How do antibiotics affect the microbiome?

The microbiome is prone to disruption, particularly from antibiotics. Even a short course can have a big impact.
5 min read
Dr Joe Inglis BVSc MRCVS
Head of Veterinary Sciences

Your dog's microbiome is a complex community of different bacteria and microorganisms that live in the gastrointestinal tract. The microbiome is very closely linked with your dog’s overall health, immune system function and digestion. Due to the nature of the gut and its constant intake of food (and other items in the case of scavenging dogs!) the microbiome is prone to disruption, which could be from the environment, because of a disease, due to lifestyle, or because of prescribed medications, particularly antibiotics. 

Antibiotics are usually prescribed to treat a bacterial infection as they are drugs that kill or incapacitate bacteria. Unfortunately, an antibiotic cannot distinguish between which bacteria are ‘good’ and which are ‘bad’ or pathogenic (disease-causing). This means that when your pet takes antibiotics to kill off the ‘bad’ bacteria causing their infection, some of the ‘good’ bacteria in the gut will also be killed. This will lead to disruption in the balance and diversity of the microbiome, which could in turn lead to a secondary health issue. This is one of the reasons why it is so important to only give antibiotics when they are necessary and not as a ‘just in case’ or preventative measure. 

Medical practitioners who study the microbiome frequently talk about how optimising health means aiming to improve the diversity of the microbiome. The diversity of the microbiome means how many different species of bacteria there are present and the richness of these populations within the gut. A wide biodiversity within the microbiome is directly linked with the health of the body and the immune system, and by following a course of antibiotics, some of this diversity can be lost. Some bacterial species’ populations will recover after the antibiotics have finished, but rarely to pre-treatment levels, whilst others will not recover, meaning diversity is lost more permanently. Ongoing bacterial imbalances within the microbiome can cause both new chronic health problems or aggravate existing ones, especially digestive issues. This is because the beneficial bacteria that are lost are involved in processes such as absorbing essential nutrients, maintaining a strong immune system and helping to fight inflammation. 

Even a short course of antibiotics can have a big impact on the microbiome. A study published in 2020 found that a 14 day course of a common antibiotic called Metronidazole caused a significant change in the microbiome, with a decrease in richness and key bacteria such as Fusobacteria, and these changes did not resolve within the 4 weeks following the end of the antibiotic course[1]. Other studies have also found that the impact of antibiotics on the microbiome is long lasting, even with the support of synbiotics, which can potentially reduce some of the antibiotic-induced gastrointestinal effects. In humans, changes have been found in the microbiome for as long as 4 years after an antibiotic course.[2] 

How much an individual antibiotic affects the microbiome is dependent on:

  • The route of administration (whether the drug was given in a tablet or injection)
  • The dose and duration of the course
  • The type of bacteria that the antibiotic targets
  • The pharmacodynamic properties of the antibiotic (how it interacts with the body and other drugs)

All antibiotics will decrease microbial diversity but some, like those that are excreted from the body in the bile acid (which goes directly into the intestine) cause a greater disruption than others. Common antibiotics that are excreted via bile acid include: Metronidazole, Erythromycin, Sulfonamides, Clindamycin and Tetracyclines. 

As well as disrupting a dog’s microbiome population, antibiotic use can also lead to antibiotic resistance developing within the gut populations, as they tend to promote the survival of bacteria with genetic variations that give them some resistance to the drug. This can happen directly, when a dog is given antibiotics to treat an infection, or indirectly when they consume meat from an animal that had been on antibiotics (as is commonly the case with beef cattle) or even through exposure to antibiotics that their owners are taking. A study in 2021 comparing the microbiome of dogs and wolves found that the dogs’ microbiome was enriched with bacteria resistant to clinical drugs used in medical and veterinary practice, whilst the wolves’ microbiome was enriched with bacteria resistant to antibiotics used in livestock[3] (probably as a result of preying on farm animals). 

Other unwanted side effects of antibiotic usage in the microbiome include overgrowth of a group of microbes called opportunistic pathogens. These are usually benign bacteria, such as Clostridium difficile and certain yeast species, that can flourish when levels of other species drop due to the effects of antibiotics. When their populations expand, they can start to overwhelm the ‘good’ bacterial species and cause significant health issues.

For the most part, all of this biome disruption happens behind the scenes, with little to see externally. Some dogs will develop diarrhoea or vomiting during or after a course of antibiotics, but others appear to be unaffected. Many dogs will remain in good health, as they may be resilient or have had a very diverse microbiome to begin with, but others may go on to develop or have a flare up of chronic disease. In some cases, more antibiotics are then given to try and resolve the dog’s deteriorating symptoms and so the health of the microbiome spirals ever downwards as more and more antibiotics are given, despite them being part of the problem.

For these reasons, it is so important to use antibiotics responsibly, and where needed only, rather than as preventatives or ‘just in case’. It is also important to select the correct antibiotic, and this is where the more modern culture of swabbing to test for sensitivity and resistance is great progress. Antibiotics save lives, there is no doubt about that, but we are depending on them far too much, and they are frequently given unnecessarily. As pet owners, as well as vets, we should always be questioning if they are needed or not, every single time their use is considered. Most importantly, we should not expect to walk out of every consultation with some tablets for our dog, as they may end up doing more harm than good in the long term.

So, the most important thing to remember for the health of your dog's microbiome (and your own) is to avoid antibiotics unless they are absolutely necessary, and ensure a fibre-rich diet to encourage the health of your dogs' good bacteria.


[1] Pilla R, Gaschen FP, Barr JW, Olson E, Honneffer J, Guard BC, Blake AB, Villanueva D, Khattab MR, AlShawaqfeh MK, Lidbury JA, Steiner JM, Suchodolski JS. Effects of metronidazole on the fecal microbiome and metabolome in healthy dogs. J Vet Intern Med. 2020 Sep;34(5):1853-1866. doi: 10.1111/jvim.15871. Epub 2020 Aug 28. PMID: 32856349; PMCID: PMC7517498.

[2] Jernberg C, Löfmark S, Edlund C, Jansson JK. Long-term impacts of antibiotic exposure on the human intestinal microbiota. Microbiology (Reading). 2010 Nov;156(Pt 11):3216-3223. doi: 10.1099/mic.0.040618-0. Epub 2010 Aug 12. PMID: 20705661.

[3] Liu Y, Liu B, Liu C, Hu Y, Liu C, Li X, Li X, Zhang X, Irwin DM, Wu Z, Chen Z, Jin Q, Zhang S. Differences in the gut microbiomes of dogs and wolves: roles of antibiotics and starch. BMC Vet Res. 2021 Mar 6;17(1):112. doi: 10.1186/s12917-021-02815-y. PMID: 33676490; PMCID: PMC7937242.

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Frequently asked questions

  • The microbiome is the name given to the collection of microbes, mostly bacteria, but also fungi and protozoa, that exist within your dog’s gut. It is a diverse and complex microbial community which can directly affect health and wellbeing. We know that 90% of a human’s body cells are microbes, with only 10% being human cells – it’s just that human cells are markedly larger than the microbes. It’s similar for our four-legged friends. Testing the microbiome gives us an idea of exactly which bacteria are present in your dog’s gut and this can help indicate existing or future health problems.

  • A healthy diversity within the microbiome has been found to be an accurate indicator of overall health and wellbeing. If your dog appears healthy, but has an imbalance in their microbiome, then this could be an indicator of a potential future health issue. If your dog has any existing health complaints, then improving the health of their microbiome can help to improve immune system health and overall wellbeing, as well as improving disease symptoms.

  • Testing and treatment have the potential to help with a whole range of different health complaints. The immune system is very closely associated with the gut, so any imbalance in the microbiome can influence immune system health, overall vitality and wellbeing. Our supplement recommendations are also tailored to your individual dog, with specific ranges designed to help with gastrointestinal inflammation, joint problems, allergies and skin complaints, to name a few.

  • All you need to do is order a kit online and fill in our questionnaire about your dog and their general health. We will then send the kit out to you by post. You then just need to collect a sample and return it to us, again by post. Once the test is performed, we will email the results directly to you.

  • You do not need to get your vet’s permission to test, or talk to them about performing the test beforehand. We do recommend that you pass on a copy of your test results to your regular vets, as it may help them in understanding your pet’s current health, and any future complaints they may have.

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