Biosynthetic potential and immune defenses across microbiomes: from ecology to biotechnology

Microbes form complex communities that sustain Earth systems, underpin the health of animals and plants, and fuel biotechnological applications. These communities, or microbiomes, are shaped by interactions between microbes, their viruses, and their hosts. Such interactions depend on genomic pathways producing bioactive natural products (biosynthetic potential) or encoding antiviral systems (immune defenses)—both key sources for therapeutic development. However, the systematic assessment of biosynthetic potential and immune defenses in environmental microbiomes has been hindered by the lack of genomic resources. This gap restricts our ecological understanding and limits access to the discovery potential of these microbiomes. Here, we leveraged sequencing data (metagenomes), including from the Tara Oceans and Tara Pacific expeditions, to generate global scale genomic resources. Focusing on the open ocean and coral reefs microbiomes, we found a diverse and novel biosynthetic potential as well as novel lineages of bacterial superproducers. We then show that these results can guide new enzymology and bioactive compounds discovery as well as shed light on ecological interactions in these microbiomes. While paving the way for studying microbial immunity at global scale, this work also highlights the molecular resources at stake under anthropogenic environmental changes and coral reef decline.