The figure above illustrates visually illustrates this: the less processed the diet, the more heterogeneous the microbiome becomes.

Environment matters.

Microbiomes differ between home cats and shelter cats:

• Home cats tend to have a higher proportion of core bacteria.

• Shelter cats show more exposure to pathogens and environmental stressors, leading to more variable microbial communities.

This reflects differences in stress, diet consistency, hygiene, and exposure to other animals.

Age matters… but only a little.

Once kittens are weaned, the gut microbiome stabilizes. Major structural changes across age groups are minimal.

However, studies note a gradual decline in the number of core taxa with age—a slow narrowing of microbial diversity. Think of it as a gentle drift, not a dramatic shift.

Health status is a major driver.

Across species (including cats), chronic gastrointestinal diseases —especially IBD— are strongly associated with dysbiosis, meaning:

• A loss of beneficial bacteria

• An overgrowth of opportunistic microbes

• A change in the overall balance and diversity of the gut community

Similar dysbiosis patterns appear in feline diabetes, periodontal disease, and even some skin conditions, illustrating how interconnected the microbiome is with whole-body health.

04

Why Does it Matter?

The real reason I care about microbiomes. Jaspurr’s gut has been on a journey… and so have we.

Understanding the microbiome isn’t just an academic exercise (though my inner microbiologist is thriving). It matters because changes in the tiny ecosystems inside our cats can affect their health, our health, and in some cases, the health of our shared environment.And of course, it matters to me because Jaspurr’s gut has been… dramatic.

Here are three reasons the feline microbiome has real-world impact:

Antibiotic Resistance

Cats and dogs don’t just share our homes—they also share their microbial DNA pool, called the resistome. Studies show that some bacteria living in a pet’s mouth, gut, or skin can carry antibiotic resistance genes (ARGs) on mobile plasmids. These genes can potentially:

• transfer to disease-causing bacteria

• make infections harder to treat

• increase risks for humans living in close contact

This is why we hear about pet-associated strains of MRSA, MDR Staphylococcus, and other resistant organisms. It’s not about blaming pets, it’s about understanding the invisible biological traffic happening in every home.

Mental Health Links (the Toxoplasma question)

Several studies (including this one) have reported an association between childhood cat ownership and a higher risk of schizophrenia-spectrum disorders later in life.

Important nuance: It’s not the cat that causes the problem, it’s the parasite Toxoplasma gondii, which cats can carry but humans can also acquire from soil, contaminated water, undercooked meat, or unwashed vegetables.

The microbiome itself may also play indirect roles in brain–gut–immune interactions, a rapidly expanding field of research.

Shared Diseases Across Cats, Dogs & Humans

Because cats, dogs, and humans share overlapping microbial families, we also share vulnerability to certain microbiome-linked conditions, including:

• obesity

• metabolic dysfunction

• inflammatory bowel disease (IBD)

• chronic enteropathies

• gum disease/periodontal inflammation

Microbial imbalances (dysbiosis) don’t respect species boundaries. What harms your pet’s microbiome may influence your own, and vice versa.

05

How to Maintain a Healthy Microbiome

Keeping your cat’s microbiome balanced isn’t just about preventing diarrhea explosions (Jaspurr, I’m looking at you). A healthy microbiome supports digestion, immunity, skin health, and even behavior. Here are evidence-based ways to help keep your cat’s internal ecosystem thriving.

Probiotics/Supplements

When Jaspurr was sick, I added a probiotic supplement (Fortiflora) to his meals — and thankfully, our vet later recommended the exact same brand. (Small victories!). His prescription diet now includes prebiotics (fiber) and probiotics (“good bacteria”), which are supported by research.

Several studies — such as this one — show that probiotics can:

• reduce inflammation

• improve stool quality

• help manage symptoms of IBD and chronic GI disease

However, probiotics alone cannot fix a microbiome disrupted by an untreated infection or underlying illness. If your cat has persistent vomiting, diarrhea, weight loss, blood in stool, or chronic tummy troubles: see your vet first to rule out pancreatitis, parasites, infection, cancer, or other serious causes.

Oral Hygiene (because the mouth is the start of the gut)

What enters the mouth doesn’t always stay in the mouth — microbes can travel to the gut, kidneys, urinary tract, and bloodstream.

Yet a recent study estimated that only 28% of cat owners brush their cat’s teeth, and even then, not consistently. I love my cats deeply, but brushing Jaspurr and Purrl’s teeth daily? Absolutely not.

Based on another study, this has consequences:

• 50% of cats over age 4 have periodontal disease

• 93% of cats over age 8 are affected

• 82% of dogs aged 6–8 have periodontal disease

Since brushing is a battle for most of us, here are expert-supported alternatives:

• Chew Aids

  • Virbac C.E.T. IntelliDent Cat Bites are designed for cats as a mildly abrasive treat intended to improve oral hygiene. One chew daily appears to be effective at reducing gingivitis.

  • Silvervine sticks — shown in recent research to be safe, enriching, non-addictive, and harmless to kidneys/liver. Experts state that they help reduce plaque mechanically and provide sensory enrichment. Plus, cats go feral over silvervine. This enrichment and dental support in one chaotic stick is quite entertaining to watch as well.

• Diet — Dental diets and kibble designed for tooth scraping can help mechanically remove plaque, though they are not a replacement for regular dental care.

Picking the right pet bowl

The ultimate proof that shallow, whisker-friendly bowls transformed my cat Jaspurr into a "shark".

You may already know this story: Jaspurr refused to eat politely until we switched to whisker-friendly, shallow bowls. Now he eats like a tiny shark.

But the material of the bowl matters too.

Based on expert recommendations:

• Food-grade stainless steel is the safest option — low risk of scratches, bacteria buildup, or chemical leaching.

• If your pet regurgitates or has neck issues — Use an elevated feeding platform (elevated for the cat, not just “elevated aesthetic”).

Cleaning & Hygiene (the microbiologist’s moment to shine)

Here’s something I used to teach pre-nursing students: Soap doesn’t kill germs — it helps them slide off surfaces. So if anything remains after washing, it can still multiply and cause infection.

In hospitals, 1 in 31 patients gets a healthcare-associated infection despite trained professionals and disinfected environments. Now imagine the average household…

Here's what experts recommend:

• Wash pet dishes after every meal — Use hot, soapy water or a dishwasher. Avoid scouring pads: scratches create perfect homes for biofilms (bacteria slime that can host pathogenic strains). For multicat homes: owning multiple bowls is game-changing.

• Wash your hands  — Before and after handling pet food. (Yes, even kibble)

• Children under 5 should not handle pet food — Their immune systems are still developing. Pregnant or immunosuppressed individuals should take extra precautions — separate dishwashing loads, careful handling, etc.

• Daily household cleaning — Toxoplasma oocysts take 1–2 days to become infectious, so regular cleaning prevents spread.

  Use mild detergents and pet-safe disinfectants that won’t damage surfaces or irritate your pets’ noses.

  (I also like Mrs. Meyer’s pet formulas for this reason.)

• Weekly deep cleaning — Scrub litter boxes with dish soap and hot water.

  Bleach can be safely used on plastic litter boxes if correctly diluted: 1 tablespoon bleach per gallon of water, followed by thorough rinsing.

  Avoid bleach or vinegar on:

  • metal (including stainless steel)

  • wood

  • stone (granite/marble)

  • painted surfaces

  • rubber seals

  • fabrics

  They’re either corrosive (bleach) or acidic (vinegar), and both can cause permanent damage.

06

Tried, Tested, and Cat-Approved Healthy Microbiome Essentials

Here are the products I personally rely on to nurture a healthy microbiome, and to catch any signs of imbalance before they become a serious problem. Every cat is different, so please check with your veterinarian for any health questions. While these OTC options can help support gut health, they cannot fully restore a disrupted microbiome. It’s always best to consult your veterinarian to rule out any serious underlying issues.

Tap or click the pictures in the scroll gallery below to shop my favorite cleaning products without leaving the page.

• PETLIBRO Stainless-steel Water Fountain: What Jaspurr and Purrl both love: their PETLIBRO Cat Water Fountain. The Dockstream 2 Smart is quite fancy and cute: 3 L stainless-steel tray, 4-layer filtration, and app-connected hydration tracking. I personally use one of their older (and cheaper) stainless-steel models, and even with one running in my bedroom, I can’t hear it at all.

• CatGuru Whisker Friendly, Stainless-steelCat Bowls: For both Jaspurr and Purrl, the ultra-shallow stainless steel bowl from CatGuru is a must-have: designed to relieve whisker-fatigue while staying hygienic (dishwasher safe, non-slip, odor-resistant). CatGuru also makes an optional raised plate that fits under this bowl, which can help cats who struggle with regurgitation. I included it here for that reason, even though it’s not microbiome-related and (thankfully!) not something I’m dealing with right now. One GI issue at a time… no vomit on top of diarrhea, please.

• Hill's Prescription Diet Gastrointestinal Biome Stress Dry Cat Food: This is the diet my actual veterinarian recommended for Jaspurr, and it works very differently from regular over-the-counter kibble. It’s designed to help settle digestive flare-ups in as little as 24 hours, thanks to a patented fiber system that acts like a prebiotic to support healthy bowel movements, plus ActivBiome+ probiotics that quickly nourish beneficial gut bacteria.

  The ingredient list is tailored for digestibility and microbiome support, and I appreciate that it does not include meat by-products. It does contain corn — something that always makes me pause when it comes to my cats’ diets — but in this prescription formula it appears to be used for its digestible carbohydrate profile and balanced fiber contribution, not as a filler.

  What makes this diet especially unique is that it supports more than just digestion. It includes omega-3 fatty acids and antioxidant vitamins A, C, and E to help with skin health and inflammation. It also contains ingredients that support relaxation (hydrolyzed casein and L-tryptophan), which can be helpful for cats whose GI issues are tied to stress — very much the case for Jaspurr.

  This food is definitely an investment, but it’s a therapeutic diet formulated for cats with real GI needs, microbiome imbalance, or stress-linked digestive flare-ups. My vet chose it specifically for Jaspurr’s situation, and after a rocky start, he finally accepted it — and I’m already seeing a difference. He’s calmer (still vocal, of course), his tummy seems more balanced, and our household has had far fewer “surprises.”

  If your cat is dealing with similar issues, this diet may be worth discussing with your own vet. Every cat is different, but I’m genuinely hopeful this continues helping Jaspurr — and that it brings relief to your kitty, too.

• Hill's Prescription Diet Gastrointestinal Biome Digestive/Fiber Care Chicken & Vegetable Stew Wet Cat Food: This is the wet prescription pâté my vet recommended for Jaspurr — I jokingly call it his “foie-gras-priced pâté,” even though he currently disagrees with me and prefers boiled chicken like a tiny Michelin-star food critic. Wet food is still important for hydration, so I’m continuing to offer it alongside his kibble while working on the transition.

  This formula uses ActivBiome+ (a blend of prebiotics and probiotics) to support the gut microbiome, plus antioxidant vitamins A, B, C, and E. It includes good fiber sources like beet pulp, pumpkin, and psyllium husk, contains no meat by-products, and is made in the USA. It does have wheat gluten — something I’m a little reserved about — but it’s the pâté selected by my vet for Jaspurr’s current GI needs.

  Although Jaspurr will have to stay on a special diet for the rest of his life (and he is so young!), I take solace in the fact that he still prefers my lovingly boiled chicken over his pricey “cat-foie-gras.”

• Purina FortiFlora Probiotics for Cats: This is my go-to powder supplement when Jaspurr's tummy is acting up, and this is the probiotic supplement my vet recommended for Jaspurr as well. FortiFlora uses a single, well-studied probiotic strain (Enterococcus faecium) that has been shown to help with antibiotic-associated digestive upset and can support some cats living with feline herpesvirus-1. It also includes taurine, which plays a role in overall digestive health.

  One of the reasons I trust this product is its microencapsulation technology. The probiotics are coated so they can survive stomach acid and reach the intestines where they actually have an effect. It’s also NASC-certified, easy to sprinkle on food, and appropriate for cats of any age, which takes a little worry off my shoulders on rough days.

• VetOne Advita Probiotic Cat Supplement: VetOne Advita offers a multi-strain probiotic blend (E. faecium, L. acidophilus, L. casei, and B. coagulans) with microencapsulation technology to help the bacteria survive stomach acid. It also includes taurine and the prebiotic inulin to support the growth and activity of beneficial gut microbes. The addition of vitamins A, C, and E provides antioxidant support that may benefit both the digestive system and the skin. It is manufactured in a NASC-certified facility, though the company uses its own certification standards and does not display the NASC seal.

• Nutramax Proviable Paste and Capsule Digestive Supplement Kit: The Nutramax Proviable Kit provides a multi-strain probiotic blend (500 million CFUs per gram in the paste and 5 billion CFUs per capsule) designed to address several GI issues simultaneously. The paste also contains pectin and kaolin, which help reduce inflammation and promote firmer stool. I’ve used the paste mixed with boiled chicken and rice for acute tummy episodes, while the capsule contents can be sprinkled on daily meals. Although it doesn’t have the NASC seal, the brand uses rigorous in-house quality standards and has operated for decades without recalls.

• WORLD'S BEST CAT LITTER® Boosters™ Health Check-in™: This litter topper is an inexpensive way I monitor urinary health at home. It mixes with regular litter and provides instant color change when blood is present (it does not assess pH). Since urinary issues in cats can be subtle, this gives me an extra level of awareness between routine vet visits.

• Virbac C.E.T. IntelliDent Cat Bites: These treats were designed specifically for cats' oral health.

• Silvervine Chews for Cats: These silvervine sticks are a simple chew toy that both of my cats love. They give Jaspurr and Purrl a fun way to gnaw and play, and it’s endlessly entertaining to watch the acrobatics that follow.

• Revolution Plus Preventive Topical: This is the preventive topical I never skip. It protects against a wide range of parasites — including fleas, ticks, ear mites, and even heartworms — and the tiny dose makes it easy to apply at the back of the neck. Jaspurr and Purrl barely notice it.

• Mrs. Meyer’s Clean Day – Pet Multi-Surface Cleaner: Because clean shouldn’t mean chemical overload. This plant-based formula cuts through messes and leaves a light orange-blossom scent. Safe for pet areas and gentle on my own hands. Win-win!