Journal
NATURE METHODS
Volume 16, Issue 12, Pages 1306-+Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41592-019-0616-3
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Funding
- Office of Science Early Career Research Program, Office of Biological and Environmental Research of the U.S. Department of Energy [DE-AC02-05CH11231]
- National Institutes of Health grants [S10RR029121, R03 CA211211]
- Janssen Human Microbiome Institute
- Center for Microbiome Innovation
- National Science Foundation grant [GRFP DGE-1144086]
- Janssen [20175015]
- Alfred P. Sloan Foundation [G-2017-9838]
- [P41GM103484]
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Integrating multiomics datasets is critical for microbiome research; however, inferring interactions across omics datasets has multiple statistical challenges. We solve this problem by using neural networks (https://github.com/biocore/mmvec) to estimate the conditional probability that each molecule is present given the presence of a specific microorganism. We show with known environmental (desert soil biocrust wetting) and clinical (cystic fibrosis lung) examples, our ability to recover microbe-metabolite relationships, and demonstrate how the method can discover relationships between microbially produced metabolites and inflammatory bowel disease.
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