One way to study commensal fungi is to separate fungal from host genes using “shotgun” metagenomics,⁵ a sequencing technique that allows researchers to study the genomes of entire microbial communities without needing to culture them first. This has already made it possible to advance the study of the human skin mycobiome⁶, the fungal component of the microbiota.

However, the interactions themselves also need to be studied, which requires an understanding of community ecology: how organisms interact within specific habitats. New insights are making it possible to study commensal strains in animals in vivo — in the gut mycobiome of lab mice,⁷ for example. Beyond standard lab-mouse work, novel model systems like hydra are also being developed to study fungal interactions within microbial communities.

Such approaches will be required to understand important changes we are making to commensal relationships: fungi, for example, play a crucial role in promoting carbon capture and in agriculture. This may be changing, however, as a consequence of synthetic phosphate use in soil.⁸ The synthetic phosphates change plants’ long-established symbiotic relationships with fungi, which may have knock-on effects for farming and for climate change.