Comparative Metagenomics of Integrated Poultry-Cattle Farms Reveals Niche-Specific Bacterial Communities, Antimicrobial Resistance, and Virulence Determinants
We employed shotgun metagenomic sequencing to analyze 30 samples from integrated poultry-cattle farms across three locations in Bangladesh (Noakhali, Cumilla, and Gazipur). Samples represented ten types spanning gut-associated (cow-dung, cloacal-swabs, droppings), environmental (soil, water), dietary (feed), and human-interface (hand-swab) compartments. Bacterial species composition, ARG profiles, and VFD distributions were characterized using comprehensive bioinformatic analyses.