What happens to your microbiome during a course of antibiotics?

Here’s what you can do to minimise the damage to get your gut health back on track fast.

By Neil Bridgeman
Aug 8, 2022 • 6 min read

Bacteria of the gut microbiota

It cannot be argued that the development of antibiotics is one of the greatest scientific achievements in medical history, however, the last 15 years have seen antibiotic usage surge by 65% during that time. It is only recently that we have begun to understand the impact that antibiotic treatment has on the human gut microbiota and the associated short and long term effects of that impact. 

Upfront, this is not an anti-antibiotics piece. It goes without saying that there are a multitude of infections that can and should be treated effectively with antibiotics that can’t necessarily be treated naturally or safely with plant or herbal medicines. But there are some simple hacks that will set you up for success if you undertake a course of antibiotics and help you recuperate faster.

“Behold, the trusty probiotic!”

Much of the research on the gut microbiota has been conducted in the last 5-10 years and each day brings a new study, with new insights on the interconnectedness and far-reaching impact these miraculous bugs in our gut have on our overall health and wellbeing.

The human gut microbiota is home to bacteria, fungi, protozoans, viruses and hardy bacteria-like organisms called archaeans. In fact, many strains call our gut home for decades, although their relative abundance can go up or down. Consider them long-term tenants!  

Our gut microbiota ostensibly have three jobs:

1/ To metabolise – they produce short chain fatty acids to fuel cellular turnover, synthesise vitamins like K and B12, influence nutrient absorption, as well as drug and bile acid metabolism

2/ To defend – they compete with pathogens for attachment sites in the gut (see the Carpark Analogy below), secrete antimicrobial compounds as well as secretory IgA production (pathogen defending immune complexes lining our gut mucosa)  

3/ To build, maintain & regulate – they maintain tight gut junctions to regulate what makes its way into our systemic blood stream from the gut, stimulate digestion and the movement of food through our gastrointestinal system as well as support the growth and turnover of our gut lining

“Pretty important stuff!”

Research in the field of the gut microbiota has confirmed that a loss of diversity amongst species within our gut leads to what is termed dysbiosis. It’s a term frequently used by nutritionists and specialists and describes the imbalance that can occur between the microbiota and its host (that’s us by the way). 

Antibiotic use is associated with reduced microbiota diversity which can increase the gut’s susceptibility to being overrun by infections, longer-term antibacterial resistance, increased allergic reactions, asthma, obesity, metabolic syndrome, mood disorders and diabetes. None of these is good news for the host! 

There is some good news. Baseline composition of the gut microbiota tends to be restored within about a month and half to roughly 6 months after the final antibiotic dose, however several strains appear not to recover. 

For up to 35% of those treated with antibiotics, antibiotic-associated diarrhoea (AAD) can be a frustrating and exhausting side-effect that can last up to 8 weeks after final dose. 

“Think of your gut microbiome a bit like a car park”

Think of your gut microbiome a bit like a car park. More often than not, you want the car park full of the right strains of beneficial bacteria so that pathogenic bacteria or microbes can’t invade and tip the balance into dysbiosis. Collectively, the reduced microbial diversity caused as a result of antibiotic treatment can facilitate this invasion and this is where probiotics can play a crucial role in keeping those car parking spaces full.

Probiotic supplementation alongside antibiotic treatment reduces the risk of AAD occurrence by ~42%. Lactobacillus helveticus and lactobacillus rhamnosus have been proven to reduce the relative occurrence and length of AAD in recent double-blind randomised controlled trials, as have other strain mixes consisting of Lactobacillus casei, rhamnosus and acidophilus. Equally as effective as these strains and unaffected by antibiotics is a handy probiotic yeast called Saccharomyces Boulardii. 

Each do their part by filling up those adhesion sites in the gut (aka the car park spots) and preventing pathogenic infections to take over. 

Optibac have an ‘On Antibiotics’ product which contains the strains mentioned above as well as Saccharomyces Boulardii. For best results and to keep those car park spaces full and diverse, consider using both during treatment. 

Of course, any use of supplementation should be done in conjunction with advice from your GP and qualified health professional. It should be noted that many supplements interact with prescription medications as well as other forms of supplements and foods. Play it safe, be armed with the latest information and seek advice where appropriate.


Elvers, K. Wilson, V. Hammond, A. 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 (9) https://doi.org/10.1136/bmjopen-2019-035677 

Evans, M., Salewski, R. P., Christman, M. C., Girard, S. A. et al. (2016) ‘Effectiveness of Lactobacillus helveticus and Lactobacillus rhamnosus for the management of antibiotic-associated diarrhoea in healthy adults: A randomised, double-blind, placebo-controlled trial’ British Journal of Nutrition, 116 (1), pp. 94–103  https://doi.org/10.1017/S0007114516001665

Hempel, S., Newberry, S. J., Maher, A. R. et al. (2012) ‘Probiotics for the Prevention and Treatment of Antibiotic-Associated Diarrhea: A Systematic Review and Meta-analysis’ JAMA, 307 (18), pp. 1959–1969 https://doi.org/10.1001/jama.2012.3507 

Klein, E. Van Boeckel, T. Martinez, E. et al (2018) ‘Global increase and geographic convergence in antibiotic consumption between 2000 and 2015’ Proceedings of the National Academy of Sciences of the United States of America, 115 (15), pp. 3463–3470 https://doi.org/10.1073/pnas.1717295115 

McFarland, L. (2010) ‘Systematic review and meta-analysis of saccharomyces boulardii in adult patients’ World Journal of Gastroenterology, 16 (18), pp. 2202–2222 https://doi.org/10.3748/wjg.v16.i18.2202 

Ramirez, J. Guarner, F. Bustos Fernandez, L. et al. (2020) ‘Antibiotics as Major Disruptors of Gut Microbiota. Frontiers in Cellular and Infection Microbiology, 10 https://doi.org/10.3389/fcimb.2020.572912 

Sniffen, J. McFarland, L. Evans, C. et al. (2018) ‘Choosing an appropriate probiotic product for your patient: An evidence-based practical guide’ PLoS ONE, 13 (12), pp. 1–22  https://doi.org/10.1371/journal.pone.0209205

DISCLAIMER: The information provided on this website is for informational purposes only and should not be used for diagnosis. It is not intended as a substitute for advice from your GP or other qualified health practitioner.

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