16S rRNA (gene) based barcoded Illumina sequencing of the microbiota in ileal and colonic luminal content of Ercc1-/7 mice after 10 weeks of Akkermansia muciniphila supplementation
DNA was isolated from ileal and colonic content using a modified repeated bead beating method . Microbiota composition was assessed using 16S rRNA sequencing on the MiSeq platform (Illumina, San Diego, CA, USA). Next, the NG-Tax pipeline was used for barcode-primer filtering, de-multiplexing, OTU picking and taxonomic classification. The generated biom-files were used for summarizing the microbiological data, i.e. alpha-diversity and beta-diversity, using the R-packages microbiome and phyloseq.