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Metagenomic analysis of intestinal microbiome in broiler chickens developing clinical and subclinical necrotic enteritis

2021 CPRF
Necrotic enteritis (NE) is an economically important, re-emerging enteric disease of broiler chickens. It is caused by Clostridium perfringens (C. perfringens) associated with predisposing factors such as high protein diet, immunosuppression and coccidiosis. Pathogenesis of NE is not fully understood and no effective preventive measures or vaccines are available. The objective of this study was to understand the pathogenesis of NE to develop effective control strategies. In order to explore this objective, we studied intestinal microbiome of broiler chickens when birds develop clinical and subclinical NE following C. perfringens exposure. We have successfully developed a subclinical and clinical NE disease model by increasing the dietary protein to promote colonization of C. perfringens in broiler chickens. Birds challenged with C. perfringens developed classical gross and histopathological lesions of NE. Intestinal contents were collected (n=8/category) from healthy birds, and birds with clinical and subclinical disease to conduct metagenomics of the intestinal microbiome. Next generation 16S amplicon sequencing was performed to assess the degree of dysbiosis. Genomic DNA was isolated from the Jejunum using a commercial kit (Qiagen Inc., Germany). Nextera XT DNA Library Preparation Kit (24 samples) from Illumina was used and microbial 16S amplicon genes were amplified with indexed and adaptor-linked universal primers targeting the V3-4 region. Amplicon libraries were sequenced using Illumina MiSeq system (Illumina, San Diego, US) for paired-end reads of 300 bp. Metagenomics data were analyzed using Geneious prime software 2020. Normal intestinal flora consisted primarily with Lactobacillaceae, Cyanobacteria and Peptostreptococcaceae, with a small amount of Clostridiaceae. Birds with NE had considerably decreased Lactobacillaceae, and increased Clostridiaceae and Enterobacteriaceae. The degree of dysbiosis was severe in birds with clinical disease compared to subclinical infection. The results of this study will provide the opportunity to study preventative measures of NE associated with C. perfringens infection.
Tags :
clinical infection,gut microbiome,necrotic enteritis,subclinical infection
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PhD Student

University of Saskatchewan

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