Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung

Cell Host Microbe. 2017 Nov 8;22(5):705-716.e4. doi: 10.1016/j.chom.2017.10.001. Epub 2017 Oct 19.


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: cartography; cystic fibrosis; mass spectrometry; metabolomics; microbiome; molecular networking.

MeSH terms

  • Adult
  • Base Sequence
  • Biodiversity
  • Cystic Fibrosis / diagnostic imaging
  • Cystic Fibrosis / metabolism
  • Cystic Fibrosis / microbiology
  • DNA, Bacterial / analysis
  • Humans
  • Imaging, Three-Dimensional / methods*
  • Lung / diagnostic imaging*
  • Lung / metabolism*
  • Lung / microbiology*
  • Lung Diseases / diagnostic imaging*
  • Lung Diseases / metabolism*
  • Lung Diseases / microbiology*
  • Male
  • Mass Spectrometry
  • Metabolome / physiology*
  • Metabolomics
  • Microbiota / physiology*
  • RNA, Ribosomal, 16S / genetics
  • RNA, Ribosomal, 18S / genetics
  • Tomography Scanners, X-Ray Computed
  • Xenobiotics / metabolism


  • DNA, Bacterial
  • RNA, Ribosomal, 16S
  • RNA, Ribosomal, 18S
  • Xenobiotics