Fig. 2
From: Modulation of the human gut microbiota by dietary fibres occurs at the species level
Effect of pH on microbial community composition. 16S rRNA gene-targeted qPCR data are shown for Bacteroides spp. (a) with inulin and (b) with apple pectin as energy sources and for Lachnospiraceae (c) with inulin and (d) with pectin. These refer to 12 fermentor runs (F1 (upshift), F2 (downshift) fermentors run in parallel for donors D1, D2 and D3 with pectin or inulin) *P <0.05, **P <0.001 (ANOVA, see Methods). Results from Illumina MiSeq sequencing of 16S rRNA gene amplicons are shown in (e) at the phylum level for F1 and F2 fermentors for each substrate; these revealed significant effects of pH when analyzed by ANOVA (see text). MiSeq data represent merged data from the same 12 fermentor runs, but also include four additional (repeat) runs for D2 inulin (F1, F2) and D3 pectin (F1, F2). Combined phylum and family level results from the sequence data are also shown for each substrate in Additional file 1: Figure S1. A list of operational taxonomic units obtained from analysis of 16S rRNA gene amplicon sequences for all samples is given in Additional file 2: Table S1