Most pathogens of poultry and other vertebrates enter the body via a mucosal portal of entry, and for the vast majority, this means either the respiratory or gastrointestinal tract (GIT). This chapter surveys the main bacterial pathogens found in the GIT of poultry, and examines the process of symbiosis between prokaryotes and the host in the gut. The chapter analyses the impact of these bacterial pathogens on the biology of the host and the effect of dysbiosis in poultry. It examines the effects of inflammation of the GIT on anaerobiosis, assesses the role of mucins, and addresses the effect of gut infections on dietary disruption as well as the impact of airborne infections of enteric bacteria on poultry.