<b>Dataset of 569 metagenome-assembled genomes from the caeca of multiple chicken breeds from commercial and backyard farming setups of Pakistan</b>

This article presents metagenomic-assembled genomes (MAGs) of prokaryotic organisms recovered from 9 different groups of chicken raised in different farm setups in Pakistan. The groups comprise three different breeds (Broilers, White Layers, Black Australorp) of chicken raised in different farming setups that include antibiotic-free control sheds, commercial, and backyard farms. The binning of the samples identified 569 MAGs with50% completion, and10% contamination. The data for each MAG includes sequences in FASTA format, tables of functional annotation of genes, along with two different strategies for recovery of phylogenetic tree for these MAGs. Major geochemical cycles at community level including carbon, sulfur, and nitrogen cycles are also recovered.