Three dimensional cartography of microbiome and metabolome data onto radiological images of the human lung

Our understanding of spatial variation of the chemical and microbial make-up of an entire human organ remains limited, in part due to the size and heterogeneity of human organs and the complexity of the associated metabolome and microbiome. To address this challenge we developed a workflow, including the adaptation of a software, to enable the cartography of metabolomics and microbiome data onto a three dimensional (3D) organ reconstruction built off radiological images. Our methodology enabled for the first time the visualization of the microbial and chemical makeup of a human lung from a cystic fibrosis patient. We detected host-derived molecules, microbial metabolites, different medications, and regiospecific metabolism of medications. Consequently, metabolomics data can now be understood in the context of microbial distributions in the lung. Our tool, which allows visualization of omics data on an organ in 3D and the browsable maps of the first 3D microbiome/metabolome reconstruction on a radiological image of a human lung are an interactive resource for the scientific community.