The etiology of Crohn's disease (CD) is still unknown. However, many factors, including a dysregulated immune system, altered microbiota, inheritance, and environmental factors, have been implicated. This work was conducted to estimate the effect of fungal microbiota on two bone mineral density markers, RANKL and sclerostin, in addition to the correlation between these markers and vitamin B12, D3, and zinc in CD patients, along with their potential effect on fungal microbiota and vice versa. Peripheral blood and carry-Blair Stool samples were collected from 88 participants (60 newly diagnosed with CD without treatment and 28 healthy controls) to detect serum levels of RANKL and sclerostin, and culture media were used to grow, isolate, and identify fungi attendant to CD and its effect on RANKL and sclerostin levels. Sociodemographic data (vitamin B12, D3, and zinc levels) were collected from patients' medical records. The results showed significant differences in RANKL and sclerostin levels in various types of fungal microbiota in CD patients along with a significant increase in RANKL and sclerostin levels in these patients. Moreover, RANKL levels were negatively significantly correlated with Zinc, while sclerostin levels correlated negatively with vit D3. The findings of this study suggest that fungal microbiota may play a role in the inflammatory process and interactions with bone density by affecting levels of RANKL and sclerostin, vitamin D3, and zinc, suggesting that the use of the fungal microbiota in the monitoring and treatment of CD patients.
