The individual response to antibiotics and diet - insights into gut microbial resilience and host metabolism

Antibiotic use disrupts microbial composition and activity in humans, but whether this disruption in turn affects host metabolic health is unclear. Cohort studies show associations between antibiotic use and an increased risk of developing obesity and type 2 diabetes mellitus. Here, we review available clinical trials and show the disruptive effect of antibiotic use on the gut microbiome in humans, as well as its impact on bile acid metabolism and microbial metabolites such as short-chain fatty acids. Placebo-controlled human studies do not show a consistent effect of antibiotic use on body weight and insulin sensitivity at a population level, but rather an individual-specific or subgroup-specific response. This response to antibiotic use is affected by the resistance and resilience of the gut microbiome, factors that determine the extent of disruption and the speed of recovery afterwards. Nutritional strategies to improve the composition and functionality of the gut microbiome, as well as its recovery after antibiotic use (for instance, with prebiotics), require a personalized approach to increase their efficacy. Improved insights into key factors that influence the individual-specific response to antibiotics and dietary intervention may lead to better efficacy in reversing or preventing antibiotic-induced microbial dysbiosis as well as strategies for preventing cardiometabolic diseases.This Review discusses the effect of antibiotic-induced perturbations of the gut microbiome on host metabolic health. The authors outline factors that might influence the response to antibiotic use and highlight prebiotic strategies that could improve microbial composition and modulate microbial recovery.Antibiotic use disrupts gut microbial composition and diversity in humans.Observational studies show associations between antibiotic use and an increased risk of weight gain and development of type 2 diabetes mellitus.Short-term placebo-controlled studies do not show a consistent effect of antibiotic-induced disruptions of the gut microbiome on body weight and insulin sensitivity in humans but suggest an individual-specific or subgroup-specific response.The individual-specific or subgroup-specific response to antibiotic use is determined by the resistance and resilience of the gut microbiome, among other factors.Dietary substrates such as prebiotics modulate gut microbial composition and function and might be used to limit the detrimental effects of antibiotic use, but will require a personalized approach to increase their efficacy.More insight into the personalized interaction between the gut microbiome and host metabolism in response to prebiotics and antibiotics might lead to effective prevention of cardiometabolic diseases.