16S of  chicken
A total of 48 chickens were fed an antibiotic-free starter diet containing 16% dry matter protein (USDA-Feed Mill) from days 1 to 18 of age and a standard grower diet containing 24% dry matter protein from days 19 to 21, as similarly described elsewhere (Oh et al., 2018). Birds were randomly assigned to four groups with 12 birds each. For E. maxima (EM) challenge group, chickens were infected by oral gavage on day 14 with 5.0  103 oocysts/bird of EM Beltsville strain 41A. For C. perfringens (CP) challenge group, chickens were infected by oral gavage with CP netB+ strain Del1 of 1.0  109 CFUs /bird at Day 18. For EM/CP dual infection (EP) group, chickens were infected with same dose of EM at Day 14 and CP at Day 18, respectively. For the nave uninfected control (NV) group, chickens were received an equal volume of PBS by oral gavage at Day 14 followed by BHI medium at Day 18 as a sham control. At Day 20, the birds were sacrificed, and the contents in the ceca were collected by scrapping and immediately put into RNALater solution based on the manufacturers instruction (Sigma, St Louis, MO). The birds were weighed at D14 (pre-EM infection), D18 (pre-CP infection) and D20 (Day 2 post CP infections). The gut lesion scores were determined in sections of intestine flanking the diverticulum using 4-point scoring system