Every living being including dogs have a microbiome, a very characteristic one. Each one is as unique as a fingerprint. The bacterial profile in the gut can tell us whether a living being suffers from certain diseases such as diabetes or Crohn’s disease, whether they are overweight or slim, or whether they eat maily plant based foods or also meat.

 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.

What Exactly is the Microbiome?

Like humans, dogs are also densely populated with Bacteria: A complex microbial community lives on the skin, throughout the digestive and respiratory tract, including the lungs. 

If the colonization changes, this can promote chronic diseases or trigger them directly. On the other hand, altered colonization can also be an indicator of disease.

The intestine has a unique role to play here: a high microbial density meets the intestine-associated lymphatic tissue, which controls the entire body’s immune response. 

For pathogens, antigens and pollutants, the intestinal mucosa simultaneously offers a huge attack surface, for whose protection and nourishment the intestinal microbiota is jointly responsible.1

Gut Microbiome

The gut microbiome refers to the collection of microorganisms, including bacteria, viruses, fungi, and protozoa, that live in the gastrointestinal tract of an animal. 


In the case of dogs – the gut microbiome is the specific community of microorganisms that reside in the gut of dogs. These microorganisms play an important role in the overall health of the animal, including digestion, immunity, and metabolism. 


Imbalances in the gut microbiome, such as changes in the types or numbers of microorganisms present, can lead to health issues in dogs.


The Microbiome makes an essential contribution to your dog's health - although its composition and exact function are not yet precisely known!

Like a tropical rainforest, the microbiome is a very complex ecosystem. It only functions through the perfect interaction of the various Microorganisms.

How do Antibiotics affect the Microbiome?​

How an antibiotic affects the composition of the gut microbiome depends on several factors:

  • The spectrum of activity of the antibiotic
  • The dose and duration of administration
  • The route of administration (intravenous/oral)
  • The Pharmacokinetics/Dynamics

Any antibiotic will reduce microbial diversity in the dog’s gut, just as in humans. But antibiotics that are excreted via bile acid, for example, affect the gut microbiota more than others.

In addition, antibiotic use selects resistant strains. After starting antibiotic therapy, resistant bacteria may predominate.

Whether this involves primarily sensitive bacteria becoming resistant through a mutation or resistant bacteria gaining the upper hand through a growth advantage has yet to be fully elucidated.2

List of some common generic Antibiotics and the types of bacteria they are effective against:

Antibiotic Bacteria targeted
Staphylococcus, Streptococcus, Neisseria
Gram-negative bacteria (such as Escherichia coli and Pseudomonas aeruginosa)
Mycoplasma, Chlamydia, Legionella, some strains of Streptococcus and Staphylococcus
Rickettsia, Chlamydia, Mycoplasma
Gram-positive and gram-negative bacteria
Gram-negative bacteria
Gram-negative and gram-positive bacteria
Gram-positive bacteria
Anaerobic bacteria, parasites.

List of Antibiotics that are Excreted via Bile Acid:

  1. Chloramphenicol
  2. Erythromycin
  3. Lincomycin
  4. Clindamycin
  5. Tetracyclines (doxycycline, minocycline, tetracycline)
  6. Metronidazole
  7. Nitrofurantoin
  8. Rifampin
  9. Sulfonamides (sulfamethoxazole, sulfisoxazole)

It is worth noting that the route of excretion and elimination can vary depending on the specific antibiotic and the individual patient.

Additionally, the efficacy of certain antibiotics may be affected by the presence of bile acids in the gut;  It is always important to consult with a veterinarian or medical professional when prescribing antibiotics.


The composition of the gut microbiome is affected by a variety of factors, including the spectrum of activity, dose, and duration of administration, and route of administration of antibiotics.

The use of antibiotics can reduce microbial diversity in the gut and select for resistant strains of bacteria. Antibiotics that are excreted via bile acid tend to have a greater impact on the gut microbiome.

Antibiotics can Permanently Disrupt the Microbiome

The fact that antibiotics upset the bacteria of the intestinal microbiome is obvious and has now been proven by numerous studies. But antibiotics also affect the mycobiome, the fungi of our microbiome: the peaceful coexistence of microbes suddenly turns into a competition.

Moreover, the disruptive effect of antibiosis on fungi seems to be even more long-term than on bacteria: The bacterial flora recovered within 30 days, fungal species showed changes even after 90 days.

In addition, scientists found that specific metabolites of bacteria, short-chain fatty acids such as propionic acid, appear to have a positive effect on the pathogenic properties of yeast fungi.3

Intestinal microbiota: normal flora, opportunistic flora and pathogenic flora
Intestinal microbiota: normal flora - opportunistic flora and pathogenic flora

The effects of antibiotic therapy on the intestinal flora continue even after the therapy has ended. As a result, it often takes longer than we expect for the gut flora to recover.

Studies indicated a duration of up to two years for the gut microbiota to return to its original state.In the worst cases, antibiotic therapy can select pathogenic germs.

A well known example is pseudomembranous colitis;  it occurs when antibiotics damage the intestinal flora to such an extent – that the bacterium Clostridioides difficile can proliferate very strongly. 

The toxins secreted by Clostridioides difficile can lead to fever, abdominal pain, diarrhea, and fluid loss.4

Disturbed Microbiota can Increase the Permeability of the Intestinal Wall

Of course, this doesn’t always happen. But we alter the microflora’s complex interplay by administering antibiotics in dogs. This disrupts signaling cascades – even if usually only for a short time – that take place between the bacteria but also between the bacteria and the intestinal cells.

As a result, pathogenic bacteria can increase in the intestine. This can cause the mucus layer on the intestinal cells to become thinner, and the tight junctions, the connections between the intestinal cells, can lose their adhesion and become more permeable to bacteria.

Leaky Gut - Tight Junctions
Leaky Gut - Tight Junctions

Why is a Healthy Intestinal Flora so important for your Dog?

Your dog needs a healthy intestinal flora for good, regulated digestion. But it also significantly influences overall health, especially on the immune defense, because the intestinal surface is the largest gateway for pathogens.

Researchers have also proven that your dog’s intestinal flora influences.

  • how well or poorly he digests or utilizes his food
  • how much of his liver is loaded with metabolic toxins 
  • whether he develops allergies or food intolerances
  • whether he gets fat easily or remains slim even as a barn thresher
  • how well his immune system functions
  • how susceptible he is to stress and whether he reacts to stress with diarrhea
  • whether and how a chronic inflammatory bowel disease develops

Maintaining a Healthy Microbiome in Dogs

Here are a few tips to help maintain a healthy microbiome in dogs:

  1. Feed a balanced diet: A diet high in fiber and low in processed ingredients and preserevatives can help promote a healthy gut microbiome.
  2. Avoid antibiotics unless absolutely necessary: Antibiotics can kill off both harmful and beneficial bacteria, disrupting the balance of the microbiome.
  3. Provide Probiotics if Necessary: Probiotics are live microorganisms that CAN POSSIBLY help to maintain a healthy balance of bacteria in the dogs gut.
  4. Limit exposure to toxins: Chemicals, pesticides, and other toxins can damage the dogs gut microbiome, so it’s important to limit your dog’s exposure to them.
  5. Exercise regularly with your Dog: Regular exercise can promote a healthy gut by increasing blood-flow and helping to move food through the digestive system.
  6. Avoid Stress for your Dog: Stress can disrupt the balance of the microbiome, so try to minimize any stressors in your dog’s life.

It’s important to note that like with humans – every dog is different and what works for one dog may not work for another. Consult with a veterinarian for personalized advice for your dog.

A Proper Dog Diet for a Strong Gastrointestinal Tract

High-quality dog food is the best way to strengthen your dog’s digestion. The better the quality of the food, the better it can strengthen your dog’s digestion and intestinal flora.

An essential component of dog nutrition is dietary fiber. These are found mainly in plant foods such as cereals, fruits and vegetables. Your dog’s intestinal bacteria love fiber! They use it to strengthen the intestinal flora and help your dog digest. These supportive fibers are called prebiotics.” This prebiotics include apples, potatoes, psyllium, pumpkin and carrots.

In addition to prebiotics, there are probiotics! Surely you have heard of probiotic milk products. These contain, for example, lactic acid bacteria and other microorganisms that settle in the intestine.

Thus, they can strengthen the intestine’s barrier function and keep pathogens in check. Your vet can also give you more detailed information about probiotics!

Healthy DOg Food

Probiotics for Dogs: Living Microorganisms

Probiotics for dogs are feed supplements containing live or viable microorganisms. If a dog is given the bacteria as a food supplement with the food; it can help balance the intestinal flora.

Some foods naturally contain probiotic strains of bacteria. For example, fermented foods, such as sauerkraut or yogurt made with certain starter cultures, contain small numbers of probiotic bacteria. Therefore, their potential positive influence on intestinal flora is often critically discussed.

On the other hand, probiotics as feed supplements contain a considerable amount of bacteria, which are often additionally protected from destruction by gastric acid. Moreover, they are available in various combinations of different bacterial strains.

The combination of Pre-and Probiotics is called Synbiotics - this is because they combine the positive properties of both substances.

Often it is helpful to use this combination because the feed additives usually complement each other.

Probiotics Concept

More Scientific Research is Necessary

The effects of different bacterial strains on human and animal health are the subject of numerous research-projects. The gut flora has a complex relationship with other external influences, such as gut health, physical activity, nutrition and mental health.

According to the current state of microbiome research, no scientifically validated statements can be made about the health effects of probiotics!

Therefore, prebiotics and probiotics – like other feed additives – should never be seen as a cure. They can only be individually selected and given in a supportive manner.


To demonize antibiotics, in principle, is by no means the intention of this article. On the contrary, antibiotics have a very important function and still save lives! Antibiotics are also certainly not the death of the intestinal microbiome in dogs!

But we have to keep in mind that we are changing the microbiome’s composition by administering antibiotics and that, at this point, we do not even know exactly how we are changing it and what consequences we are triggering.

Therefore, antibiotics should never be used recklessly; a benefit-risk consideration must always be made. If your dog has an infection, never order antibiotics from the Internet. Instead, always consult a veterinarian who will examine your dog thoroughly and select the appropriate medication. Make sure your dog has a healthy balanced diet that also provides for a healthy microbiome and, therefore, a strong immune system.

New treatment strategies should not only be aimed at fighting the bacteria but, above all, at strengthening the immune system. Then you can often avoid unnecessary antibiotic therapy.

  1. https://pubmed.ncbi.nlm.nih.gov/27592384/
  2. Long-term impacts of antibiotic exposure on the human intestinal microbiota
  3. Seelbinder, B., Chen, J., Brunke, S. et al. Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria. Microbiome 8, 133 (2020) - https://doi.org/10.1186/s40168-020-00899-6.
  4. Jernberg C et al. Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J. 2007 May;1(1):56-66.

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.


Leave a Reply

Avatar placeholder

Your email address will not be published. Required fields are marked *

Try The Best Rated Dog Food On Amazon

Ancient grains like grain sorghum, millet, quinoa and chia seed are naturally high in fiber and rich in protein. Unchanged for thousands of years, different grains provide various nutrients such as vitamins, minerals, antioxidants and omega fatty acids.