Gallus gallus cecal content (broilers in commercial settings) Raw sequence reads

Intensive broiler production practices are structured to prevent the introduction and spread of pathogens; however, they can potentially minimize the exposure of broilers to beneficial commensal bacteria. In this study, we used 16s rRNA sequencing to perform a large-scale characterization of the cecal microbiota of 35-day-old broilers from intensive production systems (IPS) and from extensive production systems (EPS), aiming to determine which microbes are normal inhabitants of the broiler ceca and which microbes might be missing from broilers in IPS.