Antibiotic perturbations to the gut microbiome

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. In this Review, Fishbein, Mahmud and Dantas discuss factors that influence restructuring of the gut microbiome on antibiotic exposure, and they explore promising therapeutic avenues aimed at minimizing antibiotic-induced damage to the microbiome or restoring the community structure post-treatment.

Automated summary

Antibiotic exposure can significantly disrupt the gut microbiome, leading to various infectious and autoimmune diseases. However, the effects of antibiotics on the microbiome can be highly variable due to its complex ecological network. Recent advancements in multi-omic approaches have allowed us to identify intrinsic and extrinsic factors that influence microbiome dynamics during antibiotic treatment and recovery. This review discusses the factors that affect the restructuring of the gut microbiome on antibiotic exposure and highlights important considerations for future antibiotic-specific studies. Additionally, potential strategies to minimize antibiotic-induced damage or restore the pre-treatment architecture of the gut microbial community are also explored.