How to protect and repair your microbiome alongside antibiotics
- Vicky Ellenport
- 23 hours ago
- 4 min read
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 and 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.
How antibiotics affect the microbiome
Antibiotics impact the gut microbiome by causing rapid reductions in microbial diversity and shifting 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 course of antibiotics.
After antibiotic treatment, gut bacterial populations can recover within a few weeks. However, some studies show it can take months to rebuild and 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, and your baseline composition strongly influences outcomes. Some people recover quickly, while others experience lingering digestive issues and other systemic symptoms.
Gut microbiome repair
As practitioners looking to support you to restore your microbiome, we focus on three things: 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 has plenty of plant foods. These are rich in fibre, including prebiotics, and contain different polyphenols that feed our beneficial bacteria.
Poor diets, lacking in prebiotics and polyphenols, can increase vulnerability to infection after antibiotic use, while conversely, plant-rich diets increase microbiome resilience to antibiotic treatment (Kennedy et al 2024).
Probiotics Research has shown that using probiotics alongside antibiotic treatment leads to a faster recovery of beneficial species (John et al. 2024). Probiotics do not re-seed, rather they support and communicate with other organisms in the gut, influencing bacterial behaviour, gene expression and immune responses.
We refer to clinical trial data to see what probiotic strains would be most supportive, including whether the antibiotics are targeting a respiratory infection or a gut infection. We commonly prescribe Saccharomyces boulardii CNCM I-745 (SB) and Lacticaseibacillus rhamnosus GG (LGG). Clinical trials have shown SB is very effective at reducing antibiotic-associated diarrhoea. SB is a yeast, so antibiotics (that only target bacteria) don't decrease its efficacy. SB doesn’t decrease the effectiveness of antibiotics either. For safety reasons, there are some cases where we wouldn’t recommend SB, including where someone’s health is very frail or where there are deep puncture wounds or cannulas in use.
Clinical trials show LGG protects against antibiotic-induced changes in the microbiome, reduces inflammation markers and positively influences microbiome balance. However, LGG is also impacted by antibiotics, so this requires frequent, high doses and timing carefully 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. Prebiotics have been shown in human studies to increase populations of beneficial bacteria and to promote the production of health-promoting short-chain fatty acids, particularly butyrate.
Prebiotics are found naturally in certain plant foods, but for protecting the gut microbiome from antibiotic-induced changes and for encouraging large-scale and long-term shifts in the gut ecosystem, we recommend prebiotic supplements (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 different 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 and help prevent antibiotic-related diarrhea. Inulin/FOS feeds up 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, and so we consider an individual’s microbiome profile, health history, diet, lifestyle, symptoms and other needs in order 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, but our recommendations may not be so well targeted.
Tracking progress
Gut bacterial populations can fluctuate rapidly for several weeks after the course of antibiotics is completed. We usually advise stool testing after a few weeks of microbiome support to check the impact of treatment, ensure the most accurate advice and inform any treatment plans going forward.
If you are about to take a course of antibiotics, or have recently completed a course, 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:
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.
Kennedy, M.S. et al. (2025) Diet outperforms microbial transplant to drive microbiome recovery in mice. Nature.
Palleja, A. et al. (2018) Recovery of gut microbiota of healthy adults following antibiotic exposure. Nat Microbiol 3.
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