Fig. 5: Dietary fibre supplementation inhibits indole production by complex human gut microbial communities both in vitro and in vivo.
a–c, Concentrations of tryptophan metabolites indole (a) and ILA (c) and tryptophan (b) in the culture supernatants of nine separate human faecal microbial communities grown in mGAM with no fibre supplementation or supplemented with a mixture of fibres or pectin. Lines and error bars indicate medians and IQRs, respectively. Statistical analysis was done using the Friedman test, with Dunn’s post hoc test (two tailed). P values are shown in the figure panels. d, Schematic representation of the experimental plan to evaluate the effect of dietary fibre on production of tryptophan metabolites in vivo. GF mice were placed in two groups (n = 5 or 6 per group) and fed a complex fibre diet (Altromin 1314) for 14 days before FMT of the mice was done with communities originating from two different human adult donors. Subsequently, the mice remained for another 27 days on the same diet for stabilization. The mice were then fed a diet depleted of fermentable fibres (D10012G) for 2 days before feeding them a complex fibre diet for ten more days. Thereafter, the mice were fed a diet with 2 g kg−1 tryptophan without pectin for 2 weeks and then a diet with 2 g kg−1 tryptophan and 50 g kg−1 pectin for two more weeks. Pectin diet compositions are described in Supplementary Table 1. Faecal samples were collected as shown in the scheme. e, The 16S rRNA gene sequencing profiles show the average relative abundance of individual ASVs in faeces across all mice at each sampling point. Only ASVs with relative abundance >5% in at least one sample are shown, and the rest are grouped into ‘others’. f, Absolute faecal indole concentrations showing means and 95% CIs, as well as the data point of each individual mouse. Statistical analysis was done using repeated-measure one-way ANOVA, with Sidak’s multiple-comparison test (two tailed; q values). The q values are shown in the figure panels. Panel d was created with BioRender.com.
