Investigating the immune factors that determine commensal microbiota assembly

胃肠道是一个复杂的共生细菌群落的家园--被称为微生物区系--为人类的新陈代谢健康和免疫功能提供有益的功能。然而，微生物区系的变化与人类一系列炎症性和自身免疫性疾病的发生或发展有关，包括炎症性肠道疾病和肥胖症，以及大脑、心脏、呼吸道和关节等外围器官的疾病。因此，迫切需要了解这个复杂的微生物群落在早期阶段是如何形成的，以及调节它的生命因素以促进它的互惠功能。哺乳动物肠道微生物区系的发展是可以预测的，先锋物种在出生后定居在肠道，随后是其他微生物的有序演替[1，2]，但塑造微生物组组装可预测动态的力量在很大程度上仍然未知。环境和饮食、宿主免疫系统以及个体微生物之间的相互作用都可能塑造微生物区系的动态，但在如此复杂的生态系统中，确定任何一个因素的具体作用是具有挑战性的[3]。最近，我们结合了下一代测序、数学建模和机器学习，以揭示微生物-微生物相互作用在塑造这种组装过程中的作用[1]。这项工作使我们能够确定特定的王国内和王国之间的相互作用，这些相互作用在早产儿微生物组组装的可预测性中发挥着核心作用。然而，我们的方法没有考虑东道主在这一过程中可能发挥的作用。

The gastrointestinal tract is home to a complex community of commensal bacteria - known as the microbiota - which provide beneficial functions for human metabolic health and immune function. However, changes in the microbiota have been implicated in the development or progression of a wide range of inflammatory and autoimmune diseases in humans, including inflammatory bowel disease and obesity, but also diseases of peripheral organs such as the brain, heart, airways and joints. Thus, an understanding of how this complex microbial community forms during the early stages, and the factors that regulate it of life to promote it's mutually beneficial functions is urgently required.The mammalian gut microbiota develops remarkably predictably with pioneer species colonizing the gut after birth, followed by an ordered succession of other microbes [1,2], but the forces that shape the predictable dynamics of microbiome assembly remain largely unknown. The environment and diet, the host immune system, and interactions between individual microbes all potentially shape the dynamics of the microbiota, but in such a complex ecosystem, identifying the specific role of any one factor is challenging [3]. Recently, we combined next-generation sequencing, mathematical modelling, and machine learning to disentangle the role of microbe-microbe interactions in shaping this assembly process [1]. This work enabled us to identify specific within- and between-kingdom interactions that are playing a central role in the predictability of microbiome assembly within preterm infants. However, our approaches did not look at the role the host might be playing in this process.