Cell Host & Microbe
Volume 22, Issue 5, 8 November 2017, Pages 705-716.e4
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Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung

https://doi.org/10.1016/j.chom.2017.10.001Get rights and content
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Highlights

  • CT scan images used to generate 3D models of human lungs for mapping omics data

  • Microbiome and metabolome data obtained from a CF lung

  • Omics data plotted on 3D lung model to visualize spatial interactions and variations

  • Region-specific metabolism of medications placed in the context of microbial distribution

Summary

Our understanding of the spatial variation in the chemical and microbial makeup 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 to enable the cartography of metabolomic and microbiome data onto a three-dimensional (3D) organ reconstruction built off radiological images. This enabled the direct visualization of the microbial and chemical makeup of a human lung from a cystic fibrosis patient. We detected host-derived molecules, microbial metabolites, medications, and region-specific metabolism of medications and placed it in the context of microbial distributions in the lung. Our tool further created browsable maps of a 3D microbiome/metabolome reconstruction map on a radiological image of a human lung and forms an interactive resource for the scientific community.

Keywords

metabolomics
microbiome
cystic fibrosis
mass spectrometry
molecular networking
cystic fibrosis
cartography

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