Chromosomal and mobile antimicrobial resistance genes in the chicken caecal microbiome

The One Health Poultry Hub aims to understand and mitigate the spread of antimicrobial resistance and food-borne pathogens across poultry production systems globally. This umbrella BioProject represents datasets generated by the Royal Veterinary College (RVC) node, including metagenomic, amplicon, and long-read sequencing of poultry microbiomes and related environments. The project forms part of the international One Health Poultry Hub consortium (UKRI GCRF, grant BB/S011269/1) and complements other partner datasets archived at the NCBI, including BioProject PRJNA1224230. Data generated under this umbrella will include raw sequence reads, assemblies, and annotated analyses, forming a comprehensive resource for comparative microbiome and antimicrobial-resistance research. These datasets are part of a paper that investigates chromosomally integrated and mobile antimicrobial resistance genes in the chicken caecal microbiomes from Bangladesh, India and Viet Nam. It includes Nanopore reads (fastq.gz), Illumina reads (fastq.gz) and the Ceacal MAGs (fasta/ ASM).