Changes in the gut mycobiome are associated with Type 2 diabetes mellitus and metformin treatment across populations.

The gut mycobiome may be involved in human health and disease. Previous studies evaluating the human gut mycobiome have small sample sizes, do not account for the use of oral pharmaceuticals, and report inconsistent findings regarding the relationship between Type 2 diabetes mellitus (T2D) and fungal species. Pharmaceuticals, including the antidiabetic drug metformin, interact with gut bacteria and can alter bacterial metabolism. The potential interactions of pharmaceuticals with the mycobiome remain unknown. These potentially confounding factors necessitate a critical re-evaluation of existing claims and validation in larger human cohorts. Thus, we reanalyzed shotgun metagenomics data from nine studies to quantify if and to what degree there is a conserved relationship between gut fungi and T2D. We used Bayesian multinomial logistic normal models to account for numerous sources of variation and confounding factors, including batch effects induced by differences in study design and sample processing (e.g., DNA extraction or sequencing platforms). Using these methods, we analyzed data from over 1,000 human metagenomic samples and performed a mouse study to demonstrate reproducibility. Metformin and T2D were consistently associated with differences in the relative abundance of some gut fungi that were predominantly members of the Saccharomycetes and Sordariomycetes classes, but generally accounted for less than 5% of total mycobiome variation. Gut eukaryotes may be involved in human health and disease, but this work takes a critical lens to previous claims and suggests that perturbations to the most abundant and prevalent fungi in T2D may be smaller than previously thought.