Analysis of the microbiome in animals

What is the microbiome and where can we find it?

The microbiome is the collection of microorganisms, primarily bacteria, viruses, and fungi that live in and on the surface of an animal. It is unique to each individual, similar to fingerprints in humans. These microorganisms are found in various parts of the body, such as the intestines, skin, oral and nasal cavities, and respiratory tract. However, the most important is the intestinal microbiome, which plays a key role in digestion, the immune system, and the overall health of the animal.

The intestinal microbiome as the foundation of a healthy organism

The intestinal microbiome affects not only digestion and nutrient absorption, but also the immune response and mental well-being of the animal. A balanced intestinal microbiome supports proper digestion and nutrient absorption, the immune system (including the production of vitamins B2, B12, and K), and protection against pathogens. Conversely, an imbalance can lead to digestive problems, allergies, autoimmune and inflammatory diseases, or even behavioural changes. The intestinal microbiome is sometimes called the "second brain" because it produces or influences the production of neurotransmitters, hormones, and other metabolites, thereby affecting various processes in the brain—thinking, memory, concentration, but also emotions and mental state, mood and behaviour, anxiety, and depression. There is also talk of a link between the microbiome and obesity, with slim individuals having a significantly more diverse microbiome than obese individuals.

Types of bacteria: Which ones are beneficial and which ones are not?

Common and beneficial bacteria include Lactobacillus, Bifidobacterium, and Faecalibacterium, which support healthy digestion and immune function. On the other hand, an overgrowth of Clostridium difficile, Escherichia coli, or Salmonella may signal a health problem such as inflammation, infection, or an imbalance in the gut.

How is the microbiome formed?

The microbiome begins to form at birth, when the infant comes into contact with microorganisms from the mother and the surrounding environment, and gradually becomes more diverse and stable. Diet, medications (especially antibiotics), stress, and the environment further influence the composition of the microbiome throughout life. A proper diet rich in fibre, minimizing stress, and limiting the use of antibiotics can help maintain a healthy microbiome. Probiotics and prebiotics also play an important role. Probiotics are live bacteria that promote the growth of healthy microflora, such as Lactobacillus or Bifidobacterium. Prebiotics are indigestible components of food that serve as food for beneficial bacteria. They are found in foods rich in fibre, such as vegetables and some grains.

Ten reasons why it is good to know your pet's microbiome

1. Detection of health problems: Microbiome analysis can reveal imbalances or the presence of pathogenic microorganisms.

2. Personalized nutrition: Understanding the composition of the microbiome allows you to tailor your pet's diet to support beneficial bacteria and overall health.​

3. Monitoring treatment effectiveness: Regular microbiome testing helps track how various treatments affect the intestinal microflora.

4. Optimization after antibiotic treatment: Antibiotics disrupt the balance of intestinal bacteria. Analysis of the microbiome after treatment can help determine how best to restore a healthy environment in the intestines.

5. Supporting reproductive health: In breeding animals, a healthy microbiome can also be important for fertility and proper development of offspring.

6. Disease prevention: Identifying changes in the microbiome can serve as an early indicator of potential health problems.

7. Managing chronic diseases: The microbiome may play a role in chronic problems such as allergies, digestive problems, or skin diseases. Its analysis can reveal hidden connections and help find more appropriate therapies.

8. Supporting the immune system: A healthy microbiome plays a key role in the immune response; its analysis and subsequent adjustment can strengthen the animal's immunity.

9. Supporting the animal's mental well-being: An imbalance in the intestinal microbiome can affect behaviour, stress, or anxiety.

10. Support for longevity and overall vitality: A balanced microbiome promotes better digestion, nutrient absorption, strong immunity, and detoxification of the body. All of this contributes to the long-term health, vitality, and quality of life of your animal.

Ordering a test

Intestinal microbiome testing is available for all types of animals.

After placing your online order for microbiome testing, we will send you a sampling kit. The sampling kit is included in the price of the test and contains:

• a sterile Copan eNAT tube with a cap, which contains a special transport medium designed to stabilize and protect DNA and RNA in samples
• FLOQSwabs sampling stick
• an envelope with a return address

Sample collection

Sample collection is simple and does not require a veterinarian. Microbiome testing can be performed on dogs, cats, horses, and any other animals. A rectal mucosa swab is taken for microbiome testing. The Copan eNAT sampling system is designed to ensure sample stability during transport and analysis. It prevents the growth of microorganisms in the tube by completely inactivating microbial activity within 30 minutes, thus enabling safe handling of samples. FLOQSwabs, which use capillary suction, are available in various sizes and shapes for convenient sampling in different animal species.

How is the microbiome analysis performed?

The microbiome analysis is performed using the Illumina 16S rRNA sequencing system, which enables comprehensive profiling of the microbial diversity of the intestinal microbiome. It contains a set of highly accurate markers, enabling the detection and quantification of beneficial and potentially dangerous microbial organisms in the sample and their differentiation at the species level.

The results report includes an analysis of the composition of the microbiome, including graphs showing the percentage representation at the level of various taxonomic ranks – kingdom, phylum, class, order, family, genus, and species.

We offer two versions of the results report:

• for experts – contains the composition of the microbiome
• for laymen – contains the composition of the microbiome and an interpretation of the results by a veterinarian

Conclusion

The microbiome plays a crucial role in the overall health of animals. Thanks to modern testing methods, we can better understand its composition and find suitable solutions to optimize the health of our pet.