Data files

Comparison of Shannon and Simpson indexes between antibiotic-free subjects (No) and subjects that used antibiotics more than six months before the sample collection (Yes) in NAFL, NASH and NAFLD groups.

See “List of identified sterols, bile acids, and acylcarnitines” for details.

Figure 1: Separation of the different classes of standards (sterols, bile acids, and acylcarnitines) based on retention time in reversed-phase liquid chromatography in the positive ionization mode.

Figure 2: Extracted ion chromatograms of the base peak spectra of detected sterols acquired from reference “BACSMLS” standards in the positive ionization mode. Peak identities are as follows: (1) cortisone, (2) corticosterone,
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Boxplot of CTG Candida-clade abundances. Statistical comparison between fibroscan stages was performed using: Kruskal-Wallis test.

Boxplot of CTG Candida-clade abundances. Statistical comparison between fibroscan stages was performed using: Kruskal-Wallis test.

Microbial community network showing the 4 subcommunity modules. Significant negative correlations are shown in blue and positive in red. The module significantly associated with NAFLD-related parameters is shown with red nodes and significant correlations between the genera and fibroscan, AST, ALT and GGT are shown in green.

Objective: The aim of this study was to present and validate a sensitive and simple liquid chromatography–tandem mass spectrometry (LC–MS/MS) method to detect the presence and distribution of NAFLD-related metabolites (sterols, bile acids, and acylcarnitines) in biological samples. These compound classes were considered as they are implicated in the development and progression of NAFLD; their detection by MS-based analytics is challenging due to the occurrence of many isomers and stereoisomers;
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Beta diversity. PLS-DA of Aitchison distance of the mycobiome composition by fibrosis stage group.

Overview of mycobiome composition at genus level in early and advanced fibrosis groups (cut-off </> 9.7 kPa).

Boxplot of Candida CTG-clade abundances. Statistical comparison between early and advanced fibrosis was performed using: Wilcoxon rank-sum test (Pwilcoxon) and generalized linear models adjusting for age, gender and obesity-related parameters (Pglm).

NAFLD: non-alcoholic fatty liver disease; NAFL: non-alcoholic fatty liver; NASH: non-alcoholic steatohepatitis; HC: healthy controls.
Beta diversity. PLS-DA of Aitchison distance of the mycobiome composition by diagnosis.
Overview of mycobiome composition at genus level in NAFLD, NAFL, NASH and HC groups.
Boxplot of Saccharomyces and Penicillium abundances. Statistical comparison between groups (HC, NAFL, NASH and NAFLD) was performed using Wilcoxon rank-sum test (Pwilcoxon) and generalized linear
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Beta diversity. PLS-DA of Aitchison distance of the mycobiome composition by diagnosis.
Beta diversity. PLS-DA of Aitchison distance of the mycobiome composition by fibrosis stage group.
Boxplot of CTG Candida-clade abundances. Statistical comparison between early and advanced fibrosis was performed using: Wilcoxon rank-sum test (Pwilcoxon) and generalized linear models adjusting for age, gender and obesity-related parameters and antibiotic intake (Pglm).