Every surface of our world is covered in microbes. While we can’t see them, bacteria, viruses, fungi, and other microorganisms are inextricably linked to nearly every aspect of the health and well-being of all living things. Thanks to new scientific advances, we now know more about microbes than ever before. This is especially important for veterinary medicine, because research on the microbiome has introduced a whole new framework for diagnosing and treating the root causes of numerous common health conditions in pets.

The majority of a dog or cat’s microbes are found throughout the intestinal tract; this community is collectively called the gut microbiome. Many researchers, doctors, and veterinarians think of and treat the gut microbiome as a metabolically active organ. This article touches on the importance of the microbiome in the overall health of pets, how it develops in young animals, and the methods veterinarians can use to support the microbiome health of patients from the very beginning of life.

The important of the gut microbiome

You’ve likely heard about the gut microbiome; the term refers to the non-host genetic material of bacteria, viruses, fungi, and protozoa (or protists) found in the intestinal tract of an animal. The microbial community that makes up the gut microbiome is an ever-changing ecosystem, with the most profound changes occurring in the first year of a pet’s life.

The microbiome development during this first year is significantly correlated to a pet’s overall health, which we will cover in more detail in the next section. However, it is important to emphasize that the microbiome health of puppies and kittens can dictate health outcomes throughout their entire adult lives. If the gut microbiome becomes imbalanced or lacks the microbial diversity typically acquired in the first year of life, it can lead to adverse clinical signs and conditions later in life. This connection between the microbiome and long-term wellness arises because the gut microbiome and immune system are intricately linked; it’s estimated that approximately 80% of immune regulation occurs in the gut.

Imbalanced microbiomes in adulthood

As with most health conditions in pets, it’s important to catch microbiome imbalances early because they can be harder to resolve as time goes on. These issues can easily become a self-perpetuating cycle of imbalance that becomes increasingly harder to resolve. Numerous microbiome-associated conditions are found in cats and dogs, such as atopic dermatitis,1 obesity,2 inflammatory bowel disease (IBD),3,4 diabetes,5,6 and even mood disorders.7,8

How does the gut microbiome develop in puppies and kittens? The best way to support the lifelong microbiome health of cats and dogs is to understand how they develop their gut microbiomes in the first place. The first exposure to microbes a puppy or kitten experiences is during birth, but major gut microbiome changes also occur during the nursing process, and during the transition to a diet beyond the mother’s milk.


Both puppies and kittens are enclosed in amniotic sacs within their mother’s uterus. In dogs, these sacs are usually broken during birth. When a litter of puppies is delivered naturally, microbes that line the birth canal are the first to colonize the gut microbiomes of the puppies. If delivered by Caesarean section, the mother’s skin microbiota are the first to colonize the puppies’ gut microbiomes.

Kittens are typically born in their amniotic sac, which is removed by their mother, who will then stimulate them to breathe by washing them with her tongue. The mother’s microbes are transferred to her kittens during this process, thus introducing them to her microbiome.

Studies have shown that delivery mode significantly affects gut microbiome colonization,9 with infants delivered by Caesarean section having more adverse health outcomes later in life.10 These findings suggest that exposure to vaginal microflora is important for the development of the gastrointestinal tract and immune system.

This is especially important when considering breeds, such as bulldogs and terriers, who are typically born by Caesarean section. Interventions to introduce newborns to vaginal microbes may be beneficial for those delivered this way. While not yet a standard practice, an absorbent material can be inserted into the birth canal of a laboring mother, and then swabbed over the skin and mouth of newborns delivered via Caesarean section to imitate the microbial exposure of a natural birth.


The next major colonization of a puppy or kitten’s gut microbiome comes from nursing. A mother’s colostrum and breast milk contain not only beneficial microbes,11 but also important nutrients,12 maternally derived antibodies,13 and metabolites that facilitate healthy gut microbiome inoculation and colonization. Because the microbes in breast milk are so important for microbiome development, neonates receiving colostrum from a different species miss out on bacteria specific to the functions of their gut microbiome.

Numerous studies highlight the association between non-breast milk-fed human infants and adverse long term health outcomes. But why is this? Researchers at the University of Luxembourg found in one study that human infants who were fed formula had a delayed diversification of their gut microbiome compared to breast-fed fed infants during the nursing stage of microbiome development.14 Other studies point to the importance of nutrients and metabolites in breast milk that are crucial for healthy immune system development, and that formula-fed infants miss out on.15

Puppies and kittens that cannot be fed breast milk, such as orphans, may need extra microbiome support as they develop and age. We’ll discuss several ways to promote the balance and diversity of cat and dog gut microbiomes later on.


The transition from milk or formula to solid food triggers the next major shift in gut microbiome composition in infants. At this stage, the gut microbiome transitions to an adult-like composition, which researchers suggest is strongly driven by nutritional factors. Not all post-weaning diets have the same effect on the neonatal gut microbiome; one study found that kittens fed a canned post-weaning diet had more advanced microbiome functions compared to those fed a kibble based post-weaning diet.16

The speed17 and age18 at which weaning occurs significantly impact the microbial diversity of the gut microbiome and immune system development. While breeds, species, and individuals all require different weaning times for their optimal microbiome development, it’s generally recommended to aim for weaning at 12 weeks in dogs and eight weeks in cats for the best gut microbial diversity outcomes.

What can cause an imbalance in the gut microbiome?

The initial gut microbiome colonization stages during birth, nursing, and weaning are critical for building a diverse community of microbes, but it is also important to understand factors that can perturb this community. Here we discuss situations that are common to puppies and kittens.


Viruses (e.g. parvo), parasites (e.g. giardia), and bacterial infections (e.g. E. coli) are known to impact the gut microbial community in cats and dogs. Often these infections trigger a host inflammatory immune response, which creates an environment favorable to pathogenic microbes. Beneficial microbes can be lost during these inflammatory states, leading to a loss of microbial diversity and balance in the gut microbiome.


While infections can affect the diversity and balance of a microbiome, so can the treatments for them. In particular, antibiotics can wipe out beneficial microbes and lower bacterial diversity in the gut microbiome. In some cases, it can take years for a gut microbial community to recover from antibiotic therapy.

When it is necessary to prescribe antibiotics in order to treat an infection, they should be used thoughtfully, especially in nursing mothers and young puppies and kittens, and by following the guidelines for antimicrobial stewardship.19,20 During and after a course of antibiotics, there are many ways to support a patient’s gut microbiome.

Diet and environmental factors

The lifestyles of young cats and dogs have important ramifications for gut microbiome health. A nutritionally balanced and diverse diet promotes an equally balanced and diverse microbial community, but it is pertinent to look for clinical signs of food allergies or sensitivities, such as diarrhea, vomiting, and pruritus. Food allergies can trigger inflammation, which negatively impacts the diversity of the microbiome, resulting in chronic enteropathy.21 Similarly, environmental allergens can also trigger an inflammatory response.

Early-life exposure to microbially-rich surroundings is important for pets to develop a strong immune system and a healthy gut.22 For example, outdoor microbes are diverse and several species of beneficial bacteria can be found in soil. Encouraging quiet, safe places for puppies and kittens to rest and play further protects them from having a stress response to their surroundings.23

Key takeaways

The gut microbiome of puppies and kittens undergoes the most change during the first year of life. From the moment of birth, microbes from the mother rapidly colonize her newborns, with the delivery method having a significant effect on the colonization process. Nursing and weaning methods drive the subsequent developmental stages of the gut microbiome, and have long-lasting effects on the newborn’s overall health into adulthood.

An imbalance in the microbiome is linked to numerous health conditions; infections and antimicrobials can also trigger an imbalance in the gut microbial community. Luckily, several evidence-based options are available to veterinarians and pet parents alike for maintaining and restoring a healthy microbiome in cats and dogs (see sidebars).

Visit animalbiome.vet to learn more about integrating a microbiome focus into your veterinary practice.

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