Antibiotic-perturbed microbiota and the role of probiotics

Hania Szajewska^#¹, Karen P Scott^#², Tim de Meij³, Sofia K Forslund-Startceva^{4

5

6

7}, Rob Knight^{8

9

10

11

12}, Omry Koren¹³, Paul Little¹⁴, Bradley C Johnston^{15

16}, Jan Łukasik¹, Jotham Suez¹⁷, Daniel J Tancredi¹⁸, Mary Ellen Sanders¹⁹

Affiliations

¹ Department of Paediatrics, The Medical University of Warsaw, Warsaw, Poland.
² Rowett Institute, University of Aberdeen, Aberdeen, UK.
³ Department of Paediatric Gastroenterology, Emma Children's Hospital, Amsterdam UMC, Academic Medical Centre, Amsterdam, The Netherlands.
⁴ Experimental and Clinical Research Center, a joint cooperation of Max Delbruck Center for Molecular Medicine and Charité - Universitätsmedizin Berlin, Berlin, Germany.
⁵ Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
⁶ Max Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
⁷ DZHK (German Centre for Cardiovascular Research), Berlin, Germany.
⁸ Department of Pediatrics, University of California San Diego, San Diego, CA, USA.
⁹ Department of Computer Science & Engineering, University of California San Diego, San Diego, CA, USA.
¹⁰ Shu Chien - Gene Lay Department of Bioengineering, University of California San Diego, San Diego, CA, USA.
¹¹ Halıcıoğlu Data Science Institute, University of California San Diego, San Diego, CA, USA.
¹² Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA.
¹³ Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel.
¹⁴ Primary Care Research Centre, University of Southampton, Southampton, UK.
¹⁵ Department of Nutrition, College of Agriculture and Life Sciences, Texas A&M University, College Station, TX, USA.
¹⁶ Department of Epidemiology and Biostatistics, School of Public Health, Texas A&M University, College Station, TX, USA.
¹⁷ W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
¹⁸ Department of Pediatrics, School of Medicine, University of California Davis, Sacramento, CA, USA.
¹⁹ International Scientific Association for Probiotics and Prebiotics, Consulting Scientific Advisor, Centennial, CO, USA. maryellen@isappscience.org.

^# Contributed equally.

PMID: 39663462
DOI: 10.1038/s41575-024-01023-x

Review

Antibiotic-perturbed microbiota and the role of probiotics

Hania Szajewska et al. Nat Rev Gastroenterol Hepatol. 2025 Mar.

. 2025 Mar;22(3):155-172.

doi: 10.1038/s41575-024-01023-x. Epub 2024 Dec 11.

Authors

Affiliations

¹ Department of Paediatrics, The Medical University of Warsaw, Warsaw, Poland.
² Rowett Institute, University of Aberdeen, Aberdeen, UK.
³ Department of Paediatric Gastroenterology, Emma Children's Hospital, Amsterdam UMC, Academic Medical Centre, Amsterdam, The Netherlands.
⁴ Experimental and Clinical Research Center, a joint cooperation of Max Delbruck Center for Molecular Medicine and Charité - Universitätsmedizin Berlin, Berlin, Germany.
⁵ Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
⁶ Max Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
⁷ DZHK (German Centre for Cardiovascular Research), Berlin, Germany.
⁸ Department of Pediatrics, University of California San Diego, San Diego, CA, USA.
⁹ Department of Computer Science & Engineering, University of California San Diego, San Diego, CA, USA.
¹⁰ Shu Chien - Gene Lay Department of Bioengineering, University of California San Diego, San Diego, CA, USA.
¹¹ Halıcıoğlu Data Science Institute, University of California San Diego, San Diego, CA, USA.
¹² Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA.
¹³ Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel.
¹⁴ Primary Care Research Centre, University of Southampton, Southampton, UK.
¹⁵ Department of Nutrition, College of Agriculture and Life Sciences, Texas A&M University, College Station, TX, USA.
¹⁶ Department of Epidemiology and Biostatistics, School of Public Health, Texas A&M University, College Station, TX, USA.
¹⁷ W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
¹⁸ Department of Pediatrics, School of Medicine, University of California Davis, Sacramento, CA, USA.
¹⁹ International Scientific Association for Probiotics and Prebiotics, Consulting Scientific Advisor, Centennial, CO, USA. maryellen@isappscience.org.

^# Contributed equally.

PMID: 39663462
DOI: 10.1038/s41575-024-01023-x

Abstract

The disruptive effect of antibiotics on the composition and function of the human microbiota is well established. However, the hypothesis that probiotics can help restore the antibiotic-disrupted microbiota has been advanced, with little consideration of the strength of evidence supporting it. Some clinical data suggest that probiotics can reduce antibiotic-related side effects, including Clostridioides difficile-associated diarrhoea, but there are no data that causally link these clinical effects to microbiota protection or recovery. Substantial challenges hinder attempts to address this hypothesis, including the absence of consensus on the composition of a 'normal' microbiota, non-standardized and evolving microbiome measurement methods, and substantial inter-individual microbiota variation. In this Review, we explore these complexities. First, we review the known benefits and risks of antibiotics, the effect of antibiotics on the human microbiota, the resilience and adaptability of the microbiota, and how microbiota restoration might be defined and measured. Subsequently, we explore the evidence for the efficacy of probiotics in preventing disruption or aiding microbiota recovery post-antibiotic treatment. Finally, we offer insights into the current state of research and suggest directions for future research.

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Conflict of interest statement

Competing interests: H.S. has participated as a clinical investigator or advisory board member or consultant or speaker for Arla, BioGaia, Biocodex, Danone, Dicofarm, Nestlé, Nestlé Nutrition Institute, Nutricia, Mead Johnson/RB, and Winclove. H.S. serves as a board member of the International Scientific Association for Probiotics and Prebiotics (ISAPP; unpaid, volunteer position). K.P.S. serves as a board member of the ISAPP (unpaid, volunteer position). T.d.M. received an unrestricted research grant from Winclove and Nutricia and serves as consulting scientific adviser for Nutricia. S.K.F.-S. has no conflicts to declare. R.K. declares the following activities: Gencirq (stock and scientific advisory board member), DayTwo (consultant and scientific advisory board member), Cybele (stock and consultant), Biomesense (stock, consultant, scientific advisory board member), Micronoma (stock, scientific advisory board member, co-founder), and Biota (stock, co-founder). O.K. declares no competing interests. P.L. declares no competing interests. B.C.J. received a grant from Texas A&M AgriLife Research (2019–2020) to fund investigator-initiated research related to saturated and polyunsaturated fats as part of his start-up funding at Texas A&M University. The grant was from Texas A&M AgriLife institutional funds from interest and investment earnings, not a sponsoring organization, industry or company. J.Ł. received support from Winclove for conducting a clinical trial. J.S. declares no competing interests. D.J.T. serves as a statistical consultant for Deerland Probiotics & Enzymes, International Flavors and Fragrances, and Synbiotic Health, and as a member of the scientific advisory board for Deerland Probiotics & Enzymes. He serves as a board member of the ISAPP (unpaid, volunteer position). M.E.S. serves as consulting scientific adviser and formerly as executive science officer for the ISAPP; she has consulted with Bayer, Pepsico, and the Bill and Melinda Gates Foundation; served on scientific advisory boards for Institute for Advancement of Food and Nutrition Sciences, United States Pharmacopeia, Danone NA, Sanofi and Cargill; and has been compensated for giving talks for Xpeer, Sanofi, European Federation of Association of Dietitians and Associated British Foods.

References

1. 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 11, e043054 (2021). - PubMed - PMC - DOI
1. Guo, Q., Goldenberg, J. Z., Humphrey, C., El Dib, R. & Johnston, B. C. Probiotics for the prevention of pediatric antibiotic-associated diarrhea. Cochrane Database Syst. Rev. 4, CD004827 (2019). - PubMed
1. Ma, Y. et al. Which probiotic has the best effect on preventing Clostridium difficile-associated diarrhea? A systematic review and network meta-analysis. J. Dig. Dis. 21, 69–80 (2020). - PubMed - DOI
1. Su, G. L. et al. AGA clinical practice guidelines on the role of probiotics in the management of gastrointestinal disorders. Gastroenterology 159, 697–705 (2020). - PubMed - DOI
1. Goldenberg, J. Z. et al. Probiotics for the prevention of Clostridium difficile-associated diarrhea in adults and children. Cochrane Database Syst. Rev. 12, CD006095 (2017). - PubMed

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Antibiotic-perturbed microbiota and the role of probiotics

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Antibiotic-perturbed microbiota and the role of probiotics

Authors

Affiliations

Abstract

Conflict of interest statement

References

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Medical