Effect of supplementation of a minimal culture medium with Raffinose compared with a glucose condition, on the gene expression of a set of bacteria of the intestinal microbiota

The aim of this RNA-sequencing study is to measure differential gene expression in 8 intestinal bacteria (Bacteroides xylanisolvens, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bifidobacterium adolescentis, Bifidobacterium catenulatum, Subdoligranulum variabile and Roseburia intestinalis, Agathobacter rectalis). The data highlight the coordinated action of genes within the same locus involved in the degradation of complex carbohydrates. These loci are well characterized in Bacteroidota species and referred to as polysaccharide utilization loci. In Bacillota and Actinomycetota species, these loci are not so clear-cut, athough the GP-PUL concept has already been proposed. Here we compare the differential gene expression in minimal culture medium supplemented with a complex carbohydrate with a minimal culture medium supplemented with glucose. This differential analysis reveals a source-specific genetic response and a coordinated expression of genes involved in carbohydrate transport, carbohydrate degradation and transcriptional activation of these complex enzymatic machineries. To investigate this differential expression, bacterial RNA was extracted after 12h of culture in minimum medium supplemented with one complex carbohydrate or glucose. RNA was extracted using RNAeasy Qiagen kit.