The Imperial College Clinical Phenome Centre (CPC) deploys nuclear magnetic resonance (NMR) and mass spectrometry (MS) based platforms for near real time mapping of the surgical patient journey. This systems medicine approach is being used to explore the biochemical and functional impact of the gut microbiome on colon cancer biology. This is because the dietary-microbiome axis is essential to the initiation of colon cancer, and the microbiota directly influence the toxicity and efficacy of both surgical and medical therapeutic interventions. The CPC is therefore developing novel diagnostic technologies that account for the gut cancer microbiome and which function in the near real time scale for intra-operative use and for use in the critical care setting. This talk will therefore provide an overview of how surgical systems medicine is providing novel insights into the importance of the gut microbiome in colon cancer and outline why host-microbiome interactions are essential for the development of next generation ‘precision'-based surgical oncological therapies.