Copper-induced microbiota shifts and its effect on pig-gut colonisation by sil and sopE encoding Salmonella

肠道菌群在排除动物宿主的细菌病原体（如沙门氏菌）方面起着至关重要的作用。养猪户对将沙门氏菌排除在猪群之外特别感兴趣，因为这种病原体会损害生产力，影响动物福利，并通过进入食物链对人类构成风险。最大限度地提高生猪生产效率，同时保持产品的健康和安全，需要完全了解沙门氏菌与猪的相互作用，包括肠道微生物群。这个项目的核心是饮食引起的微生物群组成变化和沙门氏菌遗传学对这种相互作用的影响。由于主要在猪群中出现的一种鼠伤寒沙门氏菌变种（单相鼠伤寒沙门氏菌ST34）已经在全球传播，现在占英国人类鼠伤寒沙门氏菌感染的一半以上，占所有沙门氏菌感染的十分之一以上，因此对其进行更深入的了解是非常及时的。由于通过生物安全和疫苗接种方案，英国的蛋鸡和种鸡实际上已经消灭了肠炎沙门氏菌，ST34现在是导致英国牲畜感染沙门氏菌的最常见原因。与ST34的出现相一致的是，在猪的日粮中广泛使用铜补充剂来减少断奶期间的感染，并在育肥期间作为生长促进剂。自2005年禁止使用抗生素以来，它作为生长促进剂的重要性得到了提升。ST34菌株在遗传上是独一无二的，它对铜的抵抗力更强，并且获得了一种叫做SopE的毒素。已发表的和初步的数据表明，这两个因素都有可能影响沙门氏菌在饲粮中添加治疗水平铜的猪的肠道中活动的能力。英国ST34菌株的基因组流行病学研究表明，对铜和SopE抗性增强的ST34菌株比那些丢失或从未获得相关基因的菌株具有适应性优势。此外，微生物群的不同组成部分与定植抗性有关，这取决于沙门氏菌的遗传，包括sopE基因的存在。因此，迫切需要了解的不仅是猪肠道菌群组成的变化是由铜补充饮食引起的，而且还需要了解这对沙门氏菌不同遗传变异的定植抗性的影响。这些及时的信息将有助于在农场实践方面做出基于证据的决策，从而最大限度地提高生产力、动物福利和食品安全。该项目旨在通过描述由于添加高铜含量饲料而导致的猪肠道细菌变化的特征来解决这些知识空白。这将确定对沙门氏菌产生定殖抗性的潜在介质。肠道菌群变化对沙门氏菌定植的影响将通过体外肠道模型和封闭实验室中猪群的实验性感染进行调查。最后，为了进一步研究介导肠道定植抵抗沙门氏菌的肠道细菌，我们将在体外培养肠道菌群，并通过合作在小鼠感染模型的后续实验中研究它们与沙门氏菌的直接和间接相互作用。该项目将产生大量研究人员感兴趣的数据，以解决猪产业的相关问题，如饲料转化（生产力）和生物医学，猪被用作研究人类疾病的模型。免费提供的资源将包括大量的基因组序列和猪肠道培养细菌的收集，以补充最近在猪肠道细菌收集（PiBAC）中提供的资源。

The gut microbiota plays a crucial role in the exclusion of bacterial pathogens such as Salmonella from animal hosts. Pig farmers are particularly interested in excluding Salmonella from herds because this pathogen compromises productivity, impacts animal welfare and presents a risk to the human population by gaining entry into the food chain. Maximising productivity in pig production while maintaining a healthy and safe product requires a complete understanding of the interaction of Salmonella with the pig including the gut microbiota. Central to this project are the consequences of diet-induced variation in the microbiota composition and the genetics of Salmonella on this interaction. The need for a greater understanding is extremely timely since the emergence of a variant of Salmonella Typhimurium (monophasic S. Typhimurium ST34) primarily in pig populations has spread globally and now accounts for over half of all S. Typhimurium infections in people in the UK, and over 1 in 10 of all Salmonella infections. Since the virtual eradication of Salmonella Enteritidis from layer hens and breeding flocks in the UK through biosecurity and vaccination regimens, ST34 is now the single most common cause of Salmonella infection resulting from UK livestock. Coincident with the emergence of ST34 has been the widespread use of copper supplementation in the diet of pigs to decrease infections during weaning, and as a growth promotor during fattening. Its perceived importance as a growth promotor has increased since antibiotics were banned for such use in 2005.The ST34 strain is genetically unique in being more resistant to copper and having acquired a toxin called SopE. Published and preliminary data suggest that both of these factors have the potential to affect the ability of Salmonella to exploit the gut of pigs on a diet supplemented with therapeutic levels of copper. Genomic epidemiology of ST34 strains in the UK suggests that ST34 strains with increased resistance to copper and SopE have a fitness advantage over those that have either lost or never acquired the associated genes. Furthermore, that different components of the microbiota have been implicated in colonisation resistance depending on the genetics of the Salmonella, including the presence of the sopE gene.There is a pressing need therefore to not only understand the changes in the composition of the pig gut microbiota that result from a copper supplemented diet, but also the impact that this has on colonisation resistance to distinct genetic variants of Salmonella. This timely information will lead to evidence-based decisions on farm practices that maximise productivity, animal welfare and food safety.The project aims to address these gaps in knowledge by characterising the changes in the gut bacteria of pigs that occurs as a result of supplementation of feed with elevated levels of copper. This will identify potential mediators of colonisation resistance to Salmonella. The effect of changes in the gut microbiota on colonisation by Salmonella will be investigated using an in vitro gut model and with experimental infections of groups of pigs in a containment laboratory. Finally, in order to further study bacteria of the gut that mediate gut colonisation resistance to Salmonella we will culture gut microbiota bacteria and investigate their direct and indirect interaction with Salmonella in vitro, and through collaboration in follow-on experiments using the mouse model of infection.The project will generate a large amount of data of interest to researchers addressing related questions in the pig industry such as feed conversion (productivity) and biomedicine where the pig is used as a model to study human disease. Resources made freely available will include a large number of genome sequences and a collection of cultured bacteria of the pig gut complementing those recently made available in the pig intestinal bacteria collection (PiBAC).