This repository is a repository about the bioinformatics for paper on MDPI Antibiotics "Fecal Microbiota Transplantation Reduces Campylobacter jejuni Colonization in Young Broiler Chickens Challenged by Oral Gavage but not by Seeder Birds".
The Qiime2 folder contains the pipeline for 16S rRNA sequencing analysis.
The R folder contains the R scripts for the CFU levels analysis, microbiota analysis, and the codes that were used to generate the figures in the paper.