Composition–Resistance Decoupling: Why Microbiome Recovery After Antibiotics Is Measured on the Wrong Clock

Antibiotic disturbance of the human microbiome is usually judged by whether community composition returns to baseline. We argue that this endpoint runs on the wrong clock. The same exposures, read at two levels, give opposite answers: composition recovers in weeks, while resistance persists for months. In a 2015 trial, salivary composition recovered within about 30 days while faecal communities stayed altered for up to 12 months; in a 2007 trial, one course of azithromycin or clarithromycin raised pharyngeal carriage of macrolide-resistant streptococci by 53·4 points at day 4 with azithromycin and 50·0 points at day 8 with clarithromycin, still above baseline at day 180. We call this asymmetry composition–resistance decoupling, and propose a minimum standard that measures both clocks, with denominators, until resistance returns to baseline.