The effect of the mycotoxins deoxynivalenol (DON) and zearalenone (ZEN) on the gut microbiome of 15 weaners were analysed. Animals were fed for 28 days with low and high dosages of the toxins. Animals of the control group did not receive any mycotoxin-spiked feed. The gut metaproteome composition shifted due to the high dosages of the toxins compared to the control and low mycotoxin groups and it was also more similar between the animals that received high dosages of the mycotoxins.