How to protect and repair your microbiome alongside antibiotics

When was your last course of antibiotics? Did you suffer symptoms during or after antibiotic treatment? Did you protect your microbiome health while taking antibiotics? And have you done a microbiome test to see if your gut microbiome needs any targeted support to repair? These are questions we often ask during a first consultation where we explore a client’s health history.

Antibiotics are one of the most widely prescribed medical interventions worldwide. They are a vital first-line treatment for many infections. However, they are also one of the most significant causes of major disruption to our gut microbiome. At The Microbiome Group, we always advise clients to take probiotics and prebiotics alongside antibiotic treatment to limit any damage to their microbiome health. However, we often need to support people with microbiome repair following antibiotic treatment.

Vicky with a glass containing PHGG and a probiotic capsule

Understanding Antibiotics and Their Impact on Gut Health

Antibiotics impact the gut microbiome by causing rapid reductions in microbial diversity. They shift the balance of bacterial populations in the gut away from health-promoting species. The longer the course of treatment, the more species are affected, and the longer the microbiome takes to recover. Taking a combination of different antibiotics is also more disruptive to the gut microbiome, as is repeated courses of antibiotics.

After antibiotic treatment, gut bacterial populations can recover within a few weeks. However, some studies show it can take months to rebuild. Occasionally, a course of antibiotics can lead to the extinction of certain species (Palleja et al., 2018).

Antibiotics commonly reduce key beneficial bacteria such as Bifidobacterium and Faecalibacterium, while allowing populations of opportunistic, inflammatory species such as Escherichia and Klebsiella to expand. This is why some people experience diarrhoea, which is a common complaint when on antibiotics.

Microbiome recovery is highly individual. Your baseline composition strongly influences outcomes. Some people recover quickly, while others experience lingering digestive issues and other systemic symptoms.

Gut Microbiome Repair Strategies

As practitioners looking to support you in restoring your microbiome, we focus on three key areas: diet, probiotics, and prebiotics.

Diet

The most important factor in restoring the gut ecosystem and maintaining microbiome health in the long term is ensuring your diet includes plenty of plant foods. These foods are rich in fibre, including prebiotics, and contain various polyphenols that nourish our beneficial bacteria.

Poor diets, lacking in prebiotics and polyphenols, can increase vulnerability to infection after antibiotic use. Conversely, plant-rich diets enhance microbiome resilience to antibiotic treatment (Kennedy et al., 2024).

Probiotics

Research shows that using probiotics alongside antibiotic treatment leads to a faster recovery of beneficial species (John et al., 2024). Probiotics do not re-seed the microbiome; rather, they support and communicate with other organisms in the gut. This interaction influences bacterial behaviour, gene expression, and immune responses.

We refer to clinical trial data to determine which probiotic strains would be most supportive. This includes considering whether the antibiotics are targeting a respiratory or gut infection. We commonly prescribe Saccharomyces boulardii CNCM I-74 (SB) and Lacticaseibacillus rhamnosus GG (LGG). Clinical trials have shown that SB is very effective at reducing antibiotic-associated diarrhoea. SB is a yeast, so antibiotics (which only target bacteria) don't decrease its efficacy. Additionally, SB doesn’t reduce the effectiveness of antibiotics either.

For safety reasons, there are cases where we wouldn’t recommend SB. This includes situations where someone’s health is very frail or where there are deep puncture wounds or cannulas in use.

Clinical trials show that LGG protects against antibiotic-induced changes in the microbiome. It reduces inflammation markers and positively influences microbiome balance. However, LGG is also impacted by antibiotics, requiring frequent, high doses and careful timing within the antibiotic regimen. Depending on the nature of the infection and your health needs, we may prescribe better-targeted probiotics.

Prebiotics

Prebiotic fibres selectively feed beneficial gut bacteria, helping support microbial regrowth after antibiotic exposure. Human studies have shown that prebiotics increase populations of beneficial bacteria and promote the production of health-promoting short-chain fatty acids, particularly butyrate.

Prebiotics are found naturally in certain plant foods. However, for protecting the gut microbiome from antibiotic-induced changes and encouraging large-scale, long-term shifts in the gut ecosystem, we recommend prebiotic supplements. These are usually powders that can be mixed into drinks or food.

We most commonly recommend partially hydrolysed guar gum (PHGG), lactulose, galactooligosaccharides (GOS), or inulin/FOS. Each prebiotic has different properties and targets different groups of beneficial bacteria. For example, PHGG is the most gentle on the stomach and can normalise stools, helping to prevent antibiotic-related diarrhoea. Inulin/FOS feeds a broader range of beneficial bacteria but can cause digestive symptoms, especially if used in large quantities.

At The Microbiome Group, we personalise all our treatment plans. We consider an individual’s microbiome profile, health history, diet, lifestyle, symptoms, and other needs to choose which prebiotic to recommend and at what dose. It’s always helpful to have baseline microbiome data gathered prior to antibiotic use to guide our treatment plans. However, if someone hasn’t done a microbiome stool test before commencing treatment, we can still make recommendations for prebiotics to take alongside and immediately after antibiotic treatment to help protect microbiome health. Our recommendations may not be as well targeted in these cases.

Tracking Your Progress

Gut bacterial populations can fluctuate rapidly for several weeks after completing a course of antibiotics. We usually advise stool testing after a few weeks of microbiome support. This helps check the impact of treatment, ensures the most accurate advice, and informs any treatment plans going forward.

If you are about to take a course of antibiotics or have recently completed one, please get in contact for microbiome support.

Vicky Ellenport BHSc NUT is a registered Clinical Nutritionist and Microbiome Analyst.

You can find out more about consultations with her here:

Vicky Ellenport | The Microbiome Group

References

Elvers KT, et al. (2020) Antibiotic-induced changes in the human gut microbiota for the most commonly prescribed antibiotics in primary care in the UK: a systematic review. BMJ Open. 10.1136/bmjopen-2019-035677

John D, et al. (2024). A double-blind, randomized, placebo-controlled study assessing the impact of probiotic supplementation on antibiotic-induced changes in the gut microbiome. Frontiers in Microbiomes, 3. https://doi.org/10.3389/frmbi.2024.1359580

Kennedy, M.S. et al. (2025) Diet outperforms microbial transplant to drive microbiome recovery in mice. Nature. https://doi.org/10.1038/s41586-025-08937-9

Palleja, A. et al. (2018) Recovery of gut microbiota of healthy adults following antibiotic exposure. Nat Microbiol 3. https://doi.org/10.1038/s41564-018-0257-9