A Global Synthesis of Yeast in Microbiomes

Yeasts are widespread members of microbial communities across terrestrial, aquatic, and host-associated environments, yet they remain underrepresented in microbiome studies due to low abundance and methodological biases. By combining a literature review with a meta-analysis of ~44,000 fungal metabarcoding samples from the GlobalFungi database, we show that yeasts occur in over 90% of samples, confirming their global ubiquity. Basidiomycetous lineages-especially Agaricomycotina-were most frequently detected, whereas Saccharomycotina showed stronger signals in anthropogenic, aquatic, host-associated, and food-related settings depending on the dataset. Although yeasts typically comprised only ~0.1% of fungal reads, their distributions were structured rather than uniform and reflected distinct habitat associations across environments. In ~3% of samples, yeasts exceeded 25% of reads, with genera such as Aureobasidium, Hanseniaspora, and Saccharomyces episodically dominating nutrient-rich or human-influenced environments. Cosmopolitan genera including Vishniacozyma, Solicoccozyma and Rhodotorula were broadly distributed but remain underreported in microbiome surveys. Shotgun metagenomic data further confirmed yeast presence across diverse microbiomes, with yeast-derived reads being a small fraction of total metagenomic sequences, reflecting the 'curse of low abundance'. Despite their rarity, yeasts are likely to contribute to nutrient cycling, plant growth, and host interactions. We recommend inclusive multi-kingdom approaches-improved primer design, optimised fungal DNA recovery, long-read sequencing, and quantitative tools-to better integrate yeasts into microbiome research.