At birth the intestines of all animals are sterile. The microorganism that populate the intestine are picked up from other animals as well as the environment. A day-old chick (DOC) does not have contact with the hen and will therefore not receive any microbiota from the hen. The DOC will however pick up microbiota from the environment, egg shell, hatchery and poultry house. In pigs, the bacteria that form the basis of the piglet’s microbiome are derived from the birth canal of the sow as well as from the sow’s faeces and the environment of the farrowing house.
The intestine of DOCs rapidly colonise. By 2 weeks a stable intestinal microbiome would have developed and by 30 days a stable ceacal intestinal microbiome would be fuctional. However, the presence of pathogenic bacteria (Salmonella, E. coli and Clostridium perfringens) in the farrowing house and poultry house can have a negative impact on the development of a healthy intestinal microbiome.