Fungal signature differentiates alcohol-associated liver disease from nonalcoholic fatty liver disease

ABSTRACT

The fungal microbiota plays an important role in the pathogenesis of alcohol-associated liver disease (ALD) and nonalcoholic fatty liver disease (NAFLD). In this study, we aimed to compare changes of the fecal fungal microbiota between patients with ALD and NAFLD and to elucidate patterns in different disease stages between the two conditions. We analyzed fungal internal transcribed spacer 2 (ITS2) sequencing using fecal samples from a cohort of 48 patients with ALD, 78 patients with NAFLD, and 34 controls. The fungal microbiota differed significantly between ALD and NAFLD. The genera Saccharomyces, Kluyveromyces, Scopulariopsis, and the species Candida albicans (C. albicans), Malassezia restricta (M. restricta), Scopulariopsis cordiae (S. cordiae) were significantly increased in patients with ALD, whereas the genera Kazachstania and Mucor were significantly increased in the NAFLD cohort. We identified the fungal signature consisting of Scopulariopsis, Kluyveromyces, M. restricta, and Mucor to have the highest discriminative ability to detect ALD vs NAFLD with an area under the curve (AUC) of 0.93. When stratifying the ALD and NAFLD cohorts by fibrosis severity, the fungal signature with the highest AUC of 0.92 to distinguish ALD F0-F1 vs NAFLD F0-F1 comprised Scopulariopsis, Kluyveromyces, Mucor, M. restricta, and Kazachstania. For more advanced fibrosis stages (F2-F4), the fungal signature composed of Scopulariopsis, Kluyveromyces, Mucor, and M. restricta achieved the highest AUC of 0.99 to differentiate ALD from NAFLD. This is the first study to identify a fungal signature to differentiate two metabolic fatty liver diseases from each other, specifically ALD from NAFLD. This might have clinical utility in unclear cases and might hence help shape treatment approaches. However, larger studies are required to validate this fungal signature in other populations of ALD and NAFLD.

KEYWORDS:

• Mycobiome
• microbiome
• fungi
• ALD
• NAFLD

Acknowledgments

This work was supported by National Institutes of Health (NIH) grant K12 HD85036, University of California San Diego Altman Clinical and Translational Research Institute (ACTRI)/NIH grant KL2TR001444, and Pinnacle Research Award in Liver Diseases Grant #PNC22-159963 from the American Association for the Study of Liver Diseases (AASLD) Foundation, and Pilot/Feasibility Grant P30 DK120515 from the San Diego Digestive Diseases Research Center (SDDRC) (to P.H.), by a DFG fellowship (LA 4286/1-1) and the “Clinical and Translational Research Fellowship in Liver Disease” by the AASLD Foundation (to S.L.), by the “Marga und Walter Boll-Stiftung”, project number 210-03-2016, and the “Köln Fortune” research pool, Faculty of Medicine, University of Cologne, Germany, project number 160/2014 (to M.D.), by grants from the Fond National de Recherche Scientifique Belgium (J.0146.17 and T.0217.18) and Action de recherche concertée (ARC), Université Catholique de Louvain, Belgium (to P.S.), in part by NIH grants R01 AA024726, R01 AA020703, U01 AA026939, U01 AA026939-04S1, by Award Number B×004594 from the Biomedical Laboratory Research & Development Service of the VA Office of Research and Development (to B.S.) and services provided by NIH centers P30 DK120515 and P50 AA011999.

Disclosure statement

B.S. has been consulting for Ferring Research Institute, HOST Therabiomics, Intercept Pharmaceuticals, Mabwell Therapeutics, Patara Pharmaceuticals, Surrozen and Takeda. B.S.’s institution UC San Diego has received research support from Axial Biotherapeutics, BiomX, ChromoLogic, CymaBay Therapeutics, NGM Biopharmaceuticals, Prodigy Biotech and Synlogic Operating Company. B.S. is founder of Nterica Bio. UC San Diego has filed several patents with S.L. and B.S. as inventors related to this work.

Author contributions

G.V. was responsible for data analysis, and writing and editing the manuscript; P.H. was responsible for data analysis, and writing and editing the manuscript; S.L. was responsible for collection and processing of fecal samples, data analysis, data interpretation and drafting of the manuscript; M.D. was responsible for collection of samples, data collection, interpretation of data and editing the manuscript; X.Z. provided assistance with statistical analysis; D.E.F. was responsible for bioinformatical analysis, interpretation of data and edited the manuscript; P.S. was responsible for collection of samples with alcohol use disorder and edited the manuscript; B.S. was responsible for study concept and design, interpretation of data, editing the manuscript, and study supervision.

Supplemental material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/19490976.2024.2307586

Additional information

Funding

The work was supported by the American Association for the Study of Liver Diseases [PNC22-159963]; American Association for the Study of Liver Diseases [Clinical and Translational Research Fellowship]; Biomedical Laboratory Research and Development, VA Office of Research and Development [BX004594]; Deutsche Forschungsgemeinschaft [LA 4286/1-1]; Fonds De La Recherche Scientifique – FNRS [J.0146.17 and T.0217.18]; Marga und Walter Boll-Stiftung [210-03-2016]; NIH Clinical Center [P30 DK120515 and P50 AA011999]; National Institutes of Health [KL2TR001444]; National Institutes of Health [R01 AA024726, R01 AA020703]; National Institutes of Health [U01 AA026939, U01 AA026939-04S1]; National Institutes of Health [K12 HD85036]; Köln Fortune [160/2014]; San Diego Digestive Diseases Research Center, School of Medicine, University of California, San Diego [P30 DK120515]; Université Catholique de Louvain [Action de recherche concertée (ARC)].