Exploring the developing microbiome in new-born babies

The gut microbiome contains a large diverse community of microorganisms with our bacteria being best understood. These bacteria play crucial roles for our health such as aiding in the digestion of food, production of key vitamins and metabolites and programming out immune system. However, we are not born with this microbiome and the foundation of the microbiome is shaped during birth and thereafter by how the baby is fed. Evidence suggests that an altered intestinal microbiome may activate an uncontrolled pro-inflammatory response and numerous condition have been linked with a perturbed microbial/host dynamic. Much of the conditions to date have been studied in adults. Much less is known about the interaction of the developing microbiome with the host immune response and the consequences for the host. Necrotising Enterocolitis (NEC) is a condition, which is associated with a perturbed microbiome and aberrant immune responses to the microbiome. NEC is a devastating neonatal gastrointestinal inflammatory disease, which mainly affects low birth weight (LBW) and preterm infants. NEC affects 10-15% of preterm births < 32 weeks gestation and remains the leading cause of death from gastrointestinal disease in premature infants. This disease will be used as a model system with which to explore the make-up and establishment of the microbiome and the dynamic interaction of microbes with each other and the host immune function that can trigger tolerance or inflammation

The project will use a combination of microbiome analysis, immune profiling and mathematical analysis to define the development of the microbiome and its role in inflammation. Machine learning approaches will be used in analyzing microbial data to understand the evolving microbiome in health and disease. Protocols from evolutionary biology which will be used to dissect the factors that drive the assembly processes of the microbiome. Thus the project maps well onto animal systems, health and well being.