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

Publication date: 8 November 2017
Source:Cell Host & Microbe, Volume 22, Issue 5
Author(s): Neha Garg, Mingxun Wang, Embriette Hyde, Ricardo R. da Silva, Alexey V. Melnik, Ivan Protsyuk, Amina Bouslimani, Yan Wei Lim, Richard Wong, Greg Humphrey, Gail Ackermann, Timothy Spivey, Sharon S. Brouha, Nuno Bandeira, Grace Y. Lin, Forest Rohwer, Douglas J. Conrad, Theodore Alexandrov, Rob Knight, Pieter C. Dorrestein
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.

Graphical abstract

Teaser

Garg et al. introduce the technology that enables the volume cartography of the molecules and microbes onto a radiological image such as X-ray or CT scan of human organ. They demonstrate the concept by revealing the chemistry associated with the microbial communities from a cystic fibrosis patient.


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