ECAOMIC-243
The V3-V4 hyper-variable region of the 16S rRNA gene was amplified as previously reported by our team (Mach et al., 2017a, Mach et al., 2020; Clark et al., 2018; Massacci et al., 2019; Plancade et al., 2019). The concentration of the purified amplicons was measured using a Nanodrop 8000 spectrophotometer (Thermo Fisher) and their quality was checked using DNA 7500 chips onto a Bioanalyzer 2100 (Agilent Technologies). All libraries were pooled at equimolar concentration, and the final pool had a diluted concentration of 5 nM and was used for sequencing. The pooled libraries were mixed with 15% PhiX control according to the protocol provided by Illumina (Illumina, San Diego, CA, United States) and sequenced on a single MiSeq (Illumina, United States) run using a MiSeq Reagent Kit v2 (500 cycles).