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

饲养健康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，我们不仅研究优化鸟类健康和生产性能的方法，而且同时降低对人畜共患细菌、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的健康产生积极的影响，并减少抗菌剂的使用。遗传选择和饲料配方导致了肉鸡生产的高标准，但农场和连续饲养的鸡群之间仍然存在差异。在肉鸡(专门为其肉而饲养的鸡)中，饲料转换和它们的健康状况在很大程度上取决于复杂的肠道微生物群，该微生物群在营养同化、维生素和氨基酸生产以及防止病原体定植方面发挥作用(3)。人们对亲本种鸡群以及各自的微生物群如何影响鸡的健康、生产性能以及下游肉鸡对人畜共患病细菌、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，在商业肉鸡品系(4，5)中，人畜共患细菌的定植水平存在差异。选育家禽以增加对人畜共患病细菌(如弯曲杆菌、沙门氏菌和大肠杆菌)、病毒和寄生虫的抵抗力是一个有吸引力的控制策略。商业肉鸡种群的全基因组关联研究表明，对特定人畜共患病病原体盲肠定植的抵抗力处于中等遗传控制之下(7)。此外，可遗传的抗性差异与数量性状基因座和免疫相关基因的转录有关(7)。该项目的总体目标是描述养殖者和商业肉鸡的微生物群落和宿主遗传学如何转化为优化的禽类健康和生产性能，同时降低对人畜共患细菌、病毒和寄生虫定植的易感性。这些发现可以对动物和人类的健康产生直接的积极影响。PHD目标：-(I)描述与动物健康有关的高、低性能种鸡的微生物群，以及对人畜共患细菌、病毒和寄生虫定植的敏感性。(Ii)调查种鸡孵化日对下游肉鸡微生物群、健康、生产性能和对人畜共患细菌、病毒和寄生虫定植的易感性的影响。(Iii)调查种鸡和肉鸡宿主的遗传学，以绘制与禽类健康、生产性能和对人畜共患细菌、病毒和寄生虫肠道定植的易感性相关的遗传区域图。

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.