Statistical analysis

Mice experiments: One-way analysis of variance (ANOVA) was performed between the SPF group and humanised untreated mice to evaluate the effect of faecal microbiota transfer (FMT), followed by a Tukey post hoc test. Effect of inulin supplementation was assessed using a Student’s t-test between the two groups of mice colonised with the same donor.

Microbiota analysis: Significantly affected taxa or amplicon sequence variants (ASVs) by inulin were identified using a Welch’s t-test in R, between untreated and treated groups for each donor. The p-value of the Welch’s t-test was adjusted (q-value, significant if q<0.05) to control for the false discovery rate (FDR) for multiple tests according to the Benjamini and Hochberg procedure.²²

Correlation between the variation of genera or ASVs significantly regulated by inulin and other metabolic variables was assessed by Spearman’s correlation tests with an FDR correction. A significance level of q<0.05 (adjusted p-value) was adopted for all analyses.

Human cohort: Responders and non-responders to inulin treatment were discriminated according to the body mass index (BMI) median value. Principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA) models were built based on selected variables in R. For PLS-DA, a loading >0.35 was chosen.