Temporary dietary fiber depletion prompts a rapid and lasting gut microbiota restructuration in mice

The long-term alterations of the gut microbiota and host symbiosis after a dietary perturbation remain poorly understood and characterized. In this study, we investigate the impact of dietary fiber depletion on mice fed a diet with reduced fiber content (RFD) for 3 weeks followed by a standard chow diet for 6 weeks. The fiber deprivation was accompanied by an increase in mucolytic and sulphate-reducing bacteria in the gut. The activities of enzymes targeting glycans from the host mucus were increased accordingly, and those targeting plant fibers were decreased. On the host side, we report transiently higher quantities of host DNA in feces during the RFD. The RFD also led to the rarefaction of several gut bacterial taxa and an increase in others in the Muribaculaceae family which underwent a lasting reorganization. Six weeks after the return to the chow diet, the gut microbiota of mice that had consumed the RFD was different from that of mice exclusively consuming a chow diet. The coexistence of both bacterial configurations under the same conditions suggests the existence of alternative stable microbiota states.