# Cystic Fibrosis Dataset

This dataset contains paired microbiome and metabolome data derived from lung mucus samples of patients with cystic fibrosis (CF). Adapted from:

- https://github.com/biocore/mmvec/tree/master/examples/cf

The dataset was used as a demonstration in the MMvec paper:

- Morton, J. T., Aksenov, A. A., Nothias, L. F., Foulds, J. R., Quinn, R. A., Badri, M. H., ... & Knight, R. (2019). Learning representations of microbe–metabolite interactions. Nature Methods, 16(12), 1306-1314.

The original dataset was published in:

- Quinn, R. A., Comstock, W., Zhang, T., Morton, J. T., da Silva, R., Tran, A., ... & Dorrestein, P. C. (2018). Niche partitioning of a pathogenic microbiome driven by chemical gradients. Science Advances, 4(9), eaau1908.

This dataset contains 172 samples, 2720 microbes (16S rRNA V4 ASVs), and 462 metabolites (LC-MS/MS)

The MMvec analysis revealed a strong association between _Pseudomonas aeruginosa_, a major pathogen responsible for lung infections in CF, and rhamnolipids, which are key virulence factors produced by this organism.

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Note: The actual data files are not kept in the codebase due to their sizes.
