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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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.
The authors declare no competing interests.
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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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