Simulating distal gut mucosal and luminal communities using packed-column biofilm reactors and an in vitro chemostat model

•Characterized planktonic and biofilm communities from a distal gut chemostat model.•Planktonic and biofilm communities were complex and reproducible.•Communities had distinct compositions, were representative of in vivo communities.•Communities responded to clindamycin-induced perturbation in distinctive ways.•This system was a useful model to study biofilm communities in vitro.

In vivo studies of human mucosal gut microbiota are often limited to end-point analyses and confounded by bowel cleansing procedures. Therefore, we used biofilm reactors to incorporate a simulated mucosal environment into an in vitro gut chemostat model. Communities developed were complex, reproducible, distinct, and representative of in vivo communities.