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

禁止和限制在家禽中使用抗生素生长促进剂已导致肠道疾病的再次出现，如坏死性肠炎(NE)，这是一种由产气荚膜梭菌过度生长引起的疾病，它会产生不同的毒素，导致肠壁受损。每年，全球家禽业因NE造成的损失达60亿美元，主要原因是死亡率和生产性能损失。NE有两种形式，即临床型和亚临床型，其特征分别是急性感染和死亡率高达50%，以及由于肠粘膜受损导致营养消化和吸收障碍而导致的功能丧失。对于控制NE疫情的行业来说，准确预测的早期预警系统将是有益的。目前，还没有生物标志物可以用来通过侵入性或非侵入性方法来早期检测家禽中NE的暴发。因此，这项拟议研究的长期目标是发展我们在疾病在鸡群中流行之前预测肉鸡NE发病的能力，以将其对生产和福利的影响降至最低。在三个短期目标中，未来五年将确定三种类型的生物标志物，包括与宿主相关的生物标志物、微生物生物标志物和代谢生物标志物。短期目标(1)将确定宿主相关的生物标志物，其中将包括肠道(空肠和回肠)相关的生物标志物，使用受控的NE挑战模型。短期目标(2)将确定鸡的肠道(回肠内容物、粘膜拭子)和粪便中NE的微生物标志物。短期目标(3)将确定鸡体内去甲肾上腺素的代谢(回肠含量、粪便和血液)生物标志物。短期目标-1将使用侵入性采样技术(肠道组织)，而短期目标-2和-3将使用侵入性(粘膜拭子、肠道内容物和血液)和非侵入性(粪便)技术。拟议的研究计划将利用跨学科的方法来研究肠道、微生物和代谢生物标志物。将采用各种技术，如RNAseq、16S测序、代谢组学和实时聚合酶链式反应(Real-time PCR)来识别和量化生物标志物。拟议的研究将使我们能够培训2名博士和1名硕士，掌握横跨免疫学、微生物组和代谢组学的尖端科学技术，这些技术正成为经典家禽营养之外非常可取的技能。此外，根据这项提议，每年将有1名暑期学生接受为期5年的培训，与2名博士生密切合作。了解宿主、微生物和代谢生物标志物的三大支柱将有助于理解与NE相关的生物标志物的变化。这项研究计划的发现将对开发用于商业环境的生物标记物做出更广泛的贡献，使生产商能够在NE在他们的羊群中站稳脚跟之前控制它。

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.