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Eimeria tenella  ( E. tenella ), 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 how  E. tenella  affects 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  Faecalibacterium ,  Clostridium ,  Lachnoclostridium ,  Gemmiger ,  Flavonifractor ,  Pseudoflavonifractor  and  Oscillibacter  were significantly decreased in the infected samples, whereas  Escherichia ,  Nocardia  and  Chlamydia  were 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,  E. tenella  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 of  E. tenella  and provides insight for potential new drug development. RESEARCH HIGHLIGHTSFirst simultaneous description of caecal microbiota and physiological indicators during  E. tenella  infection.Metagenomics used to explore functional properties of chicken caecal microbiota during  E. tenella  infection.Caecal microbial compositions and functional genes altered significantly after infection.Blood indicators and caecal morphology were significantly altered in the infected group. First simultaneous description of caecal microbiota and physiological indicators during  E. tenella  infection. Metagenomics used to explore functional properties of chicken caecal microbiota during  E. tenella  infection. Caecal microbial compositions and functional genes altered significantly after infection. Blood indicators and caecal morphology were significantly altered in the infected group.

avian pathology

Comparison of the caecal microbial community structure and physiological indicators of healthy and infection  Eimeria tenella  chickens during peak of oocyst shedding