BPS2026 - Consequences of sub-inhibitory concentrations of antibiotics on model gut microbiomes in zebrafish

The gut microbiome is a diverse ecosystem that influences its host’s immune system, metabolism, and overall health. Though it is known that even subinhibitory concentrations of antibiotics can perturb the gut microbiome, the mechanisms underlying these effects and the relationship between the responses of individual species and the consequences for multi-species communities remain unclear. Much of our knowledge to date comes from in vitro studies, which may not mirror the biochemical and biophysical environment within a living organism. To address this, we have performed a series of experiments using larval zebrafish as a model organism, which allows germ-free derivation and inoculation with well-defined sets of bacterial species as well as live imaging. We consider model gut bacterial communities composed of one to three zebrafish-native bacterial species, exposed to one of two common antibiotics (ciprofloxacin or tetracycline) for 24 h. Dissection and plating provide measures of bacterial abundance, and live imaging using light sheet fluorescence microscopy reveals bacterial morphology and spatial organization. We find striking differences between in vitro and in vivo antibiotic responses, in some cases with inversion of competitive advantages among specific species pairs. Imaging shows correlations with changes in bacterial morphology and behavior, such as reduced motility, that influence the ability to persist in the gut. Our results suggest that in vitro characterizations are not predictive of the responses of gut microbiota to antibiotics, and that the use of model gut communities and investigation of the biophysical properties of microbes in vivo can help make sense of such responses.