16S analysis of caecal contents of IL10 chicken

We analyzed variations in cacecal microbiota of IL10 wild type (IL10.WT) and homozygous (IL10.HOM) chicken using 16S sequencing. We collected caecal content from 5 wild type and 5 homozygous chickens, isolated total genomic DNA, and amplified V4 region of 16S gene. After removing adapters. primers, and chimera sequences in qiime2, we assigned the taxonomy to pure reads using silva database. The alpha and beta diversity analysis were performed in Rstudio using phyloseq package. The deferentially abundant phyla and genera were identified by lefse.