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

肠道微生物群在将沙门氏菌等细菌病原体从动物宿主中排除方面起着至关重要的作用。养猪户对从猪群中排除沙门氏菌特别感兴趣，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。在保持健康和安全的产品的同时最大限度地提高养猪生产的生产力，需要全面了解沙门氏菌与猪的相互作用，包括肠道微生物群。该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。由于鼠伤寒沙门氏菌的一种变异体的出现，对更好的了解的需要是非常及时的。主要在猪群中的鼠伤寒沙门氏菌（Typhimurium ST 34）已经在全球范围内传播，现在占所有S。在英国，鼠伤寒杆菌感染占所有沙门氏菌感染的十分之一以上。自从英国通过生物安全和疫苗接种方案从蛋鸡和养殖群中实际根除沙门氏菌以来，ST 34现在是英国牲畜沙门氏菌感染的最常见原因。与ST 34的出现相一致的是，在猪的饮食中广泛使用铜补充剂，以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有所增加。ST 34菌株在遗传上是独一无二的，对铜更具抗性，并获得了一种称为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利用补充有治疗水平铜的饮食的猪的肠道的能力。英国ST 34菌株的基因组流行病学表明，对铜和SopE抗性增加的ST 34菌株比那些失去或从未获得相关基因的菌株具有适应性优势。此外，根据沙门氏菌的遗传学（包括sopE基因的存在），微生物群的不同组分与定植抗性有关。因此，迫切需要不仅了解由铜补充饮食引起的猪肠微生物群组成的变化，还需要了解这对沙门氏菌不同遗传变体的定植抗性的影响。这些及时的信息将导致对农场实践的循证决策，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饲料中添加高水平铜而导致的猪肠道细菌的变化来填补这些知识空白。这将确定沙门氏菌定植抗性的潜在介质。肠道微生物群变化对沙门氏菌定植的影响将使用体外肠道模型和在密闭实验室中对猪群进行实验性感染进行研究。最后，为了进一步研究介导肠道对沙门氏菌的定植抗性的肠道细菌，我们将培养肠道微生物群细菌并研究它们与沙门氏菌的直接和间接体外相互作用，通过合作，该项目将产生大量研究人员感兴趣的数据，以解决养猪业的相关问题，如饲料转化（生产力）和生物医学，其中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集合，以补充最近在猪肠道细菌集合（PiBAC）中提供的那些。

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).