The ecology within: The impact of gut ecosystem dynamics on host fitness in the wild

单个动物通常是由小型生物组成的复杂得惊人的群落的家园。这一观察结果促使研究人员将个体视为自身的生态系统，挑战我们以新的方式思考生态过程如何驱动个体健康和适应性的变化。肠道正迅速成为个体内生态系统如何与宿主生理和健康相互作用的一个重要例子。在脊椎动物中，肠道不仅是数万亿“友好”细菌（“微生物群”）的家园，这些细菌在从消耗的食物中提取营养方面起着至关重要的作用，而且也是各种寄生虫群落的家园，它们与宿主争夺资源，并可能导致严重疾病。这种肠道生态系统对我们了解野生动物种群的生态和进化动态具有巨大的潜在意义。然而，我们目前对肠道生态系统动力学的驱动因素及其对自然种群宿主适应性的影响的理解非常有限。新一代测序方法在粪便样本中的应用代表了一种潜在的非侵入性监测野生动物肠道群落动态和饮食的革命性方法。这种方法已经彻底改变了我们对人类肠道细菌群落及其在健康和疾病中的作用的理解，但尚未应用于个体基因型、饮食、免疫和健康都受到密切监测的野生研究系统。该项目将把这种方法应用于纵向收集的野生哺乳动物粪便样本，同时监测肠道细菌、原生动物和线虫群落以及饮食的变化。这将使我们能够解决基本的悬而未决的问题，即哪些因素驱动个体体内的肠道群落动态，以及这些动态在自然条件下对健康和健身的影响。我们的研究系统，圣基尔达的Soay羊，将使我们能够定期和反复地对具有良好特征的遗传，环境经历和生殖史的已知个体进行采样。我们的项目还将涉及开发和应用一种新的统计方法，将肠道群落生态学数据与我们对宿主生态学和遗传学的理解结合起来，以及新的生态和流行病学模型，这些模型将改变我们对肠道生态系统如何影响宿主种群和自然界疾病动态的理解。我们的项目将提供第一个综合研究，绘制肠道共生和寄生虫群落，宿主饮食，免疫和野外健康之间的关系。我们的研究结果将深刻地提高我们对宿主生态系统在NERC职权范围内广泛的生态学科中的重要性的理解，包括人口、社区、疾病和进化生态学。

Individual animals are typically home to a staggeringly complex community of smaller organisms. This observation has led researchers to consider individuals as ecosystems in their own right, challenging us to think in new ways about how ecological processes may drive variation in an individual's health and fitness. The gut is rapidly emerging as an important example of how such within-individual ecosystems might interface with host physiology and health. In vertebrates, the gut is home not only to trillions of 'friendly' bacteria (the 'microbiota'), which have an essential role in extracting nutrition from food consumed, but also to diverse communities of parasites, which compete with their host for resources and can cause serious illness. The potential significance of this gut ecosystem for our understanding of the ecological and evolutionary dynamics of wild animal populations is immense. However, our current understanding of the drivers of gut ecosystem dynamics and their consequences for host fitness in natural populations is very limited. The application of new next-generation sequencing methods to faecal samples represents a potentially transformative approach to non-invasively monitor gut community dynamics and diet in wild animals. This approach has already revolutionised our understanding of the human gut bacteria community and its role in health and disease, but has yet to be applied to wild study systems in which individual genotype, diet, immunity and fitness are all closely monitored. This project will apply this approach to faecal samples collected longitudinally from an exceptionally well-studied wild mammal population to simultaneously monitor variation in gut bacteria, protozoan and nematode communities and diet. This will allow us to address fundamental outstanding questions about which factors drive gut community dynamics within individuals and the outcomes of these dynamics for health and fitness under natural conditions. Our study system, the Soay sheep of St Kilda, will allow us to regularly and repeatedly sample known individuals with well-characterised genetics, environmental experiences and reproductive history. Our project will also involve the development and application of a novel statistical approach to integrate data on gut community ecology with our understanding of host ecology and genetics, and new ecological and epidemiological models that will transform our understanding of how the gut ecosystem impacts on host population and disease dynamics in nature. Our project will provide the first integrated study mapping the relationships between gut commensal and parasite communities, host diet, immunity and fitness in the wild. Our findings will profoundly improve our understanding of the significance of within-host ecosystem across a broad range of ecological disciplines within NERC's remit, including population, community, disease and evolutionary ecology.