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How to Support Gut Health During Antibiotic Use

May 2, 2023 3 mins reading time

Antibiotics can be a double-edged sword - what can be done to help restore your digestive balance, support gut health, and help maintain beneficial gut flora?

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Inside a healthy digestive tract there are trillions of bacteria, and other microorganisms otherwise known as the gut microbiome 2. A more diverse and plentiful gut microbiome forms the foundation of a healthy immune system and general health and wellbeing3. Gut bacteria can be reduced by following a course of antibiotics, and bacteria diversity can also be impacted 4,5. Your healthy gut microbiome has some level of resilience, and can return to its previous composition, though it is not always fully restored. 

So what can be done to help restore your digestive balance, support gut health, and  help maintain beneficial gut flora during antibiotic use?

A healthy lifestyle is key. Look at your stress, sleep, physical activity and diet.

Meditate, find some time for yourself, or something else that you find relaxes you.

Aim for 7-9hours of unbroken sleep overnight 8

Exercise regularly. 150 minutes per week of moderate exercise is the official recommendation 8, though what you can manage is better than nothing. Increase your exercise slowly. 

Avoid unhealthy lifestyle choices. To learn more, read our article about common lifestyle choices that affect your gut health.

Your diet is the most important modifiable factor that can improve the composition of bacteria living in your gut 2,8. A balanced diet, focusing mostly on plant foods helps to fuel and support your gut microbiome. Aim for plenty of fruits, vegetables, wholegrains, legumes, nuts and seeds. These foods contain fibre and boost your prebiotic intake. 

Probiotics are another beneficial way to support gut health, and help to maintain beneficial gut flora during antibiotic use 1. Probiotics are the good bacteria that live in your gut. Consuming them can help to restore the digestive balance by allowing the good bacteria to thrive 1,4. Probiotics are found naturally in fermented foods such as yoghurt, kefir, kimchi, sauerkraut and kombucha or can also be taken in supplement form. The catch with probiotics is that to have a beneficial impact on your gastrointestinal tract, they need to make it through your stomach acid and small intestine to the large intestine where your gut microbes are. Not everyone can tolerate large quantities of probiotic rich foods, so that is where a supplement can be of benefit. The most common probiotic strains used in supplements are lactobacillus and bifidobacterium bacteria as they can survive digestion and reach the gut for general wellbeing. 

Always read the label. Follow the directions for use. If symptoms persist, talk to your health professional.


1. De Gunzburg et al, (2018). Protection of Human Gut Microbiome From Antibiotics, The Journal of Infections Diseases, Vol 217 (4) pg 628-636

2. Cresci, G & Izzo, K, 2018 Chapter 4: Gut Microbiome “Adult Short Bowel Syndrome Nutritional, Medical and Surgical Management”, American Press 

3. Manley, G, Lee, Y and Zhang Y, 2020. Chapter 4 – Gut microbiota and immunology of the gastrointestinal tract. Clinical and Basic Neurogastroenterology and Motility. Academic Press 2020

4. Dethlefsen et al, (2008). The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing, PLoS Biology. Vol 6:e280

5. Dethlefsen, L., and Relman, D. A. (2011). Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation, Proceedings of the National Academy of Science U.S.A. 108(Suppl. 1), pg4554–4561

6. De La Cochetiere et al, (2005). Resilience of the dominant human fecal microbiota upon short-course antibiotic challenge, Journal of Clinical Microbiol, Vol 43, pg5588–5592

7. Jernberg et al, (2007). Long-term ecological impacts of antibiotic administration on the human intestinal microbiota, Multidisciplinary Journal of Microbial Ecology. Vol 1, pg56–66

8. Shreiner, A,B, Kao, J, Y, Young, V, B, 2016. The gut microbiome in health and in disease, Current Opinion in Gastroenterology. Vol 31 (1) pg 69-75


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