Revisiting microbe-metabolite interactions: doing better than random

Morton, J.; McDonald, D.; Aksenov, A.; Nothias-Scaglia, L.-F.; Foulds, J.; Quinn, R. A.; Badri, M.; Swenson, T.; Van Goethem, M.; Northen, T.; Vazquez-Baeza, Y.; Wang, M.; Bokulich, N.; Watters, A.; Song, S. J.; Bonneau, R.; Dorrestein, P.; Knight, R.

doi:10.1101/2019.12.10.871905

bioRxiv · 10.1101/2019.12.10.871905

Revisiting microbe-metabolite interactions: doing better than random

Morton, J.·McDonald, D.·Aksenov, A.·Nothias-Scaglia, L.-F.·Foulds, J.·Quinn, R. A.·Badri, M.·Swenson, T.·Van Goethem, M.·Northen, T.·Vazquez-Baeza, Y.·Wang, M.·Bokulich, N.·Watters, A.·Song, S. J.·Bonneau, R.·Dorrestein, P.·Knight, R.

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Abstract

I.Recently, Quinn and Erb et al [1] made the case that when used correctly, correlation and proportionality can outperform MMvec when identifying microbe-metabolite interactions. We revisit this comparison and show that the proposed correlation and proportionality are outperformed by MMvec on real data due to their inability to deal with sparsity commonly observed in microbiome and metabolome datasets.

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Morton, J., McDonald, D., Aksenov, A., Nothias-Scaglia, L.-F., Foulds, J., Quinn, R. A., Badri, M., Swenson, T., Van Goethem, M., Northen, T., Vazquez-Baeza, Y., Wang, M., Bokulich, N., Watters, A., Song, S. J., Bonneau, R., Dorrestein, P., Knight, R.. 2019-12-16. Revisiting microbe-metabolite interactions: doing better than random. https://doi.org/10.1101/2019.12.10.871905

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