Global metagenomics analyses demonstrate metformin‐induced changes in the gut mycobiome in subjects with type 2 diabetes

The fungal component of the gut microbiota (mycobiome) has been less well studied than bacterial populations; however, emerging evidence suggests that the mycobiome might play an important role in metabolic disease. Intestinal fungi play an important role in modulating immune responses at mucosal and systemic sites, but the extent of host-bacterial-fungi interactions in disease pathogenesis remains unknown. Metabolic diseases such as obesity and type 2 diabetes are accompanied by an altered gut microbiome, known as dysbiosis, and recent work suggests that the gut mycobiome may also be perturbed in metabolic diseases. Correcting gut dysbiosis is hypothesized as a therapeutic target for obesity and some metabolic diseases, however, little data is available regarding the effects of medications on the gut mycobiome and associated host-bacterial-fungi interactions. Metformin is globally the most prescribed drug for type 2 diabetes mellitus (T2D), and its therapeutic effects cause decreased hepatic gluconeogenesis and consequently circulating blood glucose. Metformin treatment also impacts the gut microbiome composition, lowering circulating lipopolysaccharide and therefore reducing toll-like-receptor-mediated inflammation. To date, the potential effects of metformin on the gut mycobiome are entirely unknown. Therefore, this study aims to address this knowledge gap by characterizing the impact of metformin on the gut mycobiome of healthy adults and adults with pre-diabetes and T2D, defined by fasting plasma glucose values. We searched for published research articles with archived, publicly accessible shotgun metagenomics data and re-processed the data with one uniform bioinformatics pipeline to identify fungal taxa and relative abundance. Our analysis involved a total of 4510 samples from 13 individual studies ranging from randomized clinical trials to cross-sectional cohorts. We performed analyses on the compiled dataset to (1) characterize the impact of metformin treatment in healthy, pre-diabetic, and T2D individuals on the gut mycobiome; and (2) correlate the changes in relative abundance of fungal taxa to available clinical covariates, such as body mass index and fasting blood glucose. Secondary analysis of a randomized controlled trial of 44 newly diagnosed, treatment-naïve T2D patients who were prescribed metformin for three days demonstrated a significant effect of metformin on the gut mycobiome richness (Shannon and Simpson indices; t test p = 0.02 and p = 0.0061 respectively) and diversity (PERMANOVA p = 0.001). Additionally, the relative abundance of Saccharomyces,a well-characterized yeast genus, was significantly higher after three days of metformin treatment (Wilcoxon p = 0.019). This study provides novel insight into the interactions between human hosts, the gut microbiome, and the gut mycobiome in response to metformin, a widely used drug to treat T2D. Furthermore, these analyses may provide greater understanding of the role of the mycobiome-microbiome interaction in metabolic diseases.