The infection was performed orally via feeding tube (gavage) with a dose of 1 × 108 CFU/bird at 14 days of age as described previously (Awad et al., 2015a). At 7 days post infection 5 birds from each group were anesthetized by injection of a single dose of thiopental (20 mg/kg) into the wing vein and slaughtered by bleeding of the jugular vein. The final 10 birds/group were killed at 14 days post infection. At each time point the gastrointestinal content from the jejunum and ceca, as well as jejunal and cecal mucosa from 5 birds/group were taken to determine the gut microbiota. Intestinal segments were disclosed at the mesentery with sterile instruments and the digesta was removed. The luminal site of the intestinal segments was washed with sterile ice-cold PBS until the mucosa was completely cleaned from the digesta. The mucosa was rinsed several times with sterile ice cold PBS, after which the mucosa was collected aseptically by scraping off the mucosa using scalpel blades. All samples were stored at −80°C until further processing.