A genomic compendium of cultivated human gut fungi characterizes the gut mycobiome and its relevance to common diseases

The gut fungal community represents an essential element of human health, yet its functional and metabolic potential remains insufficiently elucidated, largely due to the limited availability of reference genomes. To address this gap, we presented the cultivated gut fungi (CGF) catalog, encompassing 760 fungal genomes derived from the feces of healthy individuals. This catalog comprises 206 species spanning 48 families, including 69 species previously unidentified. We explored the functional and metabolic attributes of the CGF species and utilized this catalog to construct a phylogenetic representation of the gut mycobiome by analyzing over 11,000 fecal metagenomes from Chinese and non-Chinese populations. Moreover, we identified significant common disease-related variations in gut mycobiome composition and corroborated the associations between fungal signatures and inflammatory bowel disease (IBD) through animal experimentation. These resources and findings substantially enrich our understanding of the biological diversity and disease relevance of the human gut mycobiome. [Display omitted] •A cultivated gut fungi (CGF) catalog (760 genomes, 206 species) was established•CGF catalog illustrates the functional and primary metabolic diversity of gut fungi•CGF catalog characterizes the gut mycobiome in Chinese and non-Chinese populations•Fungal signatures were identified in common diseases and validated in colitis mice This study offers a catalog of cultivated gut fungi (CGFs) comprising 760 genomes derived from healthy individuals. This compendium highlights the taxonomic and functional diversity and metabolic potential of human gut fungi, aids in constructing a comprehensive phylogenetic representation of the gut mycobiome, and sheds light on common disease-related variations.