Antibiotics and the gut microbiome

While antibiotics are effective in treating infections, their unintended impact on the gut microbiome increasingly recognised. Patients may experience gastrointestinal symptoms, such as bloating, cramping, or diarrhoea, during or after antibiotic use. Here’s how they can affect the gut microbiota, and how GPS can support patients’ digestive health.

Antibiotic-induced dysbiosis

Broad-spectrum antibiotics can significantly disrupt the gut microbiota by reducing species diversity, altering microbial metabolic activity, and promoting antibiotic-resistant organisms.¹ Such changes are key contributors to antibiotic-associated diarrhoea (AAD) and increase the risk of recurrent Clostridioides difficile infections.¹

Beyond short-term complications, emerging research highlights the role of antibiotic-induced dysbiosis in the pathophysiology of functional gastrointestinal disorders, particularly post-infectious irritable bowel syndrome (PI-IBS).²^,³ There is emerging research in cohort studies that suggest a strong association between antibiotic exposure and increased risk of IBS.³ The microbial changes induced by antibiotics, namely reduced diversity and altered community structure, appear to mirror the shifts observed in patients with IBS.³

These findings highlight the importance of gut microbial resilience, especially in patients with a history of GI sensitivity or recent gastrointestinal infections.

Evidence for probiotics

Probiotics may help reduce the risk of AAD, particularly in children and older adults.⁵ The following strains have demonstrated benefit in clinical trials:

• Lactobacillus rhamnosus GG (LGG)
• Saccharomyces boulardii CNCM I-745
• L. acidophilus CL1285 + L. casei LBC80R + L. rhamnosus CLR2

Strain specificity and adequate dosing are essential for efficacy, and clinicians can refer to evidence-based resources such as the US Clinical Guide to Probiotic Products for updated recommendations. ⁶

Supporting microbial recovery

While probiotic use often receives attention, dietary strategies may also support the restoration of microbial diversity:

• Prebiotic-rich foods: Encouraging fibre intake from legumes, oats, onions, and green bananas may promote the regrowth of beneficial microbes and support short-chain fatty acid production.⁴
• Fermented foods: Foods such as kefir, sauerkraut, or kimchi contain live microbial species and may assist with maintaining gut microbial diversity.
• Diversity: Consuming a wide range of plant-based foods (e.g., fruits, vegetables, whole grains, legumes, nuts, and seeds) can help support a diverse microbiome. A greater variety of plant foods provides different types of fibres that encourage the growth of a broader range of beneficial microbes.⁷

GPs can support patients during antibiotic use by recommending specific probiotic strains to prevent antibiotic-associated diarrhoea and encouraging gut-friendly foods to maintain microbiota balance. Including fibre-rich foods, prebiotics, and fermented options can promote gut health and support overall digestive wellbeing during a course of antibiotics.

– Sarah Marko, Accredited Practising Dietitian

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References

1. Ramirez J, et al. Antibiotics as Major Disruptors of Gut Microbiota. Front Cell Infect Microbiol. 2020;10:572912. doi:10.3389/fcimb.2020.572912
2. Karakan T, et al. Gut-Brain-Microbiota Axis: Antibiotics and Functional Gastrointestinal Disorders. Nutrients. 2021;13(2):389. doi:10.3390/nu13020389
3. Mamieva Z, et al. Antibiotics, gut microbiota, and irritable bowel syndrome: What are the relations? World J Gastroenterol. 2022;28(12):1204-1219. doi:10.3748/wjg.v28.i12.1204
4. Fusco W, Lorenzo MB, Cintoni M, Porcari S, Rinninella E, Kaitsas F, Lener E, Mele MC, Gasbarrini A, Collado MC, Cammarota G, Ianiro G. Short-Chain Fatty-Acid-Producing Bacteria: Key Components of the Human Gut Microbiota. Nutrients. 2023 May 6;15(9):2211. doi: 10.3390/nu15092211. PMID: 37432351; PMCID: PMC10180739.
5. Goodman C, Keating G, Georgousopoulou E, Hespe C, Levett K. Probiotics for the prevention of antibiotic-associated diarrhoea: a systematic review and meta-analysis. BMJ Open. 2021 Aug 12;11(8):e043054. doi: 10.1136/bmjopen-2020-043054. PMID: 34385227; PMCID: PMC8362734.
6. Clinical Guide to Probiotic Products Available in the United States: 2024 Edition. (2024). Alliance for Education on Probiotics (AEP). Retrieved from https://usprobioticguide.com
7. McDonald, D., Hyde, E., Debelius, J. W., Morton, J. T., Gonzalez, A., Ackermann, G., Aksenov, A. A., Behsaz, B., Brennan, C., Chen, Y., DeRight Goldasich, L., Dorrestein, P. C., Dunn, R. R., Fahimipour, A. K., Gaffney, J., Gilbert, J. A., Gogul, G., Green, J. L., Hugenholtz, P., … Gunderson, B. (2018). American Gut: an Open Platform for Citizen Science Microbiome Research. MSystems. https://doi.org/10.1128/msystems.00031-18