Dissection of caecal microbial community in chickens after Eimeria tenella infection

Eimeria spp. are responsible for chicken coccidiosis which is one of the most important enteric protozoan diseases resulting in tremendous economic losses in poultry industry. Chemotherapeutics are the most effective ways to control the disease though, microbial intervention therapy is a promising substitutive measure which is getting more and more attention. Understanding caecal microbiota alterations associated with Eimeria infection within an intact life cycle may help to identify the well-defined bacteria to develop novel treatment strategy. Overall, this study provides valuable insights into the cecal microbial community in AA broilers challenged with Eimeria tenella, utilizing 16S rRNA gene sequencing. We found that microbial shifts take place during the infection. Lactobacillus, Faecalibacterium, Ruminococcaceae_UCG-013, Romboutsia and Shuttleworthia, were decreased in the levels of abundance. Whereas, opportunistic pathogens Enterococcus and Streptococcus were increased in the levels over time in response to the infection. These findings could improve our comprehension of the microbiota–coccidia interactions during Eimeria tenella infection and provide important insights into the alternative therapeutics to control the coccidiosis.