Stool Subject S9 baseline
For 16S rRNA amplicon  based microbial profiling, DNA extracts were used to generate amplicons using a MetaVxTM Library Preparation kit (GENEWIZ, Inc., South Plainfield, NJ, United States) at Genewiz. The V3-V4 hypervariable region of the 16S rRNA gene was targeted and amplified using forward and reverse primers containing the sequences 5-CCTACGGRRBGCASCAGKVRVGAAT and 5-GGACTACNVGGGTWTCTAATCC, respectively. The DNA amplicon libraries were validated using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, United States) and quantified using Qubit 2.0 Fluorometer. Then, the libraries were multiplexed and sequenced on a MiSeq instrument (Illumina, San Diego, CA, United States) using a 2  300 paired-end configuration accordingly to manufacturers recommendations.