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Antibiotics have undoubtedly revolutionised modern medicine, saving countless lives by combating  bacterial infections. However, their negative impact on the balance of our gut microbiota is well-documented. As nutrition professionals, we have a key role in guiding individuals towards beneficial strategies to optimise their gut health after antibiotic treatment, says Jess English, RD.

In my NHD blog, I aim to provide evidence-based insights and nutritional strategies to support gut health after treatment with antibiotics.


Our gut microbiota plays a crucial role in maintaining overall health; from digestion to immune function – while its role in mental health (from maternal health onwards) continues to be investigated.1

Antibiotics, while essential for treating infections, indiscriminately target both harmful and beneficial bacteria. This has been shown to result in microbial dysbiosis; a decreased diversity of microbial species and altered metabolic activity and immune function.2 This dysbiosis may also lead to recurrent infections through a proliferation of potentially harmful bacteria such as c. difficile.3


1. Probiotics and fermented foods

Probiotics are live microorganisms found in food and supplements that, when consumed in adequate amounts, may have a positive impact on the gut microbiota by restoring the balance of beneficial bacteria.

Probiotics may also improve gut function and reduce diarrhoea associated with antibiotic use.4,5 More research is needed as to whether they are of benefit in reducing the spread of antibiotic-resistant strains of bacteria, with a need for a uniform approach to sampling. Any benefit appears to be specific to individuals, highlighting the need for genetically tailored probiotic prescriptions.6

Overall, research into the use of probiotics for restoring gut microbiota after antibiotics is ongoing, and while the results are generally promising, there is not yet a one-size-fits-all approach.

The effectiveness of probiotics appears to depend on various factors, including:

  • Strain-specific effects: Different probiotic strains may have varying effects on the gut microbiota, so it may be beneficial to choose the right probiotic strain or combination of strains for a particular condition.
  • Timing: Some research suggests that taking probiotics during antibiotic treatment may reduce the severity of disruption to the gut microbiota.7 Conversely, there is some evidence that taking probiotic after antibiotics may compromise gut mucosal recovery.8
  • Dosage: The effectiveness of probiotics may be dose-dependent and delivery method-dependent. Higher doses may have more significant effects, but this can also vary based on the individual.6
  • Individual variation: Each person's gut microbiota is unique, and the response to probiotics may vary from person to person.

Probiotics in food: Encouraging the consumption of probiotic-rich fermented foods may also aid in replenishing beneficial bacteria. Probiotic-rich foods like yoghurt, kefir, sauerkraut, kimchi, and kombucha introduce live microorganisms to the gut, potentially supporting gut health and promoting growth of beneficial bacteria. Though it’s not currently clear how many of these make it to the large intestine where they could influence microbiota, there is evidence that some do, or may provide other benefits.8

2. Prebiotic-rich foods

Prebiotics are a type of fibre that pass through the gastrointestinal tract undigested. Once they reach the large intestine, they can promote the growth of beneficial strains of bacteria.

Fermentation of prebiotics in the gut produces short-chain fatty acids (SCFAs), such as butyrate, which improve gut integrity and function.9 In contrast, antibiotics have been shown in some cases to reduce this level of butyrate production – potentially due to reduced levels of ‘beneficial’ bacteria.10

Foods such as garlic, onions, leeks, asparagus, bananas, chicory, fennel and even dark chocolate can stimulate the growth of beneficial bacteria.

3. Fibre

Adequate varied dietary fibre intake is important as it also contributes to the production of SCFAs and the increased variety of bacteria in our gut.9 As always, it’s important to build this up slowly, ensuring sufficient fluid intake.


The use of specific probiotics may be beneficial to support restoration of gut health after antibiotics. As research advances, we may see specific probiotics prescribed alongside antibiotics more regularly, including personalised prescriptions based on metagenomics.

Though limited to US availability and commercially funded, the US Probiotic Guide11 may be a helpful place to start for those wanting a list of available probiotics and their uses.

Prebiotic foods can also help to restore balance in the gut, bearing in mind that this needn't involve expensive, branded products or supplements – but can be tailored to an individual’s needs.

These tactics can be implemented alongside advice around a varied diet rich in fibre, including prebiotic-rich foods.

Overall, there are many strategies that we can use to help clients in supporting their gut health after antibiotic treatment. Interestingly, while we can assure clients that these interventions are likely to lead to positive health outcomes, it is reassuring to note that our gut microbiota appears to be mostly restored around four to eight weeks after cessation of antibiotics in many cases, without a targeted intervention.12


Jessica English, RD

Self-employed private practice dietitian with interests in IBS, maternal and child health and public health.

Website: www.mealsformotherhood.com
Instagram: @meals.for.motherhood



  1. Järbrink-Sehgal E, Andreasson A. The gut microbiota and mental health in adults. Curr Opin Neurobiol. 2020;62:102-114. doi:10.1016/j.conb.2020.01.016
  2. Ramirez J, Guarner F, Bustos Fernandez L, Maruy A, Sdepanian VL, Cohen H. Antibiotics as Major Disruptors of Gut Microbiota. Front Cell Infect Microbiol. 2020;10:572912. Published 2020 Nov 24. doi:10.3389/fcimb.2020.572912
  3. Parkes GC, Sanderson JD, Whelan K. The mechanisms and efficacy of probiotics in the prevention of Clostridium difficile-associated diarrhoea. Lancet Infect Dis. 2009;9:237-44
  4. McFarland LV. Meta-analysis of probiotics for the prevention of antibiotic associated diarrhea and the treatment of Clostridium difficile disease. Am. J. Gastroenterol. 2006;101:812-822.
  5. Hickson M, D'Souza AL, Muthu N, Rogers TR, Want S, Rajkumar C, Bulpitt CJ. Use of probiotic Lactobacillus preparation to prevent diarrhoea associated with antibiotics: randomised double blind placebo controlled trial. BMJ. 2007;335(7610):80
  6. Montassier, E., Valdés-Mas, R., Batard, E. et al. Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner. Nat Microbiol 6, 1043–1054 (2021). https://doi.org/10.1038/s41564-021-00920-0
  7. 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;11(8):e043054. Published 2021 Aug 12. doi:10.1136/bmjopen-2020-043054
  8. Bell V, Ferrão J, Pimentel L, Pintado M, Fernandes T. One Health, Fermented Foods, and Gut Microbiota. Foods. 2018;7(12):195. Published 2018 Dec 3. doi:10.3390/foods7120195
  9. Esgalhado M, Kemp JA, Damasceno NR, Fouque D, Mafra D. Short-chain fatty acids: a link between prebiotics and microbiota in chronic kidney disease. Future Microbiol. 2017;12:1413-1425. doi:10.2217/fmb-2017-0059
  10. Patangia DV, Anthony Ryan C, Dempsey E, Paul Ross R, Stanton C. Impact of antibiotics on the human microbiome and consequences for host health. Microbiologyopen. 2022;11(1):e1260. doi:10.1002/mbo3.1260
  11. Alliance for Education on Probiotics: The US Probiotic Guide (2023), available at: http://www.usprobioticguide.com/?utm_source=intro_pg&utm_medium=civ&utm_campaign=USA_CHART (accessed online 31/07/2023)
  12. Elvers KT, Wilson VJ, Hammond A, et al. 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. 2020;10(9):e035677. Published 2020 Sep 21. doi:10.1136/bmjopen-2019-035677


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