Beyond the gut microbe: Rethinking infection, microbiome harmony, and the one-health continuum

Core Tip

Core Tip: Advances in culture and sequencing have expanded microbial detection, but presence does not equal pathogenicity. Many infections reflect disruption of the human microbiome rather than invasion by a novel pathogen. Misinterpretation of isolates drives antimicrobial misuse, resistance, and ecological harm. This opinion proposes an eight-question, clinically grounded framework to distinguish pathogens from non-pathogens by integrating host site and response, ecological context, contamination assessment, and transparent reporting. Applying this approach aligns infectious-disease practice with diagnostic stewardship, one health principles, and preservation of microbial harmony from individual patients to planetary health.