Microbes form complex communities that sustain Earth systems, underpin human health, and fuel biotechnological applications. Those communities, or microbiomes, are under constant threat of infection by viruses and other genetic parasites. This immense evolutionary pressure led to a complex microbial immune system, which has received little attention in the context of natural microbiomes. Yet, to understand the impact of microbe–virus interactions on microbiome function as well as microbiome- or phage-based applications, it will be crucial to unravel the ecology of microbial immunity at the microbiome scale. Our group works at the interface of microbial immunity and microbial ecology, and uses computational biology and meta-omics technologies to elucidate how ecology shapes microbial immune strategies, from the deep ocean to the human gut.
