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Climate change is now considered to be the greatest threat to biodiversity and ecological networks, but its impacts on the bacterial communities associated with plants and animals remain largely unknown. Here, we studied the consequences of climate warming on the gut bacterial communities of an ectotherm, the common lizard (Zootoca vivipara), using a semi-natural experimental approach. We found that 2–3 °C warmer climates cause a 34% loss of populations’ microbiota diversity, with possible negative consequences for host survival.