Gut health prediction biomarkers in broiler chickens under necrotic enteritis challenge condition

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The ban and limitation in the use of antibiotic growth promoters in poultry has resulted in the re-emergence of enteric diseases such as necrotic enteritis (NE), a disease caused by overgrowth of Clostridium perfringens, which produces different toxins resulting in damage to the intestinal wall. Annually, the global poultry industry loses USD 6 billion as a result of NE, mainly due to mortality and loss of performance. There are two forms of NE, namely clinical and subclinical, characterized by acute infection with mortality reaching up to 50%, and loss of performance due to damage to the intestinal mucosa leading to impaired digestion and absorption of nutrients, respectively. For the industry to control NE outbreaks, early warning systems with accurate prediction will be beneficial. Currently, there are no biological markers (biomarkers), which can be used to detect outbreaks of NE in poultry early using invasive or non-invasive methodologies. Therefore; The long-term objective of the proposed research is to develop our capacity to predict NE pathogenesis in broiler chickens before the disease takes hold in a flock to minimize its impact on production and welfare. With three short-term objectives, three types of biomarkers will be identified in the next five years, which includes host related, microbial and metabolic biomarkers. Short-term objective (1) will identify host-related biomarkers, which will include gut (jejunum and ileum) associated biomarkers using a controlled NE challenge model. Short-term objective (2) will identify gut (ileal contents, mucosal swabs) and faecal microbial markers of NE in chickens. Short-term objective (3) will identify metabolic (ileal contents, faecal droppings and blood) biomarkers of NE in chickens. Short-term objective-1 will use invasive sampling technique (gut tissue), while short-term objectives-2 and -3 will use both an invasive (mucosal swabs, gut content, and blood) and non-invasive (faecal droppings) techniques. The proposed research program will utilize an interdisciplinary approach to study the gut, microbial and metabolic biomarkers. Various technologies such RNASeq, 16S sequencing, metabolomics and real-time PCR will be employed for identifying and quantifying biomarkers. The proposed research will allow us to train 2 PhD and 1 MSc in cutting-edge scientific technologies spanning immunology, microbiome and metabolomics, which are becoming highly desirable skills in addition to classical poultry nutrition. Furthermore, 1 summer student per year for 5 years will be trained under this proposal working closely with the 2 PhD students. Understanding of the three pillars of host, microbiome and metabolic biomarkers will be useful in understanding the changes in biomarkers that are associated with NE. The finding from this research program will have a wider contribution in the development of biomarkers for a commercial setting allowing producers to control NE before it takes hold in their flocks.