Microbiome Profiling of Mouse Cecal Samples

Mouse cecal samples (12 per group) were shipped to Clinical Microbiomics Lab (Copenhagen, Denmark) for 16S DNA sequencing according to the standard routines performed at the lab. Briefly, DNA of 88 mouse cecal samples were successfully extracted using NucleoSpin^® 96 Soil (Macherey-Nagel) with additional bead-beating steps. The V3-V4 region of the 16S rRNA genes were amplified and sequenced on an Illumina MiSeq desktop sequencer using the MiSeq Reagent Kit V3 (Illumina) for 2 × 300 bp paired-end sequencing. Data obtained from an average sequencing depth of 28,194 read pairs per sample after quality filtering (Illumina MiSeq 300PE) were used for bioinformatics analysis. An adjusted dada2 pipeline was used to process the sequence data into an amplicon sequence variant abundance table (62 (link)). The default taxonomic assignment of the detected ASVs was done using a naïve Bayesian classifier algorithm comparing the ASV sequences to the SILVA reference database (v138.1).