Samitha Somathilaka, a PhD student in TSSG and the VistaMilk SFI Centre, presented at the SFI Summit 2020.
Abstract: Bacterial populations reside in the human gut as an ecosystem, namely gut microbiome. They communicate with each other through molecules to execute the tasks required for their survival, such as carbohydrate metabolism. Collectively, all these interactions on the molecular level, here modelled as a computer network, are capable of affecting the behaviour of the human gut. Moreover, the disruption of these molecular interactions results in the imbalance of gut microbiota composition causing diseases, including type 2 diabetes. Here, we introduce a simulator to address the complexity of gut microbiome by breaking it down into several layers of molecular interactions, allowing us to understand the contribution of each one of them to the whole ecosystem. To validate the simulator performance, we use carbohydrate metabolism experimental data and neural network models to recognize the existing interactions between the molecules detected by the bacteria and the microbiome end behaviour to identify possible issues. Our analysis reveals the adaptation of the carbohydrate metabolism based on the molecules detected in the environment. This result can be applied to the precise identification of the causes of gut microbiome-related diseases to propose novel treatments based on the adjustment of the bacterial collective behaviours at the molecular level.