This study investigates the fungal component of the human gut microbiome, known as the mycobiome, and its role in intestinal ecology and human health. The researchers collected 3,363 fungal sequencing samples from 16 cohorts across three continents, including 572 newly profiled samples from China. They identified and characterized four distinct fungal enterotypes using ITS profiling, which exhibit stability across populations and geographical locations and are significantly correlated with bacterial enterotypes. Notably, the fungal enterotype dominated by *Candida* (Can_type) is enriched in the elderly population and is associated with an increased risk of multiple diseases, particularly those affecting the intestinal barrier. Bidirectional mediation analysis revealed that the fungi-contributed aerobic respiration pathway associated with the Can_type enterotype may mediate the association between compromised intestinal barrier and aging. The findings highlight the structured nature of the gut mycobiome and its clinical relevance to human health.This study investigates the fungal component of the human gut microbiome, known as the mycobiome, and its role in intestinal ecology and human health. The researchers collected 3,363 fungal sequencing samples from 16 cohorts across three continents, including 572 newly profiled samples from China. They identified and characterized four distinct fungal enterotypes using ITS profiling, which exhibit stability across populations and geographical locations and are significantly correlated with bacterial enterotypes. Notably, the fungal enterotype dominated by *Candida* (Can_type) is enriched in the elderly population and is associated with an increased risk of multiple diseases, particularly those affecting the intestinal barrier. Bidirectional mediation analysis revealed that the fungi-contributed aerobic respiration pathway associated with the Can_type enterotype may mediate the association between compromised intestinal barrier and aging. The findings highlight the structured nature of the gut mycobiome and its clinical relevance to human health.