Comparison of the caecal microbial community structure and physiological indicators of healthy and infectionchickens during peak of oocyst shedding.

Abstract

(), an important intestinal parasite of chicken caeca, causes coccidiosis and brings large economic losses to the poultry industry annually. Gut microorganismal alterations directly affect the health of the body. To understand howaffects its host, we analysed the changes in caecal microbial diversity and the physiological and morphological changes during the peak of oocyst shedding. Infected and healthy chickens differed significantly in caecal pathology and blood indicators. At the genus level, the abundances of,,,,,andwere significantly decreased in the infected samples, whereas,andwere significantly increased. Functional gene pathways related to replication, recombination and repair, and transcription were significantly decreased, and functional genes related to metabolism were highly significantly reduced in the infected samples. Furthermore, in the infected samples,reduced the haemoglobin levels and red blood cell counts, greatly reduced the beneficial bacteria and increased the potentially pathogenic bacteria. This study provides a research basis for further understanding the pathogenic mechanisms ofand provides insight for potential new drug development.First simultaneous description of caecal microbiota and physiological indicators duringinfection.Metagenomics used to explore functional properties of chicken caecal microbiota duringinfection.Caecal microbial compositions and functional genes altered significantly after infection.Blood indicators and caecal morphology were significantly altered in the infected group.