Canine Skin Allergies: 10 Scientifically Proven Tips To Improve Your Dog’s Skin Microbiome

October 24, 2023

By Sarah Griffiths, DCH

Does your dog have skin issues? Have you been told that they have allergies? Did you know that skin-related disease is a common cause of euthanasia in North America? It can cause such stress for both animal and pet parent, leading sometimes to devastating loss.

Despite “skin allergies” being a common diagnosis, they may be MUCH less common than you think. The real problem might lie in the widely misunderstood workings of the skin microbiome. Science tells us that the skin microbiome of healthy dogs is up to 5 times more diverse and rich than dogs with skin allergies. (1) Diversity = health when it comes to the microbiome.

The good news is that skin problems are often preventable and manageable with a little bit of creative thinking and a bird’s eye view of what’s really happening. Today’s article is for those who are lost in the vicious cycle of stress that can occur when caring for a pet with canine skin disease. Let’s think outside the box to get solutions that may make the difference for your pet.

What are the most common skin issues in dogs?

Skin issues could include:

  • itching
  • hair loss
  • dandruff
  • dry or greasy coat
  • bacterial/fungal infections
  • blackening of the skin
  • redness and swelling
  • excessive scratching
  • hot spots
  • ear infections
  • bad body odor
  • foot-licking and chewing
  • head shaking
  • concurrent gut issues eg. “sensitive” stomach, chronic diarrhea/vomiting, pancreatitis

One or more of these can be indicators that your dog’s microbiome is struggling. So what are the options and how do you navigate it? Let’s explore.

Environmental Vs. Food-Related “Allergies”

You may have been told that your dog has seasonal, environmental or food-related allergies. You many have even had expensive tests done to discover what your dog is allergic to and what kinds of pathogens might be inhabiting their skin (eg. staphylococcus or yeast). You might have had several allergy tests done, each one showing contradicting information as to what your pet is allergic to. You may notice there are certain times they seem better and worse but it’s very hard to correlate the cause.

Did you know that your dog’s immune system, including the skin and gut microbiome is dynamic, not static? This is why allergy tests can look different from one test to the next. It is a snapshot in time rather than a definitive answer to what your dog is allergic to.

The microbiome is highly adaptable and can become more or less educated depending on the input it receives. Choosing suppressive measures to control skin symptoms – like immune and microbiome-suppressive drugs will cause the picture to get muddier and the possibility for resolution gets further out of reach. It can snowball into MUCH more serious immune-mediated issues.

Did You Know The Skin and It’s Microbiome are Considered Organs?

It’s true! We need to treat them both with the respect we would with any other organs in the body.

The skin plays the very important roles of:

  • maintaining a healthy barrier between the outside environment and the body’s internal homeostasis
  • temperature regulation
  • moisture homeostasis
  • UV protection
  • Sensory system connected to the parasympathetic nervous system
  • Infection detection (immune system)

The skin microbiome roles are vast but’s main role is to balance bacteria, fungus and pathogens so the skin and blood do not succumb to infection. Essentially, it’s part of your dog’s immune system. A 2014 study showed that dogs with healthy skin have 5 times more diversity and richness in their skin microbiome than those diagnosed with skin allergies. (1) Unfortunately, this is still not widely taken into consideration in conventional veterinary circles.

The Epithelium

What the heck is the epithelium? Your dog’s body has countless linings throughout the body that protect them from the external environment. The epithelial linings of the body include all the smooth muscle and mucosal linings including:

  • Gut (esophagus, stomach, intestines and bowel)
  • Respiratory pathways (sinus, bronchioles, lungs)
  • Circulatory pathways (heart, arteries and veins)
  • Urinary pathways (kidneys, ureters, bladder, urethra)
  • Reproductive organs (ovaries, uterus, cervix, vas deferens, etc.)
  • Internal organs (liver, pancreas, gall bladder, spleen, etc.)
  • Endocrine glands (pituitary, thyroid, adrenal, etc.)
  • Nervous system (brain, spine, nerves)
  • Lymph system
  • Auditory system (ears, Eustachian tubes, etc.)
  • The skin (epidermis)

Each one of these surfaces houses a unique microbial community that we are just starting to discover. Causing damage to these linings or their mucosal layers renders the surface inhabitable for the microbes that keeps your dog’s body in homeostasis. Epithelial inflammation and destruction of the microbiome leaves your dog susceptible to immune dysregulation and infections from pathogenic bacteria, fungus and viruses. The scope of this is almost unfathomable given the entirely systemic nature of the microbiome. This is why it is imperative to consider all environmental risk factors that affect microbiome health.

Causes of Skin Flare Ups – What Science is Telling Us

The rollercoaster of skin disease usually begins with some slight itching weeks or months after:

  • a major illness
  • a food change
  • a vaccine
  • topical chemicals (eg. flea and tick)
  • one round (or more) of antibiotics or non-steroidal anti-inflammatory drugs (NSAIDs)
  • excessive bathing
  • environmental sterilization (chemical cleaners, air fresheners, etc.)
  • toxic environmental exposure (eg. herbicides, pesticides, fungicides)
  • a stressful life event (metabolic changes)
  • and/or a combination of two or more of these factors at once
  • genetics plays a role: bulldogs, Staffordshire terriers, poodles, terriers, Labradors and retrievers are also susceptible to skin issues.

All of the above factors can negatively alter your dog’s microbiome status in the gut and on the skin. This process is known as dysbiosis. (2)

Microbiome Abuse – It Has Serious Consequences

In my experience, skin disease is not the core issue in cases of allergic dogs. It is a consequence of a history of microbiome abuse which can even be generational. This happens through uninformed decision-making and unperceived physical trauma when taking care of our animals and ourselves.

Any time we make health-related decisions for our dogs, we need to consider whether it’s supportive or suppressive to the microbiome. Some of the most detrimental things you can do in terms of long-term microbiome health are to feed starchy processed foods from a young age (3), use chemical-based cleaning and laundry products in your home and to use antibiotics without weighing the risks and the benefits. The microbiome can quickly fall into dysfunction, leading to serious long-term issues that can be difficult to resolve. To avoid this scenario and find solutions to an existing skin problem, we have to look at how the animal got to his current state. That involves stepping into our time machines and having a really good look at their history.

When a new client comes to me with canine skin disease, I meticulously go through the medical history of that dog. I mean meticulously. This gives me an understanding of all the circumstances in which microbiome abuse has occurred in the past and present.

I ask:

  • What do they eat?
  • What have they eaten in the past?
  • When did the allergy issues start?
  • Have they been subjected to one or more rounds of antibiotic treatments?
  • What did their mother eat?
  • Have they or their mother ever lived in a highly stressful or sterilized environment such as an animal shelter?
  • Do they have recurrent gut issues?
  • How often do they get bathed?
  • What kind of shampoo is being used?
  • What is their home environment?
  • What cleaners and detergents are used in the home?
  • How often are they receiving flea and/or tick treatments? (internal or external)
  • Are fertilizers used on the lawn where the dog walks?
  • Are air fresheners, synthetic fragrances or petroleum-based candles used in the home?
  • Is there carpet in the home?
  • Is there the possibility of mould in the home?
  • What kind of water are they drinking and bathing in?
  • Are they taking immune-suppressive medications?

These are all pieces of the puzzle that help me build a picture of how they got to where they are at. Then, we can reverse engineer the issues. These are all questions you should be asking if you want to improve you own health too!

Conventional Treatment of Chronic Skin Disease in Dogs: The Hamster Wheel

Often, by the time I see a canine skin case, they have been on a medical rollercoaster. Most pet parents turn to alternatives out of frustration when things aren’t working medically or when they see the negative side effects associated with conventional treatments. Conventional care of chronic disease is sometimes necessary for quality of life but an integrative plan to wean off of harmful drugs is not only possible but necessary for your dog to live a quality life into their senior years. All conventional treatments for canine skin disease have serious side effects that can affect your dog’s quality of life and longevity.

Some of the most commonly used drugs for canine skin disease have serious side effects:

Antibiotics – given for a number of reasons including chronic diarrhea and secondary bacterial skin infections. Antibiotics are prescribed with little consideration of an animal’s microbiome status and can create quite a mess for dogs dealing with skin disease or gut disease.

Antibiotics compromise the microbial communities in the body (4) (5) and we now know through science that the microbiome is involved in every body system to help maintain homeostasis. When it is compromised, it can contribute to an already-existing immune-mediated disorder. It can become a health hamster wheel when pet parents bring their animals for veterinary help and a skin infection is present, antibiotics are prescribed, the infection seems resolved, the animal looks better but then the infection rears its head again later on, sometimes much worse than before and sometimes in a deeper manner such as GI disturbance, pancreatitis, liver disease or even auto-immune disease. This is because antibiotics don’t just target pathogenic (harmful bacteria), they also kill the microbes that are supposed to be doing that job in the first place. The more antibiotics are given, the further the microbiome is compromised and this can lead to chronic dysbiosis, antibiotic resistance, prescriptions for more powerful drugs, more serious infections and continued chronic infections and inflammation.

Pet parents are often told that the deeper immune-mediated and gastro-intestinal side effects are not related to skin disease but this couldn’t be further from the truth. To be successful in helping a dog in this scenario, the whole picture needs to be addressed as one disease: microbiome disturbance.

Chronic and severe allergy cases are often managed with prescriptions for immune-suppressive drugs including steroids (prednisone and cortisone), Apoquel, Cytopoint and even medicated shampoos and processed prescription diets full of low-quality extruded and hydrolyzed ingredients. These options do not promote a healthy gut and strip the skin microbiome of the good bacteria that’s trying to balance the terrain of the skin. While it can temporarily appear to provide relief, these sterilizing and immune-suppressive methods drive the microbiome and the immune system into further chaos. (6) (7) (8) ( It can become a dumpster fire!

Your Home Environment Plays a Bigger Role Than You Think!

I am thorough when assessing an allergic dog’s home environment. The home is where you and your animals sleep, eat and rest. If the environment is contributing to sterilizing the microbiome, it can lead to serious consequences for both you and your dog. This means air quality, water quality, clothing, bedding, shampoos, detergents, carpet fibres, moulds and more.

The use of petroleum-based cleaners, fragrances and candles is the first thing that should be eliminated for gut, respiratory and skin health. Airborne chemicals are shown to be major allergy promoters and can even change gene expression. They damage both the skin and respiratory microbiomes and tissues, especially in early life. (9) (10) (11) (12)

Antibacterial agents can also negatively affect the skin and respiratory microbiomes of humans and animals, increasing risk of skin and respiratory diseases. (13)

Petroleum-based fabrics also cause the same issues so ensure that your dog’s bedding and clothes are made from organic materials that do not contain petroleum products (eg. polyester). (14)

Chlorine and chloramine in drinking and bathing water are also major offenders when it comes to microbiome health. They are shown to alter the skin and gut microbiome and may even contribute to cancer. (15) (16) (17) (18)

Sterile Environments (City Vs. Country Life)

Science reveals that kids that live in the country, on farms and with animals have lower risk of asthma and respiratory allergies. This is NOT a coincidence. It’s a perfect example of how increasing microbial diversity protects you and your animals – without a lot of expensive supplements. (19)

Alternatively, gardeners gain more microbial access through putting their hands in the dirt. (20) The same happens when your dog digs in healthy dirt and/or eats it!

Honoring and Healing the Microbiome: 10 Scientifically Proven Tips to Help Your Pet

  1. Diet, Diet, Diet: Contrary to conventional belief, fresh, high protein, low starch diets have been scientifically proven to improve the immune status of dogs and their microbiomes. Period. End of story. Any professional that tells you otherwise should update their education. There are a number of published studies proving this fact and more being published every year. The risks of pathogenic infection due to fresh food diets is much less common than you think and much less disturbing than the long term effects of feeding highly processed feeds. The question of WHY animals are succumbing to E. coli, salmonella and other pathogens should be questioned in relation to the microbiome status of individual animals. The benefits of feeding a properly balanced fresh food are undeniable, especially when it comes to microbiome health. (21) (22) (23) (24) (25) (26) I encourage you to find a veterinarian that will support you in your decisions to feed fresh food and not blame infections and poor health on it. It is not scientific and it will not help your dog!
  2. Getting Dirty! Regular exposure to living dirt has been show to rapidly effect the skin microbiome in gardeners. It was also shown that the effects can receded within 12 hours if soil exposure is not revisited. (20) One soil microbe was even shown to improve the immune system AND work as a natural anti-depressive. (27) Healthy soil is the ultimate in probiotics because the diversity is almost limitless if you’re able to expose your pet to multiple environments each week. Remember, science shows that microbial diversity is what sets your pet up for health success. Probiotics can be beneficial but it can get complicated if your pet is extremely compromised. Overwhelming the system with just a few strains of probiotics can be counter-productive in some cases. If you’ve had this experience, seek help from a professional. Your dog has likely developed a rather sterile microbial culture throughout their body and will need a systematic approach to get back on track.
  3. Filter Drinking and Bathing Water: To reduce damage to your pet’s gut and skin microbiome, purchase filters for both your shower and for your drinking water. Make sure that they remove both chlorine and chloramine and increase water pH.
  4. Change Your Cleaners and Detergents: If you’re using petroleum-based laundry detergents or cleaning agents in your home, it’s time to switch to organic plant-based options for the sake of your entire family.
  5. Use Gentle, Organically-Based Shampoo: Ditch the antimicrobial and antifungal shampoos. Remove petroleum-based products and fragrances (phthalates and parabens) from your pet’s bathing regime. Choose fragrance-free, plant-based options that don’t disturb the microbiome.
  6. Remove All Synthetic Fragrances from the Home: This includes, chemical air fresheners, perfumes, candles, aerosols, cleaners and detergents. Choose organic options instead.
  7. Addressing Nutritional Deficiency (Especially Minerals): Mineral and vitamin deficiencies can be indicated in skin disease. Be sure that this factor is not worsening your pet’s problem. Address it by doing blood tests to establish a baseline on your pet’s nutritional status, especially when it comes to omega 3 fats, B vitamins, zinc and iodine.
  8. Prebiotics, Not Probiotics: If your dog is extremely compromised, probiotics might not be a preliminary solution. Removing detrimental environmental factors, making diet changes and diversifying the microbiome through nature walks is a much better place to start. To promote healthy microbial colonies, use a diverse variety of foods including prebiotic fibres to feed the health-promoting microbes in the gut and, by proxy, on the skin. Healthy prebiotics may include herbs, medicinal mushrooms, psyllium fibre, bark fibres and organic leafy green vegetables.
  9. Consider Titer Testing Instead of Vaccination: Vaccinations are not benign treatments. They increase immune inflammatory responses in your dog’s immune system that also interface with the microbiome of individual animals, making it, potentially, even more risky for animals with compromised microbiomes. (28) (29). If your pet has allergies, a vaccine could send them over the edge. Consider titer testing if your pet has already been vaccinated. Severely allergic animals are NOT candidates for re-vaccination. It is irresponsible to subject them to this procedure if they are suffering from immune-mediated disease, regardless of what some animal care professionals might say.
  10. Avoid Flea and Tick Treatments: Not only do flea and tick treat treatments affect your pet’s microbiome but they also negative affect immune and neurological systems. Since 2008, more than 2000 animal deaths in North America have been directly linked to flea and tick treatment exposure. And it is most likely way under-reported. These chemicals poison the blood of the host (your dog) in order to kill fleas and ticks. If you believe that these chemicals can perform this function without affecting your pet’s microbiome, think again. Consider plant-based topical pest deterrents and a healthy fresh-food diet to deal with fleas and ticks instead.

There is Hope!

I hope today’s article helps you to see a bird’s eye view surrounding chronic skin disease in dogs. If you see improvements using these tools, please be sure to reach out and let us know!


  1. PLoS One: The Skin Microbiome in Healthy and Allergic Dogs, 2014
  2. Frontiers in Veterinary Science: The Role of the Canine Gut Microbiome and Metabolome in Health and Gastrointestinal Disease, 2019
  3. Journal of Veterinary Internal Medicine: Puppyhood diet as a factor in the development of owner-reported allergy/atopy skin signs in adult dogs in Finland, 2021
  4. Journal of Veterinary Internal Medicine: Effects of metronidazole on the fecal microbiome and metabolome in healthy dogs, 2020
  5. The Veterinary Journal: Effects of antimicrobials on the gastrointestinal microbiota of dogs and cats, 2023
  6. Frontiers in Microbiology: Long-term prednisone causes fungal microbiota dysbiosis and alters the ecological interactions between gut mycobiome and bacterium in rats, 2023
  7. Frontiers in veterinary Science: Side effects to systemic glucocorticoid therapy in dogs under primary veterinary care in the UK, 2020
  8. Journal of the American Veterinary Medical Association: Oclacitinib 10 years later: lessons learned and directions for the future, 2023
  9. Current Environmental Health Reports: The impact of early-life exposure to antimicrobials on asthma in children, 2019
  10. European Journal of Allergy and Clinical Immunology: Prenatal paraben exposure and atopic dermatitis-related outcomes among children, 2021
  11. Environmental Research: Microbiome alterations associated with phthalate exposures in a US-based sample of Latino worker, 2022
  12. Ecotoxicology and Environmental Safety: Indoor particulate matter induces epigenetic changes in companion atopic dogs, 2023
  13. Current Environmental Health Reports: The impact of early-life exposure to antimicrobials on asthma and eczema risk in children, 2019
  14. Environmental Research: The T-shirt microbiome is distinct between individuals and shaped by washing and fabric type, 2020
  15. Rutgers University Libraries: Effect of chlorine water consumption on phenotypic and microbiome development, 2019
  16. Experimental Dermatology: Yin and Yang of skin microbiota in “swimmer’s acne”, 2022
  17. World Journal of Gastrointestinal Oncology: Colorectal cancers and chlorinated water, 2016
  18. Water Research: Chlorination by-products in drinking water and risk of bladder cancer – A population-based cohort study, 2022
  19. Evidence Based Medicine: Early exposure to dogs and farm animals reduces risk of childhood asthma, 2016
  20. Urban Agriculture and Regional Food Systems: Garden soil bacteria transiently colonize gardeners’ skin after direct soil contact, 2023
  21. BMC Veterinary Research: Raw meat based diet influences faecal microbiome and end products of fermentation in healthy dogs, 2016
  22. Veterinary Record: Owners’ perception of acquiring infections through raw pet food: a comprehensive internet-based survey, 2018
  23. Australian Veterinary Journal: Raw beef bones as chewing items to reduce dental calculus in beagle dogs, 2016
  24. Journal of Animal Science: 225 fecal microbiota and metabolites of adult dogs fed extruded, mildly cooked, and raw diets, 2017
  25. Animals: Fresh food consumption increases microbiome diversity and promotes changes in bacteria composition on the skin of pet dogs compared to dry foods, 2022
  26. Frontiers in veterinary Science: Effects of a whole foo diet on immune function and inflammatory phenotype in healthy dogs: A randomized, open-labeled, cross-over clinical trial, 2022
  27. Frontiers in Physiology: Effects of immunization with the soil-derived bacterium Mycobacterium vaccae on stress coping behaviours and cognitive performance in a “Two-Hit” stressor model, 2020
  28. Vaccines for Veterinarians: Adverse consequences on vaccination, 2021
  29. Journal of Leukocyte Biology: The potential of the microbiota to influence vaccine responses, 2018