The human gut harbours a vast community of bacteria, fungi, archaea and viruses, collectively known as the human microbiota. It is well-established that the microbiota has a crucial role in host health and disease, for example via the production of metabolites that shape host physiology. In contrast to the bacterial members, our knowledge of the contributions of fungi and their compounds to host function, host health and diseases as well as the underlying mechanisms are elusive. To fill this knowledge gap, Zhou et al. developed a new culture method that enables cultivation of previously unculturable gut fungal species. Using this system, they showed that filamentous Fusarium spp. fungi are common colonizers of the gut. Importantly, they found that the fungi produce a secondary metabolite that protects against metabolic disease in mice.

Next, the authors set out to establish whether the fungi are transient residents or whether they can adapt to the intestinal environment for colonization. They showed that the fungi can grow at 37 °C and under anaerobic conditions, which suggests that F. foetens can colonize the colon. In agreement with this, the gavage of germ-free mice with F. foetens gut isolates led to the enrichment of the fungus in colon contents, but only low levels were detected in other parts of the gut and it was not detected in other host tissues or in the plasma.