The Pet Microbiome Explained: How Gut Health Impacts Your Furry Friend’s Overall Wellness

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What is the Microbiome?

The microbiome is a natural microbial spacesuit that allows plants and animals to survive on Earth. Without the right microbes living on and inside your body, you wouldn’t be able to fight disease or infection, digest food, produce hormones and neurotransmitters, or many other functions essential to survival.

We live in a world dominated by microbes.  They colonize almost every inch of the planet, from the bottom of the oceans to the highest mountain summits. They even create communities inside of us – over 90% of the cells in our bodies and our pets’ bodies are microbes. Many of these microbes live in symbiosis with our cells; they do some of the work, and we do some of the work. We could not survive without their help.  We provide habitat and nutrients, and they perform many necessary functions.  This habitat and the microbes that live in it are called the microbiome.  The microbes themselves are called microbiota.  The microbiota includes bacteria, yeasts, fungi, protozoa, viruses, and more.

There are many different habitats, or biomes, all over the body, including in the ears, on the skin, in the mouth, in the digestive tract, and in the lungs. Each is home to a range of microbes, just as different biomes on Earth have different plants and animals. The ones that thrive in a desert environment are much different than those that thrive in an arctic or jungle environment.  Like these environments, a wide range of microbial life can survive and inhabit each biome.  Some of these may be beneficial microbes with which we have shared a symbiotic relationship for hundreds of thousands of years.  Some may be invasive microbes that are not species-appropriate and out-compete the beneficial microbes, lowering their numbers or driving them to extinction.  Unfortunately, this is becoming common in humans and pets due to inappropriate diets and our modern lifestyle.   This disruption of balance is called dysbiosis and is a potential cause of many diseases, including inflammatory bowel disease, Leaky Gut syndrome, obesity, and cancer.

The gut microbiome contains most of the microbes that share life with you, your dog, or your cat.   In fact, the human gut is “one of the most densely populated microbial habitats known on earth.”  When someone says “the microbiome,” they typically mean the gut microbiome.

Roles of the Gut Microbiome

As multicellular life has become more complex over the past two billion years, we’ve relied on symbiotic microbes to carry out some essential functions. These relationships go back millions of years to the point where many basic functions require a healthy, balanced microbiome. We still don’t understand all of the microbiome’s roles, but we know of many important ones.

  • Digestion – Microbes in your dog or cat’s gut break complex nutrients into basic ones that your pet can use.  Without a healthy microbial balance in the gut, your pets won’t be able to digest their food thoroughly, which means fewer nutrients for your dog and more nutrients ending up on your lawn.
  • Aiding Gut Health – Gut microbes produce new nutrients, like B & K vitamins, and short-chain fatty acids, such as butyric acid, that nourish gut cells.  They also produce T cells that work with the body’s immune system, signaling where damage needs repairing.
  • Aiding the Immune System – The microbiome is an extension of the immune system that helps identify threats and benign substances like pollen, which is why dysregulation of the microbiome is associated with allergic response.  In one study, mice who lacked a specific microbial transmitter in their gut showed a dangerous allergy to peanuts.  Researchers then wiped out the gut bacteria of healthy mice, and they became susceptible to peanut allergy as well.  Read more about the link between gut microbes and allergies here: How Diet and Environment Impact Allergies in Dogs and Cats.  Microbes in the gut also out-compete and even target pathogenic bacteria.  For example, one virus in the gut targets dangerous e.coli bacteria, destroying it before it can grow out of hand.  Additionally, gut microbes create compounds that circulate through the body and provide protective benefits.

    If your pet’s microbiome is out of whack, they will likely see more skin issues, allergies, or digestive problems.

  • Supporting Overall Health and ResistanceGut microbes play a role in balancing the other microbiomes of the body by supplying nutrients, beneficial compounds, and communication.  Microbes on the skin, in the ears, lungs, respiratory tract, and mouth perform other vital functions and offer protection, and the gut microbiome supports each of these communities.  These relationships are referred to as the gut-lung axis or the gut-skin axis.
  • Balancing Mood and Behavior – The gut microbiome communicates directly with the brain via the massive vagus nerve network.  This communication highway allows the brain to influence intestinal activities, including activity of functional immune effector cells; and the gut to influence mood, cognition, and mental health.”The Gut-Brain Axis: Influence of Microbiota on Mood and Mental Health.   
  • This connection is one of the reasons that dogs who eat fresh, raw foods can be easier to train.   Oregon State University conducted a fascinating study on the gut microbiomes of shelter dogs, discovering that aggressive dogs had distinctly different gut microbes than friendly dogs (The gut microbiome correlates with conspecific aggression in a small population of rescued dogs, 2019).  
    In this 2023 study comparing the microbiota of raw-fed and kibble-fed dogs, the microbial dominance observed in the kibble-fed dogs was the same as in the aggressive dogs in the previous study. In contrast, the microbial dominance observed in non-aggressive dogs was the same in the raw-fed group.
    In another study at Caltech, researchers wiped out the gut bacteria of healthy mice and saw their serotonin levels drop by 60%.  When researchers reintroduced healthy microbes to the gut, serotonin returned to normal. Serotonin is an important hormone and neurotransmitter that plays a role in sleep, appetite, feelings of well-being, anxiety, heart health, weight, and more. Over 90% of the body’s serotonin is produced in the gut, and a healthy microbiome seems essential to production.

    The research clearly suggests that animals with diverse, species-appropriate microbiomes enjoy better, more stable moods and a higher quality of life.

These are just a few examples of the importance of a balanced microbiome.  If the microbiome is out of balance, health and quality of life can plummet in one or more critical areas.  However, the microbiome is only one piece of the puzzle, so if your pet struggles, it’s essential to look at the whole picture.

Dysbiosis and Leaky Gut

Microbiomes differ between individuals based on genetic factors, diet, location, age, and lifestyle.  Your microbiome may be more similar to your partner’s than your parent’s.  As you age, your microbiome will change with you.  By owning a dog or cat, you will also share microbes back and forth with them.  A healthy microbiome is typically one that is species-appropriate and diverse.  However, it’s possible to foster a microbiome that does more harm than good by eating inappropriate foods, living a sedentary lifestyle, and being exposed to compounds and toxins that damage or hinder microbes.  This lack of healthy balance is becoming the norm for ourselves and our pets.

Think of it like a farmer intending to grow a vegetable garden.  If he adds the wrong seeds, fertilizer, and harsh pesticides, he may end up serving buckthorn and poison ivy for Thanksgiving dinner.   His field may become overrun by invasive plants and pests that mangle his crops, soil, and equipment.  The farmer’s choices have led to a damaging lack of natural balance in his environment.

Dysbiosis is a lack of balance within the gut microbiome.  When species-inappropriate microbes reproduce more than beneficial microbes, it leads to a microbiome that is out of harmony with the body.   Compounds that the body needs aren’t produced in sufficient quantities, and other irritating or damaging compounds may start to build up and cause issues.  Communication between the microbes and the immune system will decrease, and many other negative changes will occur.  The result is an unhappy pet. 

There are three basic types of dysbiosis: loss of good bacteria, overgrowth of harmful microbes, or an overall loss of diversity.

Causes of Dybiosis

Many factors can contribute to gut microbiome imbalance, including, but not limited to, the following.  If your dog or cat suffers from dysbiosis, they won’t receive all the benefits of a thriving microbiome and may build up microbes that harm the body.

  • Inappropriate diet – Processed foods and foods high in carbohydrates are common contributors to dysbiosis as they feed the wrong microbes.
  • Preservatives and food additives
  • Antibiotics or medications – Some beneficial microbe species may die completely from antibiotics.
  • Infections
  • Damage to the digestive system
  • Stress
  • Exposure to toxins
  • Sedentary lifestyle

Symptoms of Dysbiosis

Some symptoms appear in the gut where you would expect, but some may be surprising since gut balance affects so many different systems. Dysbiosis can also contribute to many disease states, such as obesity, cardiovascular problems, inflammatory bowel disease, and cancer. Pets may exhibit one or several of these symptoms, which may be mild or severe.

  • Fatigue
  • Poor digestion, gas, or loose stool
  • Digestive upset or reflux
  • Diarrhea or vomiting
  • Food sensitivities
  • Skin rashes or itching
  • Repeat ear infections
  • Anxiety or depression
  • Achy joints

Unfortunately, dysbiosis is becoming very common due to processed diets and antibiotic use.  If a pet suffers from dysbiosis long enough, they can develop Leaky Gut.

What is Leaky Gut?

The intestinal wall is the only thing that separates bacteria, viruses, and your pet’s undigested meal from his bloodstream.  It is a semi-permeable structure that allows fully digested food particles and bacterial metabolites to enter the body to be used for energy and as building materials.  You can think of it like a wall of security guards, letting the good stuff through and keeping dangerous and undigested materials out.  This wall is extremely thin in many places, only one cell thick.  A thin coating of mucus protects the wall.

Normally, beneficial microbes help nourish and protect the gut lining.  In pets with dysbiosis, the good microbes are replaced with neutral or harmful microbes, which create compounds that irritate the gut lining and eat away the protective mucus.   As the gut lining becomes more inflamed, the gaps between intestinal cells grow larger, making the gut more permeable, like holes in a fishing net.  Larger particles, such as undigested food, bacteria, and viruses, begin to cross directly into the bloodstream and circulate through the body.  This damage to the lining also blunts the immune system’s ability to communicate with the gut and recognize friend from foe.

The result is devastating.  Throughout the body, the immune system attacks the benign particles that slip through the larger holes.  Undigested food proteins found in the bloodstream are labeled as enemies, causing sensitivities and allergy symptoms whenever that protein is eaten.  The immune system’s reaction triggers inflammation – one of the body’s primary defenses –  all over the body.  The disrupted gut microbiome disrupts other microbiomes, most notably the skin microbiome.  

Pets with Leaky Gut may suffer from several food and environmental allergies, which may increase in number and severity over time. Typically, pets in this state will see some relief after switching to a new or “novel” protein, only to start showing symptoms again after a few months.

Symptoms of Leaky Gut

Each pet may exhibit different symptoms, which may be constant or intermittent, making it challenging to identify Leaky Gut; it can masquerade as many other ailments. Suppose your pet shows one or more of these symptoms and has taken medications or antibiotics in the past or has eaten a highly processed or high-carbohydrate diet such as kibble or canned foods. In that case, testing the microbiome balance is a good idea.  

Though dysbiosis is not the only cause of Leaky Gut, the two often go hand in hand, so many symptoms are the same.  Most pets will suffer from one or more GI issues, though some may only see issues on the skin.

  • Fatigue
  • Poor digestion or loose stool
  • Bad breath
  • Sensitive stomach
  • Digestive upset or reflux
  • Bloating or gas
  • Diarrhea, constipation, or vomiting
  • Food sensitivities
  • Food and environmental allergies
  • Autoimmune disease
  • Skin rashes or itching
  • Loss of fur
  • Repeat ear infections
  • Bladder infections
  • Behavioral issues
  • Anxiety or depression
  • Achy joints
  • Weight loss
  • Nutritional deficiencies

As you can see, the list of potential symptoms is long and not concentrated in any one area.  The longer Leaky Gut goes on, the more damage it can do to the gut lining and the longer it may take to reverse.  It took time to create the situation, and it’ll take time to reverse it.

Not every pet exhibiting these symptoms has Leaky Gut, as many other conditions can cause one or more of the above symptoms. Luckily, microbiome testing now allows you to check for dysbiosis.

How to Improve the Gut Microbiome

Improving and balancing the microbiome usually includes a few steps.  At its most basic, you remove exposure to anything that may contribute to imbalance, add beneficial microbes and possibly target and reduce harmful microbes, add the right foods to encourage the growth of good microbes and support the body to heal the damage.

Testing the Microbiome

Several helpful tests now exist for dogs and cats that allow us to see what and how many microbes are present in the gut and determine if dysbiosis and possibly Leaky Gut are potential causes of your pet’s symptoms. Testing works by mailing a fresh stool sample to a laboratory where technicians carefully examine the microbial DNA in the sample, allowing them to get a snapshot of the inner workings of your dog or cat’s gut.  

AnimalBiome has been at the forefront of the microbiome testing industry since Dr. Holly Ganz founded it in 2015. It offers accurate testing, a one-on-one consultation after every test, and solutions for balancing the gut, such as fecal transplants from healthy dogs and cats. To learn more about fecal transplants, check out our interview with Dr. Odette Suter about the microbiome.

Starve “Bad” Microbes

Technically, there aren’t any “bad” microbes; everyone has a place. Even potentially harmful bacteria like E. coli normally live in a healthy gut.  But when microbes that should be in the extreme minority start to take over, it’s essential to make some changes to balance the system.  One of the most common contributors to unhealthy gut bacteria balance is food. 

Every single bite your dog or cat eats will feed microbes, good or bad. If you’re feeding natural, fresh, species-appropriate foods, you’ll feed the microbes that benefit your pet. If you feed heavily processed, starch-laden foods, you’ll feed microbes that promote imbalance and damage. So, one of the first steps for pets suffering from dysbiosis is to adjust their diet.  By cutting out processed foods and foods high in carbohydrates, you starve the bad microbes, reducing their numbers and allowing the beneficial microbe communities to grow.

Reduce Exposure to Harmful Compounds

As we work to regain balance in the gut, it’s important to reduce exposure to compounds that may damage or interfere with the microbes’ ability to thrive. Food preservatives and additives, pesticides, and even cleaning chemicals used around the house can inhibit the growth of beneficial microbes. Pesticides are common in our environment and often used on pet food ingredients, but they can also harm the microbiome.  Steve’s Real Food only uses pesticide-free produce in our recipes.


Reducing exposure also includes proteins and foods that your pet is sensitive to.  Now is not the time to rotate back to a protein that they have reacted to in the past.  Most sensitivities are not permanent and may go away once the gut balance is restored and the damage is healed. Still, as you’re working to improve the gut, it’s vital to reduce inflammation in the body as much as possible.  

Stress is another important factor in gut health—work on reducing stress in your pet’s life and your own life.

Probiotics for Dogs - Restore Beneficial Microbes

If your pet has severe enough dysbiosis or has taken medications or antibiotics in the past, it may be necessary to add diverse gut microbes through diet.  Think of the gut as a fish tank; just adding the right foods won’t be enough if the fish aren’t even in the tank.

Though several companies make dog and cat-specific probiotics, a fecal transplant is currently the best option for pets who need to re-establish their gut balance.  A fecal transplant involves taking poop from a healthy dog or cat who has a well-balanced and tested gut microbiome and introducing that to the recipient pet.  Typically, fecal transplants are available in capsule form and are not unpleasant for the recipient pet.  They also make a huge difference; in some cases, improvements are seen within just a few days.  

AnimalBiome and Adored Beast Apothecary offer excellent dog and cat-specific probiotics and complete protocols to help balance the microbiome.   We highly recommend working with one of these companies. Restoring gut balance can be a long road for some pets, and as the harmful microbes die off, they may actually cause more irritation, making it look like it’s not working or getting worse. Thus, it’s helpful to have experienced minds in your corner.  For more information, check out our interview with Julie Anne Lee, founder of Adored Beast.

Feed the Right Foods

Successfully balancing the gut microbiome long-term will 100% depend on food choices.  Even if you reintroduce the beneficial microbes, if the right food isn’t passing through the gut, they’ll have nothing to eat and die off quickly.  Using our fish tank example, if you add a wonderful diversity of fish but then just drop donuts into the tank, you’ll lose many of your fish very quickly.  

Every bite feeds microbes, so choosing foods that will support the right ones is essential. Now is when a species-appropriate diet becomes crucial. Sure, your dog can handle a moderate to high-carbohydrate diet, but that will absolutely feed the wrong microbes, and before you know it, you’ll be right back where you started.

What is the Best Pet Food to Promote Gut Balance?

Luckily, this isn’t a very controversial topic.  Microbiome testing has led to a clear correlation between diet and microbial diversity.  We want to decrease carbohydrate-fermenting microbes and increase protein- and fiber-fermenting microbes.  Those are the ones most closely associated with healthy dogs and cats.  That means a diet high in meat, organ, and bone and rich in prebiotic fiber diversity.  

Gut microbes thrive on minimally or non-processed foods, so look for raw or gently cooked diets.  Again, avoid food additives, preservatives, and too many synthetic supplements.  Real, foods provide the best variety of naturally occurring compounds and prebiotic fiber.  As an example, look at our Original Beef formula.   This raw diet is 80% meat, organs, and bone and will encourage plenty of protein-focused microbes.  It’s also 15% real, fresh produce like romaine lettuce, broccoli, carrots, and apples.  These ingredients add an incredible array of prebiotic fiber, the preferred food for beneficial bacteria.   Microbes convert some of this prebiotic fiber to butyric acid, which nourishes gut cells to keep them healthy. Finally, it’s low-carbohydrate and will discourage the rise of inappropriate microbes. 

Just as important as the ingredients is how the food is processed.  Every processing step reduces the value of the ingredients to the point where heavily processed foods like extruded kibble lose much of their value.  So many nutrients must then be replaced using synthetic vitamins.  The more processed, the harder it is for the gut to use, and the less beneficial it will be for the microbes. Imagine putting your dog’s food under a microscope; ideally, you should clearly see cells.  

Diet doesn’t have to be all-or-nothing, though.  For pets suffering from severe dysbiosis, it’s a good idea to go fully raw or feed as much raw as you can, but don’t let the perfect be the enemy of the good.  If feeding a fully minimally processed fresh diet is impossible, just include what you can.  Many studies have shown improvements from replacing just 25% of a processed diet with fresh foods.  

Fermented Foods

Fermented foods have been partially “predigested” by microbes. This results in food full of beneficial microbes, and the end product of these good microbes is postbiotics.  A small amount of fermented foods added regularly to your dog or cat’s diet bestows some of the benefits of a thriving microbial community and can be a fantastic boost for any pet.  


Our fermented Protein Bites include a unique blend of “wild fermented” superfoods provided by Gussy’s Gut.  Most fermented foods are created using a few strains of cultured bacteria or yeast that reproduce quickly and dominate fermentation.  A wild ferment uses the dozens of microbial species naturally present in the organic produce, resulting in a beautifully diverse, changing blend of soil-based microbes dominating the fermentation.  

For more information on fermented foods for pets, check out our interview with Dr. Ian Billinghurst, the Father of RAW, and Rob Ryan, founder of Gussy’s Gut.

Final Thoughts

If you have a dog or cat that suffers from some of Leaky Gut or dysbiosis symptoms, the best first step is to do a microbiome test.  Testing is the most precise and easiest way to understand what is happening inside their gut and address their specific needs.  Due to antibiotic use and modern diets that are high in processed foods, both dysbiosis and Leaky Gut are common but often go undiagnosed.   

In the long run, treating the root of the problem will be better than covering up the symptoms with medications.

Here are more resources for information about dysbiosis, Leaky Gut, and allergy symptoms.

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