Is the Nasal Microbiome the Secret to Treating Nasal Infections in Pet Bunnies?

Did you know that one of the most common illnesses in pet bunnies has to do with arguably the cutest part- their nose? That’s right, bunny noses are actually more susceptible to infection or inflammation simply because of the way they are shaped. [1] Not only that but since bunnies cannot breathe through their mouths, if their nose becomes stuffy (unlike other animals), nasal inflammation in bunnies creates a pretty common and possibly life-threatening issue!

nasal infections in bunnies

Nasal inflammation and respiratory infections in rabbits, known as Chronic Rhinosinusitis (CRS), have many symptoms that bunny owners and veterinary professionals should look out for.

What Are the Symptoms of Chronic Rhinosinusitis in Bunnies?

  • Sneezing
  • Runny/wet nose (nasal discharge)
  • Reduced airflow/heavy breathing
  • Slobbering or excessive saliva
  • Discharge from the eyes or other parts of the face
  • Nose bleeding

If your bunny is experiencing these symptoms, seeking medical guidance for treatment is essential! But, to develop the BEST treatments for CRS in bunnies, we need to first understand the cause of CRS.

What Causes CRS in Pet Bunnies?

Sometimes, CRS in bunnies can be due to non-infectious causes, like inhaling foreign bodies, occasional allergies, or even dental issues.
Infectious CRS, on the other hand, is linked to adverse changes in nasal bacteria or fungi. [2,3] Recent research has shown that changes to the nasal microbiome and fungal mycobiome occur when bunnies suffer from CRS. Two recent research articles have identified that bunnies with CRS show significant changes in their nasal microbiome, including increases in inflammatory pathogens like Pseudomonadales spp. and Burkholderia, [4] as well as reductions in commensal bacteria, like Moraxella spp. and Neisseriaceae spp. [5]

While no study to date has identified changes to the fungal mycobiome of bunny noses, particular infectious fungi have been shown to contribute to nasal inflammation in other animal models, including Alternaria spp. [6]
So, if CRS is due partly to alterations to the nasal microbiome and mycobiome, how do veterinary professionals I.D. certain bacteria or fungi that contribute to CRS?
The current identification of infectious pathogens and subsequent treatments that many veterinary professionals employ may fall short.
The good news is that the influence of the nasal microbiome and mycobiome on CRS in bunnies poses a great opportunity for veterinary professionals to update how they, 1, identify and, 2, treat these types of infections!

Identifying Bacteria That Contribute to CRS in Bunnies

Traditionally, veterinary professionals use traditional culture methods (like PCR) to identify pathogens that could be contributing to rabbit respiratory infections. While these methods can typically I.D. bacteria that could be present in your bunny patient’s nose, they don’t often show the ENTIRE picture.

For one, not all bacteria grow sufficiently well in the lab conducting the PCR technique.

Not only that, but PCR culturing can only detect the bacterial strain associated with the primer in the kit provided to the veterinary professional. For instance, if the veterinary professional suspects an Escherichia coli infection, they can request analysis for that particular marker.

Thus, while culture methods can effectively identify pre-determined, common pathogens, using this technique makes it impossible to detect uncommon or novel bacterial or fungal markers.

And, since research is so new in this area, and we don’t know which exact bacteria or fungi contribute to CRS, culture methods may fail to I.D. the most appropriate bacterial or fungal marker to target with treatment.

Effective and Accurate Diagnostic Tools for Nasal Infections in Pet Bunnies

Fortunately, more advanced technologies can (and should) be used to identify more uncommon bacterial or fungal taxa that may contribute to CRS, like next-generation sequencing (NGS). [7] The MiDOG All-in-One Microbial Test utilizes NGS technology to detect and quantify microbial DNA through untargeted and comprehensive sequencing and quantitative comparisons to reference databases. The MiDOG NGS technology provides a valuable opportunity to identify many more markers that could contribute to CRS with this untargeted sequencing approach. The MiDOG microbial test is based on scientific research that provides veterinary professionals with DNA evidence to treat bunny CRS more effectively and accurately!

How to Treat Rabbit CRS Infections

Typical treatments to treat CRS that target bacteria, like antibiotics, have been widely used to eliminate pathogens contributing to the infection. However, while antibiotic treatments have been successful, veterinary professionals must consider two important factors that could impact their efficacy.

1. It is essential to prescribe the most appropriate antibiotic to accurately target the specific bacterial marker contributing to the respiratory infection.

This can be difficult to do when using culturing methods, but fortunately, with the MiDOG test results, veterinary professionals can prescribe the right antibiotic.

2. Antibiotics can inadvertently alter the microbiome or mycobiome and often lose effectiveness over time.

This is known as antimicrobial resistance, or AMR. Some typical AMRs that common pathogens have include:




Tomacrolides, Fluoroquinolones, Pleurmutilins, & Tetracyclines [8]


Tetracyclines [10], Fluoroquinolone [11]


Vancomycin, Ampicillin & Trimethoprim [12]

While respiratory infections can impact the lives of pet bunnies significantly, knowing what to look for in terms of symptoms is the first step to treating these furry friends!
Fortunately, there have been many advancements in treatments to help our pet bunnies heal from CRS. Of course, it is also important to consider other factors besides the microbiome and mycobiome, including the health history of your pet bunny.

Working with your veterinary professional and using NGS technology, like the MiDOG All-in-One Microbial Tests, is a great first step in identifying the root cause of the respiratory infection so you can optimize your treatment plan and help your bunny best!


  1. Xi J, Si XA, Kim J, Zhang Y, Jacob RE, Kabilan S, Corley RA. Anatomical Details of the Rabbit Nasal Passages and Their Implications in Breathing, Air Conditioning, and Olfaction. Anat Rec (Hoboken). Jul 2016;299(7):853-68. doi:10.1002/ar.23367

  2. Zhao YC, Bassiouni A, Tanjararak K, Vreugde S, Wormald PJ, Psaltis AJ. Role of fungi in chronic rhinosinusitis through ITS sequencing. Laryngoscope. Jan 2018;128(1):16-22.

  3. Cho DY, Hunter RC, Ramakrishnan VR. The Microbiome and Chronic Rhinosinusitis. Immunol Allergy Clin North Am. May 2020;40(2):251-263.

  4. Cho DY, Mackey C, Van Der Pol WJ, et al. Sinus Microanatomy and Microbiota in a Rabbit Model of Rhinosinusitis. Front Cell Infect Microbiol. 2017;7:540.

  5. Lux CA, Johnston JJ, Waldvogel-Thurlow S, et al. Unilateral Intervention in the Sinuses of Rabbits Induces Bilateral Inflammatory and Microbial Changes. Front Cell Infect Microbiol. 2021;11:585625.

  6. Didehdar M, Khoshbayan A, Vesal S, Darban-Sarokhalil D, Razavi S, Chegini Z, Shariati A. An overview of possible pathogenesis mechanisms of Alternaria alternata in chronic rhinosinusitis and nasal polyposis. Microb Pathog. Jun 2021;155:104905.

  7. Damerum, A., Malka, S., Lofgren, N., Vecere, G., & Krumbeck, J. A. (2023). Next-generation DNA sequencing offers diagnostic advantages over traditional culture testing. American Journal of Veterinary Research, 84(8), ajvr.23.03.0054. Retrieved Sep 21, 2023

  8. Gautier-Bouchardon, A. V. (2018). Antimicrobial resistance in Mycoplasma spp. Microbiology spectrum, 6(4), 6-4.

  9. Mitchell, J. D., McKellar, Q. A., & McKeever, D. J. (2012). Pharmacodynamics of antimicrobials against Mycoplasma mycoides mycoides small colony, the causative agent of contagious bovine pleuropneumonia. PloS one, 7(8), e44158.

  10. Létourneau, V., Nehmé, B., Mériaux, A., Massé, D., Cormier, Y., & Duchaine, C. (2010). Human pathogens and tetracycline-resistant bacteria in bioaerosols of swine confinement buildings and in nasal flora of hog producers. International journal of hygiene and environmental health, 213(6), 444–449.

  11. Dai, L., Sahin, O., Grover, M., & Zhang, Q. (2020). New and alternative strategies for the prevention, control, and treatment of antibiotic-resistant Campylobacter. Translational research : the journal of laboratory and clinical medicine, 223, 76–88.

  12. Berrocal, A. M., & Gaitan, J. R. (2008). MORAXELLA 372.02. In Roy and Fraunfelder’s Current Ocular Therapy (pp. 52-53). WB Saunders.

Categories: Exotic Pets, Rabbits, Respiratory Infection

animal diagnostics

Validated by Veterinarians

“Clients expect their veterinarians to stay up to date on all matters that affect the health and well being of their non-human family members. The current technique that we have used to determine the presence and antibiotic sensitivity of organisms causing disease in our pets is over a century old.

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Bernadine Cruz, DVM, Laguna Hills Animal Hospital Laguna Woods, CA

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Michael Morgan, DVMQuail Animal Hospital, Tustin, CA

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Thank you very much MiDOG, for sharing the opportunity to try your technology.”

Martha Smith-Blackmore, DVM, President of Forensic Veterinary Investigations, LLC – Boston, MA

The MiDOG All-in-One Microbial Test is our new gold standard of pathogen identification. The results are so accurate and valuable – especially with assessing both bacterial and fungal infections with the same sample.

Thank you MiDOG!”

Kathy Wentworth, DVM, Diplomate ABVP Canine and Feline Practice – PetPoint Medical Center, Irvine, CA

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Cathy Curtis, DVM – London, UK

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The cost and turnaround time are about the same as a culture test, but I get much more data. The test has great performance and I believe the NGS technology will be a game changer for veterinarians treating dogs with lesions or other infections.”

Michael Kavanagh, DVM, Practice owner – Saddleback Animal Hospital, Tustin, CA

“It’s helpful to have an NGS spectrum because it gives you a broader insight of what’s happening and what might be going on.”

Richard Harvey BVSc DVD DipECVD PhD FRSB FRCVS – European Specialist in Veterinary Dermatology – Head of Dermatology, Willows Veterinary Centre & Referral Service – Solihull, England UK

“I have been using MiDog for over 4 years now and exclusively as my test of choice for all cultures for 3 years.  It is so great to submit a culture and feel confident there will be a result when it comes back, especially for urine cultures.  The reports were intimidating at first because they contain so much information.  After the first few, I am now quickly able to glance over it and pick out the highlights.  I can then come back later and pour over all the details.  I have been extremely pleased with my patients’ results using the test as well.  I don’t envision ever going back to traditional culture and susceptibilities again.”

Brian M. Urmson, DVM, Columbiana Veterinary Associates

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Dr. Wayne Rosenkrantz, Animal Dermatology Clinic – Tustin

“She [Dr. Krumbeck] really did a great job of making complicated concepts accessible and demonstrating the value of your services. I’m really looking forward to working with MiDOG on my research project!”

Dr. Yaicha Peters, Animal Dermatology Clinic – San Diego

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Dr. Richard Harvey, BVSc DVD DipECVD PhD FRSB FRCVS; European Specialist in Veterinary Dermatology

“We’re seeing that, if we prescribe too many antibiotics or they’re taken too frequently, animals are developing inappropriate or pathogenic strains of bacteria. We’re also seeing that our antibiotics are just not working against them anymore… It’s a good example of why we need better diagnostic testing, like MiDOG, so that we’re selecting the correct antibiotic every time our patients have an infection.”

Dr. Alissa Rexo, DVM, CVA, DACVD, Mid-Atlantic Veterinary Dermatology

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Dr. Joerg Mayer, Entomologist and Microbiologist at the University of Georgia

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Dr. Jeremy Rayl – Veterinarian, Block House Creek Animal Hospital, Cedar Park, Texas