雞球蟲病是造成養雞產業相當大損失的重要疾病之一。主要是造成雞隻腸道上皮細胞中度至嚴重損壞，導致增重與飼料效率降低，並經常引發雞群高的發病率和死亡率。本試驗應用Illumina MiSeq system 分析球蟲對於土雞盲腸與泄殖腔內微生物菌相的影響。DNA樣品取自雞隻盲腸有球蟲感染與沒有受到球蟲感染的盲腸與泄殖腔內容物。以16S rRNA共通的引子組與Illumina MiSeq system 定序分析獲得每個樣品組大量的細菌類群的DNA片段定量型材(quantitative profiles)。採用分層聚類和主成分分析已鑑定出的類群的相對百分比豐度。在盲腸沒有球蟲感染的雞隻盲腸內容物的微生物菌相中，以擬桿菌屬(Bacteroides)最豐富，其次分別為牛黄瘤胃球菌屬(Ruminococcus)、Alistipes及梭孢桿菌屬(Clostridium)。而在盲腸有球蟲感染的雞隻盲腸內容物的微生物菌相中，則以Clostridium最豐富，其次分別為Bacteroides及Alistipes。在盲腸沒有球蟲感染的雞隻泄殖腔內容物的微生物菌相中，以Clostridium最豐富，其次分別為 Bacteroides、Subdoligranulum及乳桿菌屬(Lactobacillus)。而在盲腸有球蟲感染的雞隻泄殖腔內容物的微生物菌相中，也是以Lactobacillus最豐富，其次為Clostridium、Turicibacter及Bacteroides。球蟲感染明顯地影響雞隻盲腸與泄殖腔內微生物菌相的分布與豐度。本研究所呈現球蟲感染對雞腸道菌群的影響，可作為雞隻球蟲病防治的重要參考資訊。

Coccidiosis, one of the most important chicken diseases, causes considerable economic loss in the chicken industry. Coccidiosis causes serious mucosal damage and predisposes chickens to enteropathogen infection. In this study, Illumina sequencing approach was used to evaluate effects of coccidiosis on the intestinal microflora of native chicken. Total DNA was isolated from the cecal and cloaca contents of infected and uninfected birds, respectively, PCR amplified with an universal 16S rRNA barcodes, and sequenced by Illumina MiSeq. Quantitative profiles of bacterial taxa were obtained using an analysis pipeline written in Perl. The relative abundance of the identified taxa was analyzed using hierarchical clustering and principal component analysis. Samples from the cecal contents of uninfected chickens were dominated by bacterial species belonging to the genera Bacteroides, Ruminococcus, Alistipes and Clostridium; cecal contents of infected samples were dominated by species from the genera Clostridium, Alistipes and Bacteroides. On the other hand, samples from the cloaca of uninfected chickens were dominated by bacterial species belonging to genera Clostridium, Bacteroides, Subdoligranulum and Lactobacillus; the infected cloaca samples were dominated by species from the genera Lactobacillus, Clostridium, Turicibacter and Bacteroides. Coccidia infection affects not only the richness of the microbial communities but also its composition in the cecum and cloaca. These results prove the coccidia influence on the microbial communities of chicken gut and provide important information for the prevention and cure of chicken coccidiosis.

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