Implementation of a Pipeline Integrating Gut Metagenome Data, Host Immunogenetic Characteristics and Clinical Gut Inflammatory Biomarkers for Stratified Clinical Management

The combined analysis of microbiome, immunological parameters and host genetics in patients has potential for applying personalized approaches of prevention, diagnostics or therapy in the future. However, the acquisition and analysis of these patient characteristics in a scientifically sound, technically reliable, cost-effective, practicable and future-oriented fashion are a far from trivial task. Therefore the objectives of the study are (i) to optimize a sample and data acquisition and analysis pipeline that fulfills these criteria (using samples from healthy volunteers); (ii) validate the pipeline in a cohort of children undergoing stem cell transplantation, yielding information on host immuno-genetics, gut immune function and the human gut microbiome; (iii) deduct the most critical parameters for host-microbiome interplay from this complex dataset.