Fig. 6

Differentially enriched species between rats before (Day − 3) and after (Day 42) sibutramine treatment. A Phylogenetic tree representation of differentially expressed taxa between samples at the start and end of the treatment. Differential enrichment at every classification level (Phylum, Class, Order, Family, Genus and Species) was calculated with R package DESeq2 using a linear model (~ Day + rat number). P values were adjusted by Benjamini-Hochberg correction and only species with P.adj < = 0.05 were considered significantly different, then tables with log2 and library size normalized counts (rlog) for every taxon were extracted [44, 49]. These were fed into GraPhlAn for phylogenetic tree visualization. External annotation corresponds to Log2 fold-change values for every differentially expressed species. Species of interest were indicated in the circular tree by stars and coloured according to their Log2 Fold change (Log2 fold-change < 0, blue; Log2 fold-change > 0, red). Concentric circles each represent a taxonomical level, starting from Phylum (Proteobacteria, light blue; Firmicutes, yellow; Bacteroidetes, red; Actinobacteria, green), then proceeding outwards to Class, Order, Family, Genus and Species. Notably, Bacteroidetes as a whole are significantly increased by the end of the treatment (see red star in the innermost circle). B Boxplots showing levels of differentially enriched Bacteroides species, before and after sibutramine treatment. Grey lines connect dots corresponding to the same rat. Counts used were log2 transformed and normalized by library size [49]