The gut mycobiome is shaped by interactions with the bacterial community in twins.

The human gut microbiome comprises bacteria, viruses, and fungi, yet the fungal component (mycobiome) remains poorly characterized. Here, we investigated gut fungal composition and fungal-bacterial interactions in healthy monozygotic and dizygotic twins. Fungal communities showed substantially higher inter-individual variability than bacterial communities. Zygosity, age, and shared environment had no major influence on fungal abundance, similarity, or dominant genera. Candida was the most abundant genus (mean 5.2% in 161 individuals), followed by Geotrichum (3.7% in 132), whereas Saccharomyces was detected less frequently (0.8% in 92). Most bacterial genera were negatively correlated with Candida and Geotrichum, with stronger negative associations observed at higher bacterial abundances (up to rho = -0.6 for Alistipes). Network analysis revealed complex negative correlations among Bacteroides, Prevotella, and Candida. Overall, our findings reveal a highly variable gut mycobiome independent of host zygosity, pointing to a competitive bacterial-fungal interplay as a key regulator of fungal homeostasis in humans.