Various bacteria, viruses, and fungi coexist inside your dog's body to form the microbiome. Some organisms are commensal organisms that coexist with or within another organism without endangering it or providing it with any advantages. Many other microorganisms develop symbiotic relationships or mutual benefits between two organisms, while others spread disease.

Although the gut microbiota is commonly mentioned in animal health, the dog's body also contains microorganisms in its skin, reproductive system, conjunctiva, mouth cavity, and nasal passages. For the gut microbiome to be balanced, there must be a balance between the good and harmful bacteria in your dog's body.

It is usual for bacteria to colonize the gastrointestinal tract shortly after birth and remain there throughout life. Recently, the importance of gut microbiomes has become widely recognized, earning it the nickname "the forgotten organ."

In this scenario, a symbiotic relationship exists between the microbiota and its host, which is your dog. There is a rich environment in which the bacteria thrive. The host relies on them to maintain metabolic homeostasis and develop normal immune, endocrine, and nervous systems. A healthy gut flora prevents pathogens from invading the body.

Dogs' gut microbiomes are complex communities of bacteria, viruses, and fungi that are constantly evolving. Despite the initial colonization of bacteria occurring at birth, your dog's microbiota is highly adaptable over its lifetime due to genetics, environment, and age. Dietary changes significantly impact the composition of the gut microbiome, affecting how the gut microbiome processes protein, carbohydrates, and fat, ultimately affecting the body’s overall health and biological functions.

The microbiota composition depends on the ratio of macronutrients provided in the diet and how well the body digests those nutrients. It is essential to gradually adjust your dog's diet so that the gut bacteria can adapt to the change. 

If you switch from a kibble (carb-rich diet) to a completely raw diet (high in protein and fat), your dog’s gut bacteria might have difficulty digesting it, resulting in diarrhea or other GI tract disorders.

Dysbiosis is a condition caused by an imbalance in gut flora. The immune system function is directly affected by gut flora imbalances. Dysbiosis is frequently caused by the use of antibiotics, which significantly decrease gut flora diversity and richness.

Dysbiosis in dogs has been linked to obesity, metabolic diseases, cancer, GI tract disorders, and neurological diseases.

The Gut Microbiome and the Gastrointestinal Tract

In addition to the fermentation of fiber, bacteria in the gut produce short-chain fatty acids (SCFAs), lactic acid, biotin, vitamin K, and amino acid metabolites. SCFAs decrease intestinal pH and slow pathogenic (disease-causing) bacterial growth. The bacteria also produce thiamine and vitamin B12.

Bacteria within the gut lining assist with transporting the nutrients across the intestinal wall, allowing them to enter the bloodstream. 

Dysbiosis is typically accompanied by chronic or acute intestinal inflammation, diarrhea, inflammatory bowel disease, and leaky gut.

The gut microbiome plays a significant role in supporting the immune system; it makes up 70-90% of the body's immune system. Gut-associated lymphatic tissue (GALT) is found in the mucosa of the GI tract and is a source of lymphocytes, T-cells, and B cells that are part of the immune system. As antibodies are secreted into the lumen of the intestine and then into the bloodstream, the GALT regulates their local production.

Bacteria can act as pro- and anti-inflammatory agents in a healthy and balanced microbiome, preventing excessive inflammation while responding rapidly to infections.

Immune system functions are responsible for allergies. Many "food allergies" are actually food intolerances caused by dysbiosis.  In the case of undigested macronutrients, especially proteins, the immune system will interpret the food particles as allergens, triggering inflammatory reactions in the skin, sinuses, and gastrointestinal tract.

A brain-gut microbiome axis has been discovered by studying how tryptophan and threonine are metabolized by microbes and how they interact with other neurotransmitters.

The brain-gut axis concept describes how gut bacteria communicate with the brain. The gut produces a variety of essential chemicals and hormones, including:

Serotonin- also known as the "happy chemical," helps to promote emotional well-being. There is wide recognition of the effects of serotonin on the brain. Many antidepressants and antianxiety medications aim to maintain brain serotonin levels. About 90% of the serotonin produced by the body is derived from the intestines, either by bacteria directly producing the chemical or by the body consuming its precursor, tryptophan.

Dopamine- responsible for motor functions, decision-making, and hormone regulation, is a neurotransmitter and precursor to other substances, including epinephrine. In the body, at least 50% of dopamine is produced by the GI tract.

GABA- A neurotransmitter or chemical called Gamma-aminobutyric acid (GABA) regulates stress and anxiety. Your dog's sleep patterns are also affected by GABA. Intestinal bacteria regulate GABA.

Norepinephrine- a neurotransmitter responsible for increasing heart rate and blood pumping and increasing blood pressure when required. In addition, it helps the body produce more energy by breaking down fat and improving blood sugar levels.

Acetylcholine plays a crucial role in cell-to-cell communication. 

Understanding how gut flora contributes to the production and regulation of serotonin, dopamine, GABA, norepinephrine, and acetylcholine helps understand how gut microbiomes impact your dog’s behavior.

The diet significantly influences the composition of the gut microbiota your dog is consuming, such as a raw diet versus commercial kibble. The microbial composition of dogs fed raw, more natural food is significantly more varied and abundant than that of dogs on a kibble diet. The crucial neurotransmitters and other compounds necessary for your dog's health and well-being are produced more effectively when bacteria in their communities grow more regularly on raw foods.

Healing the Imbalanced Gut Microbiome with a Whole Fresh Food Diet

Healing and supporting the gut microbiome in dogs through a whole-food diet involves providing a nutritionally balanced and diverse range of whole foods. A healthy and balanced diet can positively impact the composition and function of the gut microbiome, promoting a thriving community of beneficial bacteria. Critical components of a whole-food diet to support the gut health of dogs include providing a species-appropriate diet, prebiotics, probiotics, a variety of proteins and other nutrients, and omega-3 fatty acids.

Dogs are omnivores with specific dietary needs. A whole-food diet should reflect their evolutionary diet, consisting of a balanced combination of high-quality proteins and healthy fats with minimal carbohydrates. The diet should consist of raw meaty bones, muscle meat, secreting organs, seafood, and a fiber source, either fur or vegetables. 

Prebiotics are substances that nourish and support the growth of beneficial bacteria in the gut. Include prebiotic-rich foods such as mushrooms, chicory root, garlic, or larch arabinogalactan found in carrots, pears, corn, coconut, shiitake mushrooms, and some herbs like echinacea and astragalus. Burdock root, dandelion greens, apples, bananas, and asparagus are also good prebiotic foods.

Fermented foods contain beneficial probiotic bacteria that can contribute to a healthy gut microbiome. Consider incorporating small amounts of fermented foods like kefir, yogurt, or sauerkraut into the dog's diet. Ensure these foods are free of additives like sugars and artificial preservatives.

Offering a variety of protein sources helps diversify the nutrients and beneficial microbes in the gut. Rotate between animal proteins such as beef, poultry, lamb, fish, and organ meats. Adding seafood to the diet provides Omega-3 fatty acids that reduce inflammation and promote overall health, including gut health.

Development of the Gut Microbiome of Puppies

Developing a healthy gut microbiome in puppies is essential for their health, well-being, and longevity. Methods to promote a healthy gut microbiome in your puppy include:

Choose the right food: Providing your puppy with high-quality, balanced, and easily digestible food is critical for developing a healthy gut microbiome. A nutritionally balanced raw diet that contains a variety of protein sources, fiber, prebiotics, and probiotics is ideal. 

Avoid overfeeding: Overfeeding your puppy can lead to gastrointestinal issues and disrupt the balance of the gut microbiome. Feed meals based on your puppy's age, weight, and activity level. You must feed large and giant breed pups to promote slow growth and avoid skeletal disorders.

Gradual diet changes: If your puppy was weaned onto kibble, gradually transitioning to a raw diet will allow her gut microbiome to adjust. Sudden changes can lead to gastrointestinal upset and imbalances in the gut microbiome.

Provide access to clean water: Clean and fresh water should always be available to puppies. Proper hydration is essential for maintaining a healthy gut microbiome.

Avoid unnecessary antibiotics: Overuse of antibiotics can disrupt the gut microbiome and lead to the growth of harmful bacteria. Only use antibiotics when necessary and under the guidance of a veterinarian.

Consider probiotics: Adding a probiotic supplement to your puppy's diet can help promote the growth of beneficial gut bacteria and support digestive health. 

The gut microbiome of cesarean-section puppies may differ from that of babies born naturally, as they miss exposure to the mother's vaginal and fecal bacteria during birth. This initial bacterial exposure is thought to play a crucial role in shaping the gut microbiome of newborn puppies.

Some studies have shown that C-section puppies may have lower levels of beneficial bacteria, such as Bifidobacteria and Lactobacilli, and higher levels of opportunistic bacteria, such as Escherichia coli. This can result in an imbalance in the gut microbiome, which may increase the risk of specific health issues, including diarrhea, allergies, and immune disorders.

It is essential to start interventions as soon as possible to promote a healthy gut microbiome in C-section puppies. Colostrum must be provided to the c-section puppies, ideally from nursing, as it can help to transfer the beneficial bacteria required to promote a healthy gut microbiome to the puppies. A substitute commercial colostrum is necessary if the female does not allow her pups to nurse.

A microbiome is the sum of the microbes that share a dog’s body. The gut microbiome is just one example of the many microbiotas within the body.

Although genetics and environmental factors can affect gut flora composition, diet is the most influential factor.

Establishing and maintaining a healthy gut microbiome at a young age is essential for a dog’s overall health as it affects almost all biological functions and the normal development of the immune, endocrine, and nervous systems. 

Differences in the gut microbiota of dogs (Canis lupus familiaris) fed a natural diet or a commercial feed revealed by the Illumina MiSeq platform  

Effect of sequentially fed high protein, hydrolyzed protein, and high fiber diets on the fecal microbiota of healthy dogs: a cross-over study  

Raw meat based diet influences faecal microbiome and end products of  fermentation in healthy dogs  

Comparison of the effects of four commercially available prescription diet regimens on the fecal microbiome in healthy dogs  

Effects of the Dietary Protein and Carbohydrate Ratio on Gut Microbiomes in Dogs of Different Body Conditions   

Long‐Term Consumption of High Protein Disrupts Dog Gut Microbiome and Metabolites  

Rapid Reconstitution of the Fecal Microbiome after Extended Diet-Induced Changes Indicates a Stable Gut Microbiome in Healthy Adult Dogs  

Gut Microbiome of Healthy and Arthritic Dogs  

Differences in the gut microbiomes of dogs and wolves: roles of  antibiotics and  starch 

The Relationship Between the Gut Microbiome-Immune System-Brain Axis and Major Depressive Disorder  

 The Role of the Canine Gut Microbiome and Metabolome in Health and Gastrointestinal Disease  

Analysis of the gut microbiome in dogs and cats  

The Effects of Nutrition on the Gastrointestinal Microbiome of Cats and Dogs: Impact on Health and Disease  

Brady, C. (2020). In Feeding dogs: dry or raw? The science behind the debate (pp. 167-169).  Farrow Road Publishing.

Various bacteria, viruses, and fungi coexist inside your dog's body to form the microbiome. Some organisms are commensal, coexisting with or within another without endangering it or providing it with any advantages. Many other microorganisms develop symbiotic relationships or mutual benefits between two organisms, while others spread disease.

Learning About the Gut Microbiome

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