Colonisation efficiency of 
The microbial activity in ileostomy effluent was analysed by metatranscriptome analysis in the samples obtained on the first and last days of the intervention periods. Functional metatranscriptome mapping (FMM) of the small intestine microbiome were obtained for each sample by genome, protein and pathway mapping. To understand how well the microbial composition identified by 16S rRNA reflected the taxonomic distribution within the metatranscriptome, a detrended correspondence analysis (DCA plot) was used and it revealed a substantial overlap between the compositional profiles (Supplementary Figure SInter subject FMM differences was the predominant source of variation, explaining almost 25% of the overall FMM variance (Additional file 