Investigating the immune factors that determine commensal microbiota assembly

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.