Microbiome Stewardship: re-defining high-risk antibiotics

Healthy human gut microbiomes are essential for overall wellness and must be safeguarded by incorporating preservation into clinical decision-making processes and policies. Given the paradigm shift of single-acting bacteria causing infectious diseases to a new understanding of interacting communities of bacteria that build up stable network structures and functions to prevent diseases, a One-Health umbrella has emerged that interconnects all life through their respective microbiota. The preservation of this homeostasis is a term coined Microbiome Stewardship. Although multi-causal, antimicrobial use has the most disruptive effect on the microbiome, quickly changing microbiome structure and function as well as promoting antimicrobial resistant gene (ARG) generation and abundance. Clinically, Microbiome Stewardship could lead to new strategies around antimicrobial administration route and enhanced consideration of whether anaerobic coverage is required, especially routine empiric coverage. Antimicrobial resistance (AMR) and perturbation of the microbiome effect short- and long-term patient outcomes and should drive the drug development process and repurposing of current antimicrobials. In the new scientific era of systems biology providing increasingly accessible and cost-effective studies, evaluation of the microbiome during the antimicrobial drug development process should become the new standard. Microbiome Stewardship incorporation into clinical practice and drug development will advance patient outcomes and AMR prevention on an individual and public health platform.