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Antibiotic perturbations to the gut microbiome

Nature Reviews Microbiology volume 21, pages 772–788 (2023)Cite this article

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Abstract

Antibiotic-mediated perturbation of the gut microbiome is associated with numerous infectious and autoimmune diseases of the gastrointestinal tract. Yet, as the gut microbiome is a complex ecological network of microorganisms, the effects of antibiotics can be highly variable. With the advent of multi-omic approaches for systems-level profiling of microbial communities, we are beginning to identify microbiome-intrinsic and microbiome-extrinsic factors that affect microbiome dynamics during antibiotic exposure and subsequent recovery. In this Review, we discuss factors that influence restructuring of the gut microbiome on antibiotic exposure. We present an overview of the currently complex picture of treatment-induced changes to the microbial community and highlight essential considerations for future investigations of antibiotic-specific outcomes. Finally, we provide a synopsis of available strategies to minimize antibiotic-induced damage or to restore the pretreatment architectures of the gut microbial community.

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Fig. 1: Antibiotic-mediated destruction of the gut microbiome opens an opportunistic niche.
Fig. 2: Integrated understanding of how antibiotics remodel the microbiome.
Fig. 3: Assessing the effect of antibiotics on horizontal gene transfer rates.
Fig. 4: Approaches aimed at maintaining or restoring gut microbiome structure on antibiotic treatment.

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Acknowledgements

Work in the authors’ laboratory was supported in part by awards to G.D. through the National Institute of Allergy and Infectious Diseases (NIAID; award numbers U01AI123394 and R01AI155893), the Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD; award number R01HD092414), and the National Center for Complementary and Integrative Health (NCCIH; award number R01AT009741) of the National Institutes of Health (NIH); through the National Institute for Occupational Safety and Health (NIOSH) of the US Centers for Disease Control and Prevention (CDC; award number R01OH011578); and through the Agency for Healthcare Research and Quality (AHRQ) of the US Department of Health & Human Services (DHHS; award number R01HS027621). S.R.S.F. was supported by an award from Paediatric Gastroenterology Research Training Program (T32DK077653) through the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding agencies.

Author information

Author notes

  1. These authors contributed equally: Skye R. S. Fishbein, Bejan Mahmud.

Authors and Affiliations

  1. The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA

    Skye R. S. Fishbein, Bejan Mahmud & Gautam Dantas

  2. Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA

    Skye R. S. Fishbein & Gautam Dantas

  3. Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA

    Gautam Dantas

  4. Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA

    Gautam Dantas

  5. Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA

    Gautam Dantas

Authors
  1. Skye R. S. Fishbein
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  2. Bejan Mahmud
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  3. Gautam Dantas
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Contributions

S.R.S.F. and B.M. researched data for the article. S.R.S.F., B.M. and G.D. substantially contributed to discussion of content, wrote the article, and reviewed and edited the manuscript before submission.

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Correspondence to Gautam Dantas.

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Fishbein, S.R.S., Mahmud, B. & Dantas, G. Antibiotic perturbations to the gut microbiome. Nat Rev Microbiol 21, 772–788 (2023). https://doi.org/10.1038/s41579-023-00933-y

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