*4.3. 16S rDNA Amplification*

The V3+4 region of the 16S rRNA gene was amplified using 10 ng of bacterial template DNA with degenerate region-specific primers (341F: 5 -ACTCCTACGGGAGGCAGCAG-3 and 806R: 5 -123 GGACTACHVGGGTWTCTAAT-3 ), containing barcodes and Illumina flow cell adaptor sequences [58], in a reaction consisting of 25 (stool) or 35 (tissue) PCR cycles (98 ◦C 15 s, 58 ◦C 20 s, and 72 ◦C 40 s) using the NEBNext Ultra II Q5 Master Mix (New England Biolabs, Ipswich, MA, USA). Amplicons were purified with Agencourt AMPure XP Beads (Beckmann Coulter, Brea, CA, USA), normalized and pooled before sequencing on an Illumina MiSeq device using a 600-cycle paired-end kit and the standard Illumina HP10 and HP11 sequencing primers.
