Paneth cell gene expression with and wihout zinc in different microbiome contexts (antibiotics, germ-free, normal)

We investigated the differences in paneth cell gene expression in different intestinal microbiome contexts and with and without zinc supplementation. We used mice housed in an SPF animal house that wre untreated, mice housed in ans SPF animal house that were treated with antobiotics for 3 weeks and germ-free mice to investigated the effect of the microbiome on paneth cell gene expression. Zinc is an essential element for paneth cell fuction. Mice of each group were further divide in zinc supplemented and non-zinc supplemented drinking water subgroups. This allowed us to check if zinc would enhance the differences between SPF, atibioicts and germ-free mice or reduce them. In total there are six groups of interest: SPF housed mice that recieved Milli-Q water or zinc supplemented water (3 biological replicates per group). SPF housed mice that recieved Milli-Q water or zinc supplemented water ans had their microbiome depleded with broad spectrum antibioics 3 wees before sampling (4 biological replicates per group). germ-free mice that recived Milli-Q water (3 biological replictes) or zinc supplemented water (4 biological replictes)