In humans and other animals, the gut comprises a diverse ecosystem of microbiota that supports a range of physiological functions and contributes to disease when perturbed.

Recent studies have suggested that antibiotics can cause widespread perturbations to the gut microbiome even at sublethal doses, but the mechanisms remain unclear.

Researchers report tin PNAS the use of direct imaging to track how gut bacterial species in larval zebrafish respond to low concentrations of ciprofloxacin, a common antibiotic.

The authors found that antibiotics drive greater losses in slow-growing, resident bacterial communities by causing viable bacterial cells to aggregate into large clusters, which are expelled by the mechanical actions of the intestines.

Based on these qualitative results, the authors present a quantitative biophysical model that reproduces the data and potentially offers a general framework for studying gut microbiome homeostasis.

The study provides a mechanism by which slow-growing, resident gut bacterial populations can be driven to collapse by sublethal antibiotic concentrations, such as those that accumulate in the environment due to agricultural and biomedical uses, according to the authors.

https://www.pnas.org/content/early/2019/10/04/1907567116