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We propose an eight-principle framework to distinguish pathogen from non-pathogen: (1) Clinical localization; (2) Temporal host response; (3) Exclusion of alternative sources; (4) Ecological context; (5) Host susceptibility; (6) Contamination assessment; (7) Transparent reporting of methods and quantitative thresholds; and (8) Ethical use of diagnostic technology. Adoption of this framework to any specialty, including gut, promotes accurate infection identification, stewardship, and transparency. 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