A genomic compendium of cultivated human gut fungi characterizes the gut mycobiome and its relevance to common diseases
The gut fungal community is an important component of human health, yet its functional and metabolic capacities remain inadequately elucidated, primarily due to the dearth of reference genomes. Here, we leveraged cultivation and sequencing of fecal samples from healthy individuals to create a massive compendium of 760 fungal genomes. This cultivated gut fungi (CGF) catalogue encompassed 206 species from 48 families, with 69 previously unidentified species. We characterized the functional and metabolic phenotypes of the CGF species and used the catalogue to construct a phylogenetic perspective of the gut mycobiome by examining over 6,000 and 5,000 fecal metagenomes from Chinese and non-Chinese populations, respectively. Additionally, we identified substantial common disease-related variations in the gut mycobiome and established a validated association between fungal signatures and inflammatory bowel disease via animal experiments. These resources and findings substantially enhance our knowledge of the biological diversity and disease relevance of the human gut mycobiome.
This research employs a workflow designed to calculate fungal abundance within metagenomic samples, and includes a test dataset for demonstration purposes.
Genomic annotation, including annotations for GTF, CAZy, KEGG, Pfam, eggNOG, and SMGCs.
This research incorporates profiles depicting the abundance of intestinal fungi across different taxonomic strata, alongside the categorization files of samples subject to analysis for Inflammatory Bowel Disease (IBD).
The R code corresponding to the main image and the
.RDatafile used.