Intestinal microbiota composition
Baseclear (Leiden, The Netherlands) performed the DNA extraction from the ileostomy effluents, using DNA Fecal/Soil Microbe Kits (Zymo, CA, USA) according to manufacturer’s instruction and also generated and Illumina-sequenced (MiSeq) the 16S rRNA gene amplicon libraries (V3–V4 region, primer 341F and 805R). The results were analysed using CLC Genomics Workbench version v7.5.1 and the CLC Microbial Genomics Module version 1.5 (CLC bio, Arhus, Denmark). Briefly, the paired end reads were merged into one by CLC Workbench with default setting, and CLC pipeline was used for primer and quality trimming. The remaining high-quality sequences were clustered into operational taxonomic units (OTU) using the SILVA 16S v132 97% database as mapping reference database. A total number of paired-end, unique reads of ~ 14 M, with an average of 36,309 reads/samples, were clustered in 11,939 operational taxonomic units (OTUs) of which 10218 with more than 2 counts. After removal of the outlier samples the reads were clustered in 9270 OTUs. When investigating the interventions’ effect on the endogenous microbial community, the PDB-related OTUs were removed followed by recalculation of the relative abundances of the remaining OTUsOTUs representing Correlation analysis between the qPCR estimated copies of its genome and Unfortunately, similar analysis could not be performed for the OTUs assigned to 