Uncovering the Roles of Gut Fungi using Shotgun Sequencing Data

We are pleased to announce that Dr. Virginia Pedicord, from the University of Cambridge, United Kingdom, will join 13th World Congress on Targeting Microbiota - ISM 2026 as a speaker.

Characterization of fungal constituents of the gut microbiota has historically required separate sequencing methods involving PCR amplification of the internal transcribed spacer (ITS), small subunit (SSU) and/or large subunit (LSU). To capitalize on available shotgun metagenomic data and reduce the need for separate amplicon sequencing, we developed MycoMAPS (Mycobiome Mapping-based Abundance Profiling from Shotgun sequencing) an optimized bioinformatic pipeline incorporating a curated gut-specific fungal reference database. MycoMAPS resolves common challenges in shotgun-based fungal detection to deliver accurate, strain-resolved fungal abundance profiles directly from existing sequencing data.

As proof-of-concept, we applied MycoMAPS to investigate gut fungal colonisation in preterm infants. MycoMAPS revealed that bacteria-targeting antibiotic exposure was associated with a marked increase in the occurrence of Candida albicans, consistent with fungal expansion following disruption of the bacterial community. Different classes of antibiotic, however, had widely varying impacts on fungal colonisation. These findings illustrate how MycoMAPS can uncover clinically relevant bacterial-fungal interactions directly from existing shotgun metagenomic data.

MycoMAPS addresses an important gap in human microbiome research, providing a validated, scalable framework for mycobiome profiling from shotgun sequencing data that can be readily applied to existing and future cohorts without the need for additional sequencing.