Like all mammals, cats and dogs have a microbiome. However, research into the animal intestinal flora – in contrast to that of humans – is still in its infancy. Nevertheless, scientific research has already shown clear links between a disturbed animal intestinal flora and the development of various clinical pictures, such as diarrhea, chronic inflammatory bowel diseases or dermatitis.

The gut microbiome is susceptible to disruption due to  lifestyle, and environment and is associated with many diseases. On the other hand, gut bacteria can be specifically influenced and promoted through diet.

It’s becoming increasingly clear that an unhealthy gut microbiome can be the root cause of many digestive issues in dogs. This article delves into the diagnosis and treatment options for dogs with imbalanced gut microbiomes, otherwise known as dysbiosis.

By understanding the importance of maintaining a healthy gut microbiome in dogs, we can help keep our furry friends happy and healthy.

Intestinal Microbiome in Dogs

Many areas of the body in dogs are colonized with a wide variety of bacteria. These include the surface of the skin and all mucous membranes directly exposed to the environment, e.g., the respiratory or urogenital tract. The totality of all these microorganisms is called the microbiome.

However, the gastrointestinal tract is the leading site of colonization of the microbiome. Starting from rather low-germ areas such as the stomach and duodenum, the concentration of bacteria increases sharply from the small intestine to the colon.

Recent studies show that the number of microbes localized in the colon can exceed that of the host body cells by a factor of 10. More than 25% of canine feces are composed of shed intestinal bacteria, with anaerobes making up the much larger proportion at 99%.

Considering the totality of all metabolic processes of this bacterial association, the intestinal microbiome has a higher metabolic capacity than the liver.1

Gut Microbiome

The intestinal microbiome is a metabolic organ with significant impact on host health.

Importance and Function of the Intestinal Flora

Did you know that the tiny microorganisms living in your dog’s gut play a huge role in their overall health? It’s true! Recent scientific studies have uncovered the many ways in which the intestinal microbiome contributes to a dog’s well-being.

From boosting metabolism to regulating the immune system, a healthy gut microbiome is essential for your dog’s overall health and happiness. So next time you’re thinking about your dog’s health, remember to give some love to their gut microbiome too!

A whole Series of Complex Metabolic and Immunoregulatory Processes are Influenced Positively or also Negatively by the Intestinal Flora:

The Power of Colonization Resistance

Commensal bacteria in the intestine serve as a vital barrier, preventing the colonization and growth of harmful germs such as Campylobacter or opportunistic pathogens like Candida albicans. This protection is mainly achieved through three mechanisms:

  • Occupying receptors on the mucosa
  • Inhibiting pathogen growth through the production of bacteriostatic or microbicidal compounds
  • Competing for essential nutrients, vitamins, and growth-promoting factors

Fueling the Body: The Importance of Nutrient Supply

A well-balanced gut microbiome helps to support metabolism and blood flow to the intestinal mucosa.

Bacterial breakdown products of carbohydrates and proteins enter the cells of the colon mucosa by diffusion, providing over 50% of the energy needed by the enterocytes of the colon.

Furthermore, short-chain fatty acids produced by the bacteria stimulate intestinal peristalsis and aid in proper digestion.

The Intestine-Associated Immune System

In addition to providing nutrients, the gut microbiome also plays a crucial role in supporting the host’s immune defenses.

The mere presence of the gut microbiota helps to maintain an immunological defense barrier against foreign germs by constantly training the gut-associated immune system.

Additionally, pathogens are actively repressed by stimulating the synthesis of antimicrobially active peptides such as β-defensins and immunoglobulins (sIgA).2


The Intestinal Microbiome in dogs plays a crucial role in their overall health and well being. Recent scientific studies have shown that the Gut Microbiome contributes to a variety of metabolic and immunoregulatory processes in Dogs!

This Prozesses Include: Colonization resistance, Nutrient Supply, and Support for the Host's Immune System.

A Well-Balanced Gut Microbiome is Essential for Maintaining a Dog's Health and Happiness.

Dysbiosis in the Intestine of Dogs

When the balance of bacteria in a dog’s gut is thrown off – this can lead to a number of issues. The condition, known as dysbiosis, can cause the gut microbiome to be unable to perform its protective and nutritional functions properly.

As a result, the gut’s defenses may be weakened, allowing harmful pathogens like bacteria, viruses, fungi, and parasites to thrive.

This weakened barrier function can also allow antigens, toxins, and other harmful substances to pass from the gut into the body, causing a variety of health problems, such as diarrhea, constipation, and chronic inflammatory bowel disease.

It even can lead to skin and coat problems, and allergic reactions.

The Intestine-Associated Immune System

The microbiota is in direct contact with the intestinal mucosal layer, the immune system, and luminal substrates.

Therefore, changes in one or more of these factors ultimately affect the composition of the microbiota, and dysbiosis is often an early marker of an abnormal intestinal environment associated with the disease.

Gut Bacteria may contribute to Gastrointestinal Disease through the following Mechanisms:

Type of Dysbiosis Possible Consequences
Abnormal substrates in the intestinal lumen (e.g., undigested nutrients, drugs)
Increase in Bacterial Metabolites causing Diarrhea
Loss of microbiota function due to a loss of commensal bacteria
Reduced conversion of primary to secondary bile acids leading to overgrowth by enteropathogenic germs

Deficiency of anti-inflammatory metabolites
Increase in total bacterial load in the small intestine
Increase in bacterial metabolites causing diarrhea

Increased inflammatory immune response
Increase in mucosal adherent bacteria
Increased inflammatory immune response

Diagnosis - Assessment of the Microbiome

There are several ways to assess a dog’s microbiome, but some are more effective than others.

Microbiological-Cultural Analysis

The first choice in diagnosing gastrointestinal complaints such as recurrent diarrhea is a microbiological-cultural analysis of feces.

The microbiological-cultural analysis allows rapid and cost-effective identification of many enteropathogenic germs, such as Salmonella, Yersinia and Campylobacter, and facultative pathogenic bacteria, such as Klebsiella or Hemolytic E. coli.

Determining mucosal, inflammatory, and digestive markers such as fecal calprotectin, alpha-1-antitrypsin, bile acids, and canine pancreatic elastase are helpful in many cases.

In any case, parasitoses should also be excluded by microscopic or immunological examination of the feces for endoparasites.

Microbiology; Colourful bacterial cultures


Many veterinarians still use bacterial cultures of feces to diagnose dysbiosis, but they are ultimately not helpful for assessing the microbiome!

The majority of intestinal bacteria are strictly anaerobic in nature and therefore require special culture media for cultivation. Consequently, only a small percentage of the actual relevant bacterial species can be cultured in diagnostic laboratories.

Molecular Sequencing of 16S rRNA Genes

Molecular biology techniques based on 16S rRNA gene analysis can identify and quantify bacteria regardless of their cultivation conditions.

Molecular techniques based on 16S rRNA gene sequencing provide comprehensive information about the microbial composition of a fecal sample and are mainly used in the context of science and research.

Several companies offer sequencing for microbiome assessment on a commercial basis for individual animals. Still, there currently needs to be uniform and standardized methods (e.g., DNA extraction, PCR primers used) in these laboratories.


Since no reference ranges are defined for animals, and each laboratory company produces different reports, interpretation of the results is difficult.

In addition, inter-assay variations often occur, and analytical validation data for these assays are not accessible.

For these reasons, microbiome assessment based on sequencing is not currently recommended for Dogs.

The Canine Microbiota Dysbiosis Index

The Dysbiosis Index (DI) is a quantitative PCR-based assay currently commercially available in North America and Europe and is now used in numerous clinical studies.

“The Dysbiosis Index is the only validated assay for the assessment of dysbiosis in dogs.”

The Dysbiosis Index quantifies the presence of seven intestinal bacterial strains whose quantity and composition are often altered in dogs with chronic enteropathies or after treatment with broad-spectrum antibiotics.

By precisely determining the concentration of C. hiranonis, the dysbiosis index also provides information on the ability of the intestinal microbiota to convert primary bile acids into secondary bile acids.3


With the Canine Microbiota Dysbiosis Index, a real-time PCR-based detection method has been established that is also well suited for the clarification of intestinal dysbacteria in dogs.

The following bacterial species are examined and quantified:

  • Escherichia coli
  • Faecalibacterium prausnitzii
  • Fusobacteria spp.
  • Blautia spp.
  • Turicibacter spp.
  • Clostridium hiranonis
  • The total bacterial count present in the intestine

Therapy of a Dysbiosis in Dogs

What therapeutic options are helpful in the case of proven intestinal dysbiosis? After an initial symptomatic therapy with anti-inflammatory and mucosa-supporting substances such as humic acids, zeolite or healing earth, microbiological therapeutics are an option.

The direct supplementation of anaerobic microflora such as Faecalibacterium prausnitzii, Blautia or Turicibacter is not yet possible.

Due to the complex interactions in the microbiome, it is not helpful to target a single bacterial group. As the interaction of the individual groups of bacteria has yet to be scientifically researched, valid statements on effectiveness are impossible.

Any intervention in the gut microbiome, whether via feed conversion, prebiotic feed supplementation, or probiotics, directly or indirectly affects all individuals in the bacterial collective.

Dysbiosis is also often only one component of intestinal disease, and usually, a multimodal therapeutic approach directed against the underlying cause is required in these cases.

In dogs with Exocrine Pancreatic Insufficiency (EPI), for example:
Pancreatic Enzyme Supplementation improves clinical signs, and often the intestinal microbiome also normalizes after a few weeks.

Treatment options for dogs with dysbiosis include dietary modifications, Pre- and Probiotics, Antibiotics, and Fecal Microbiota Transplantation (FMT), with each of these treatment approaches acting through different mechanisms. 

In many cases, combination treatments yield the best therapeutic effects.

Treatment Options of Dysbiosis in Dogs:

Treatment Effective Mechanism Potential Side Effects
Change in Diet
High digestibility results in less residual substrate that would promote bacterial overgrowth

Elimination diets - with new or hydrolyzed ingredients

Eliminate dietary antigens if the underlying disease is immune-mediated
None - if there is no feed hypersensitivity or food allergy

Growth of beneficial bacteria

Prebiotics are converted into SCFA

Fibers bind harmful bacterial metabolites
Soluble/insoluble fibers may initially cause flatulence and diarrhea
Probiotics / Autogenous vaccines
Can improve barrier function

Side effects are rare, but often it is not clear which patient would benefit best from which strain
Reduction of total bacterial load and the amount of mucosal adherent bacteria

Long-term changes in the microbiota

Renewed growth of bacterial load after antibiotic discontinuation

Increased antibiotic resistance
Fecal microbiota transplantation (FMT)

Alteration of the luminal microbiota

Efficacy depends on underlying disease, but side effects are rare

Little effect on mucosal-adherent bacteria/br>
Recurrent dysbiosis if concomitant inflammatory event persists

1. Change in Diet

A change in diet should always be the treatment of the first choice. Various studies show that between 50 and 70% of dogs with chronic enteropathy are food-responsive.

Highly digestible diets that contain hydrolyzed or “new” proteins, i.e., proteins never fed to the animal before, are most commonly used.

Most of these diets are hypoallergenic and provide a reduction in the number of undigested nutrients in the intestinal lumen, thereby reducing the potential for bacterial overgrowth.4

2. Probiotics

Probiotics can be administered alone in low-grade cases or combination with dietary modification. However, because the number of bacteria added with a probiotic is relatively small compared to the existing intestinal flora, probiotics have little direct effect on the microbiome’s composition.

However, the metabolites of the added bacteria can have beneficial effects on the intestinal mucosa, such as shortening the duration of acute diarrhea and reducing antibiotic-associated gastrointestinal side effects such as vomiting or diarrhea.

Unfortunately, there need to be more high-quality studies on the numerous preparations offered on the market; therefore, it is challenging to make scientifically valid statements on the use of probiotics.

3. Prebiotics

Prebiotics are indigestible carbohydrates that promote the growth of beneficial microorganisms. They are divided into soluble/insoluble and fermentable/non-fermentable fibers. Fermentable prebiotics are converted to short-chain fatty acids by colon bacteria.

Most commercial gastrointestinal diets contain prebiotics, but for some specific conditions (e.g., colitis), particularly high-fiber diets may be beneficial. For example, supplementing a diet with psyllium husk as a source of soluble fiber at a daily dosage of 0.5-1 g /kg body weight may improve fecal quality in animals with colon disease.

The appropriate product should be introduced initially at a lower dosage and gradually increased until the desired consistency is achieved.

3. Antibiotics

Antibiotics such as tylosin and metronidazole have traditionally been recommended for treating chronic enteropathies, but their use as first-line agents is now quite controversial.

Although these antibiotics may improve clinical symptoms – probably due to a reduction in the bacterial load – recurrences often occur after treatment, when the bacteria grow again, since antibiotics rarely eradicate the underlying disease process.

4. Fecal Microbiota Transplantation (FMT)

Fecal microbiota transplantation (FMT) can help against dysbiosis in some cases and restore the normal microbiota.

Fecal Microbiota Transplantation

This method involves transferring feces from a healthy donor into a recipient’s intestine via oral capsules, endoscopically, or by enema.

In human medicine, FMT has a high success rate (>90%) for recurrent Clostridium Difficile infections. Still, it is proving less effective for Inflammatory Bowel Disease due to the underlying intestinal inflammatory process.

In dogs, FMT is still a relatively new therapy, and the therapeutic success of FMT is highly dependent on the underlying disease.5


The intestinal microbiome plays a critical role in host health. For example, many animals with gastrointestinal diseases can develop dysbiosis, resulting in an abnormal microbial function that can then contribute to clinical signs.

The dysbiosis index is a helpful diagnostic tool in many affected patients. Since various underlying causes may be involved, in many cases, a multimodal and often long-lasting therapy is required to improve the microbiota’s composition effectively.

  1. Guard BC, Suchodolski JS. HORSE SPECIES SYMPOSIUM: Canine intestinal microbiology and metagenomics: From phylogeny to function. J Anim Sci. 2016 Jun;94(6):2247-61. doi: 10.2527/jas.2015-0029. PMID: 27285902.
  2. Honneffer JB, Minamoto Y, Suchodolski JS. Microbiota alterations in acute and chronic gastrointestinal inflammation of cats and dogs. World J Gastroenterol. 2014 Nov 28;20(44):16489-97. doi: 10.3748/wjg.v20.i44.16489. PMID: 25469017; PMCID: PMC4248192.
  3. MK AlShawaqfeh, B Wajid, Y Minamoto, M Markel, JA Lidbury, JM Steiner, E Serpedin, JS Suchodolski, A dysbiosis index to assess microbial changes in fecal samples of dogs with chronic inflammatory enteropathy, FEMS Microbiology Ecology, Volume 93, Issue 11, November 2017, fix136,
  4. Jergens AE, Heilmann RM. Canine chronic enteropathy-Current state-of-the-art and emerging concepts. Front Vet Sci. 2022 Sep 21;9:923013. doi: 10.3389/fvets.2022.923013. PMID: 36213409; PMCID: PMC9534534.
  5. Chaitman J, Gaschen F. Fecal Microbiota Transplantation in Dogs. Vet Clin North Am Small Anim Pract. 2021 Jan;51(1):219-233. doi: 10.1016/j.cvsm.2020.09.012. Epub 2020 Oct 29. PMID: 33131919.
Categories: Microbiome

Doctor Xeeshan

Doctor Xeeshan

I am Doctor Xeeshan, located in Lahore, Punjab, Pakistan. In this blog, I am providing authentic information about dog breeds, diseases, medications, etc.


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