Breeders to broilers: optimising chicken health and performance to reduce susceptibility to zoonotic bacteria, viruses, and parasite colonisation.

健康饲养的牲畜对经济和社会繁荣至关重要。随着世界人口的增长（到2050年约为90亿），家禽将成为蛋白质的主要来源，我们不仅要研究优化鸟类健康和性能的方法，还要同时降低对人畜共患病细菌，病毒和寄生虫定植的易感性（1）。这种降低的敏感性可以对动物和人类健康产生积极影响，并减少抗菌剂的使用。基因选择和饲料配方导致了高标准的肉鸡生产，但在农场和连续的鸡群之间仍然存在差异（2）。在肉鸡（专门饲养的鸡肉）中，饲料转化率及其健康状况在很大程度上取决于复杂的肠道微生物组，该微生物组在营养同化，维生素和氨基酸生产以及预防病原体定植中发挥作用（3）。关于亲本种鸡群以及各自的微生物组如何影响鸡的健康，性能和对下游肉鸡的人畜共患病细菌，病毒和寄生虫定植的易感性知之甚少。我们之前的研究已经开始证明商业肉鸡品系之间和品系内人畜共患病细菌定殖水平的差异（4，5）。选择性饲养家禽以提高对人畜共患病细菌的抗性（例如，弯曲杆菌、沙门氏菌和埃希氏菌）、病毒和寄生虫是一种有吸引力的控制策略（6）。在商业肉鸡种群中进行的全基因组关联研究（GWAS）表明，对特定人畜共患病病原体盲肠定殖的抗性处于中度遗传控制之下（7）。此外，抗性的遗传差异与数量性状基因座和免疫相关基因的转录有关（7）。总体项目的目标是研究育种者和商业肉鸡微生物组和宿主遗传学如何转化为优化的鸟类健康和性能，同时降低对人畜共患病细菌，病毒和寄生虫定植的易感性。这些发现可以对动物和人类健康产生直接的积极影响。PhD目标：- （i）确定高性能和低性能种鸡的微生物组与动物健康的关系，以及对人畜共患细菌、病毒和寄生虫定植的敏感性。(ii)调查种禽孵化日对下游肉鸡微生物组、健康、性能和对人畜共患病细菌、病毒和寄生虫定植的易感性的影响。(iii)研究种鸡和肉鸡宿主遗传学，绘制与禽类健康、生产性能和对人畜共患病细菌、病毒和寄生虫肠道定植易感性相关的遗传区域。

Healthily maintained livestock are essential for economic and societal prosperity. As the world population grows (around 9 billion by 2050), poultry will become the main source of protein and it is paramount we not only investigate methods to optimise bird health and performance, but simultaneously reduce susceptibility to zoonotic bacteria, virus and parasite colonisation (1). This reduced susceptibility can positively impact animal and human health and lessen antimicrobial usage.Genetic selection and feed formulation have led to high standards of broiler production, however there still exists variability between farms and successive flocks (2). In broilers (chickens specifically raised for their meat), feed conversion and their health status is heavily dependent on the complex gut microbiome which plays a role in nutrient assimilation, vitamin and amino acid production and prevention of pathogen colonisation (3). Very little is known about parent breeder flocks and how the respective microbiome can impact chicken health, performance and the susceptibility to zoonotic bacteria, virus and parasite colonisation of downstream broilers. Our previous studies have begun to demonstrate the differences that exist in the levels of zoonotic bacteria colonisation from across and within commercial broiler lines (4, 5). Selective breeding of poultry to increase resistance to zoonotic bacteria (e.g., Campylobacter, Salmonella and Escherichia), viruses and parasites is an attractive control strategy (6). Genome-wide association studies (GWAS) in commercial broiler populations have indicated that resistance to caecal colonisation of specific zoonotic pathogens is under moderate genetic control (7). Moreover, heritable differences in resistance have been associated with quantitative trait loci, and the transcription of genes related to immunity (7). The overarching project aim is to characterise how breeders and commercial broiler microbiomes and host genetics translate to optimised bird health and performance in conjunction with a reduced susceptibility to zoonotic bacteria, virus and parasite colonisation. These findings can have a direct positive impact on both animal and human health. The PhD Objectives: - (i) Characterise the microbiomes of high and low performing breeder chickens in relation to animal health, and susceptibility to zoonotic bacteria, virus and parasite colonisation.(ii) Investigate the impact of breeder hatching day on downstream broiler microbiomes, health, performance and susceptibility to zoonotic bacteria, virus and parasite colonisation. (iii) Investigate breeder and broiler host genetics to map genetic regions associated with bird health, performance and susceptibility to zoonotic bacteria, virus and parasite gut colonisation.