Effects of challenge with Clostridium perfringens, Eimeria and both on ileal microbiota of yellow feather broilers

In the poultry industry worldwide,Clostridium perfringenshas been causing major economic loss as it can cause necrotic enteritis (NE). The coccidial infection has been considered as the most important predisposing factor of NE caused byC. perfringens. In this study, we aimed to advance our knowledge on ileal microbiota of yellow feather broilers underC. perfringensand/orEimeriachallenge. Total of 80 healthy day old yellow feather broilers were randomly assigned to four groups including: Control,C. perfringenschallenge group (C. Per),Eimeriachallenge group (Cocc), andC. perfringensplusEimeriachallenge group (Comb). On day 14, the Cocc and Comb group broilers were orally gavaged 1 ml PBS solution containing 25,000 oocysts ofEimeria brunettiand 25,000 oocysts ofEimeria maxima. Starting on day 17, the C. Per and Comb group broilers were orally gavaged 10 mL ofC. perfringensper bird (4 × 107CFU/mL, ATCC®13124™ Strain) every day for 6 days. 16S rRNA gene sequencing was performed on extracted DNA of ileal digesta samples. The results showed thatC. perfringensalone did not affect the alpha diversity of ileal microbiome in yellow feather broilers but co-infection withEimeriasignificantly decreased the diversity of ileal microbiota.C. perfringensandEimeriachallenge also decreased the relative abundance of beneficial bacteria includingBacteroidetesat the phylum level andFaecalibacteriumat the genus level. At the species level, the relative abundance ofCandidatus Arthromituswas significantly decreased in theEimeriachallenged groups. This microbial shift information of ileal microbiota underC. PerfringensandEimeriachallenge provide important reference data for the development of therapeutic approaches to necrotic enteritis in yellow-feather broiler chickens.