Direct impact of antibiotics on host immune response

Antibiotics are widely prescribed and used in animal studies because they are thought to target microorganisms while not affecting the host directly. Here, we treated germ-free (GF) and conventionally colonized (CONV) mice with vancomycin to determine whether antibiotics can affect host physiology directly. We found that vancomycin disrupted circadian immune system activity in the intestines of GF and CONV mice, in opposing manners. Interestingly, this disruption in GF mice was not driven by core-clock genes. Instead, we found that food intake primed the intestinal immune system for antigen presentation in a microbiota-independent manner and that this priming was subdued by vancomycin. Finally, we found that immune priming via food intake was correlated with blood glucose levels and that vancomycin treatment disrupted metabolic activity in the colons of GF mice. Thus, the host intestinal immune system anticipates ingestion of microbes via food, even in the absence of these microbes, and antibiotics directly disrupt this process.