Mouse stool sequencing before and after EAE

We assessed the fecal gut microbiome composition of 18 wild-type mice (16 controls and 17 antibiotics treated) before and after EAE adoptive transfer using the QIAseq 16S/ITS screening panel (QIAGEN), sequenced on a MiSeq (Illumina). Briefly, samples were thawed and total DNA of 1 or 2 stool pellets was extracted with a QIAamp PowerFecal Pro DNA Kit (QIAGEN). Sequencing libraries were generated with the QIAseq 16S/ITS Screening Panels kit. For each sample, 1 ng of total DNA was amplified with each of the three Screening Panel pools and subsequently combined and indexed. The indexed libraries were pooled equimolarly, and 15pM were loaded and sequenced PE 276 on a MiSeq v3 600-cycle kit (Illumina). Taxonomy was assigned using the IDTAXA classifier (DECIPHER package) with the GTDB-RS89 reference database. The processed data were integrated into a phyloseq object for further analysis.