Fig. 1

Antibiotic perturbation to the microbiome needs to be considered in context. Certain factors are important to consider throughout life (overarching factors). Other factors such as diet and the functional and species diversity and redundancy are important to consider when the antibiotic perturbation is applied. The duration, spectrum, and route of antibiotics are vitally important in the context of how the microbiome responds during an intervention. The post-antibiotic environment including availability and colonization of pathogens, frequency of horizontal gene transfer (HGT), MDROs, and beneficial microbes is important to consider the resilience and response after antibiotic cessation. These factors influence the structure and function of the microbiome before, during, and after antibiotics throughout life. Created with BioRender