Abstract
Even short courses of antibiotics are known to reduce gut microbiome diversity. However, there has been limited mathematical modelling of the associated dynamical time-response. Here, we take inspiration from a ‘stability landscape’ schematic and develop an impulse-response model of antibiotic perturbation. We fit this model to previously published data where individuals took a ten-day course of antibiotics (clindamycin or ciprofloxacin) and were sampled up to a year afterwards. By fitting an extended model allowing for a transition to an alternative stable state, we find support for a long-term transition to an alternative community state one year after taking antibiotics. This implies that a single treatment of antibiotics not only reduces the diversity of the gut flora for up to a year but also alters its composition, possibly indefinitely. Our results provide quantitative support for a conceptual picture of the gut microbiome and demonstrate that simple models can provide biological insight.
