AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities.

Heinken, A.; Acharya, G.; Ravcheev, D. A.; Hertel, J.; Nyga, M.; Okpala, O. E.; Hogan, M.; Magnusdottir, S.; Martinelli, F.; Preciat, G.; Edirisinghe, J. N.; Henry, C. S.; Fleming, R. M. T.; Thiele, I.

doi:10.1101/2020.11.09.375451

bioRxiv · 10.1101/2020.11.09.375451

AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities.

Heinken, A.·Acharya, G.·Ravcheev, D. A.·Hertel, J.·Nyga, M.·Okpala, O. E.·Hogan, M.·Magnusdottir, S.·Martinelli, F.·Preciat, G.·Edirisinghe, J. N.·Henry, C. S.·Fleming, R. M. T.·Thiele, I.

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Abstract

The human microbiome influences the efficacy and safety of a wide variety of commonly prescribed drugs, yet comprehensive systems-level approaches to interrogate drug-microbiome interactions are lacking. Here, we present a computational resource of human microbial genome-scale reconstructions, deemed AGORA2, which accounts for 7,206 strains, includes microbial drug degradation and biotransformation, and was extensively curated based on comparative genomics and literature searches. AGORA2 serves as a knowledge base for the human microbiome and as a metabolic modelling resource. We demonstrate the latter by mechanistically modelling microbial drug metabolism capabilities in single strains and pairwise models. Moreover, we predict the individual-specific drug conversion potential in a cohort of 616 colorectal cancer patients and controls. This analysis reveals that some drug activation capabilities are present in only a subset of individuals, moreover, drug conversion potential correlate with clinical parameters. Thus, AGORA2 paves the way towards personalised, predictive analysis of host-drug-microbiome interactions.

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Heinken, A., Acharya, G., Ravcheev, D. A., Hertel, J., Nyga, M., Okpala, O. E., Hogan, M., Magnusdottir, S., Martinelli, F., Preciat, G., Edirisinghe, J. N., Henry, C. S., Fleming, R. M. T., Thiele, I.. 2020-11-10. AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities.. https://doi.org/10.1101/2020.11.09.375451

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