Characterization of the gut mycobiome in patients with non-alcoholic fatty liver disease and correlations with serum metabolome

Background. The relationship between the gut mycobiome and non-alcoholic fatty liver disease (NAFLD) is largely unexplored. Methods. In this study, we used a publicly available shotgun metagenomic sequencing dataset of fecal samples to compare the gut fungal communities of 90 NAFLD patients with those of 90 healthy controls. We examined their correlations with gut bacterial communities, host serum metabolites, and the interactions of key taxa within these networks. Results. Our results revealed a remarked dysbiosis in the gut mycobiome of NAFLD patients, characterized by a significant increase in four fungal taxa, including Pseudopithomyces sp. c174, Mucor sp. c176, Aspergillus sp. c25, and uncultured Ascochyta c213. Multi-omics analysis showed that the gut mycobiome significantly contributes to the host serum metabolome. Pseudopithomyces sp. c174 was notably associated with some beneficial blood metabolites, such as glycoursodeoxycholic acid and alpha-linolenic acid, whereas the NAFLD-enriched pro-inflammatory phenylacetic acid was linked to Aureobasidium sp. c170 and Basipetospora sp. c193. Network analysis revealed significant alterations in the gut microbiome of NAFLD patients, highlighting the potential roles of Alternaria alternata c42, Penicillium sp. c5, and uncultured Malassezia c303. Moreover, predictive models that integrated both bacterial and fungal taxa improved prediction accuracy, emphasizing the crucial role of gut fungi in NAFLD. Conclusions. Our findings provide a comprehensive understanding of the link between the gut mycobiome and NAFLD progression, which is essential for guiding future therapeutic research.