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Significance The vast numbers of microbes that reside in the intestines of humans and other animals influence normal physiological functions and, when perturbed, can contribute to many disorders. Antibiotics can dramatically alter gut communities, even at concentrations far below lethal doses, for reasons that remain unclear. We directly imaged native bacterial species inside living larval zebrafish as they reacted to low concentrations of the common antibiotic ciprofloxacin. We found that antibiotics enhanced aggregation of live bacterial cells, resulting in their increased expulsion from the gut by the intestine’s mechanical contractions. Our observations and biophysical model suggest that gut bacterial populations may be especially sensitive to environmental antibiotic contamination, as cell-scale responses are amplified by the material transport characteristic of gastrointestinal systems.

Sublethal antibiotics collapse gut bacterial populations by enhancing aggregation and expulsion