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

<i>Eimeria tenella</i> (<i>E. tenella</i>), 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 <i>E. tenella</i> 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 <i>Faecalibacterium</i>, <i>Clostridium</i>, <i>Lachnoclostridium</i>, <i>Gemmiger</i>, <i>Flavonifractor</i>, <i>Pseudoflavonifractor</i> and <i>Oscillibacter</i> were significantly decreased in the infected samples, whereas <i>Escherichia</i>, <i>Nocardia</i> and <i>Chlamydia</i> 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, <i>E. tenella</i> 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 <i>E. tenella</i> and provides insight for potential new drug development. <b>RESEARCH HIGHLIGHTS</b>First simultaneous description of caecal microbiota and physiological indicators during <i>E. tenella</i> infection.Metagenomics used to explore functional properties of chicken caecal microbiota during <i>E. tenella</i> 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 <i>E. tenella</i> infection. Metagenomics used to explore functional properties of chicken caecal microbiota during <i>E. tenella</i> infection. Caecal microbial compositions and functional genes altered significantly after infection. Blood indicators and caecal morphology were significantly altered in the infected group.柔嫩艾美耳球虫（Eimeria tenella, E. tenella）是鸡盲肠的重要肠道寄生虫，可引发球虫病，每年给家禽养殖业造成巨额经济损失。肠道微生物群落的改变直接影响机体健康。为探究柔嫩艾美耳球虫对宿主的影响机制，本研究分析了卵囊脱落峰值时期盲肠微生物多样性的变化，以及宿主的生理与形态学改变。感染组与健康鸡只在盲肠病理特征与血液指标上存在显著差异。在属水平上，感染样本中粪杆菌属（Faecalibacterium）、梭菌属（Clostridium）、拉克洛梭菌属（Lachnoclostridium）、芽殖杆菌属（Gemmiger）、黄质杆菌属（Flavonifractor）、假黄质杆菌属（Pseudoflavonifractor）以及摆动杆菌属（Oscillibacter）的相对丰度显著降低，而埃希氏菌属（Escherichia）、诺卡氏菌属（Nocardia）和衣原体属（Chlamydia）的相对丰度则显著升高。感染样本中，与复制、重组和修复以及转录相关的功能基因通路显著下调，而与代谢相关的功能基因极显著降低。此外，柔嫩艾美耳球虫感染会降低宿主的血红蛋白水平与红细胞计数，大幅减少有益菌并增加潜在致病菌。本研究为进一步阐明柔嫩艾美耳球虫的致病机制提供了研究基础，也为潜在的新型药物开发提供了思路。**研究亮点** 首次同步描述了柔嫩艾美耳球虫感染期间的盲肠微生物群与生理指标变化。 利用宏基因组学（metagenomics）探究鸡柔嫩艾美耳球虫感染期间盲肠微生物群的功能特性。 感染后盲肠微生物组成与功能基因发生显著改变。 感染组的血液指标与盲肠形态学特征均发生显著改变。 首次同步描述了柔嫩艾美耳球虫感染期间的盲肠微生物群与生理指标变化。 利用宏基因组学（metagenomics）探究鸡柔嫩艾美耳球虫感染期间盲肠微生物群的功能特性。 感染后盲肠微生物组成与功能基因发生显著改变。 感染组的血液指标与盲肠形态学特征均发生显著改变。