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Special Issue Perspective | Novel Systems Biology Techniques

Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology

Marnix H. Medema
Marnix H. Medema
aBioinformatics Group, Wageningen University, Wageningen, The Netherlands
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DOI: 10.1128/mSystems.00182-17
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ABSTRACT

Microbial and plant specialized metabolites, also known as natural products, are key mediators of microbe-microbe and host-microbe interactions and constitute a rich resource for drug development. In the past decade, genome mining has emerged as a prominent strategy for natural product discovery. Initially, such mining was performed on the basis of individual microbial genome sequences. Now, these efforts are being scaled up to fully genome-sequenced strain collections, pangenomes of bacterial genera, and large sets of metagenome-assembled genomes from microbial communities. The Medema research group aims to play a leading role in these developments by developing and applying computational approaches to identify, classify, and prioritize specialized metabolite biosynthetic gene clusters and pathways and to connect them to specific molecules and microbiome-associated phenotypes. Moreover, we are extending the scope of genome mining from microbes to plants, which will allow more comprehensive interpretation of the chemical language between hosts and microbes in a microbiome setting.

mSystems® vol. 3, no. 2, is a special issue sponsored by Janssen Human Microbiome Institute (JHMI).

  • Copyright © 2018 Medema.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

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Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology
Marnix H. Medema
mSystems Mar 2018, 3 (2) e00182-17; DOI: 10.1128/mSystems.00182-17

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Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology
Marnix H. Medema
mSystems Mar 2018, 3 (2) e00182-17; DOI: 10.1128/mSystems.00182-17
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  • Top
  • Article
    • ABSTRACT
    • PERSPECTIVE
    • FROM INDIVIDUAL GENOMES TO PANGENOMES AND METAGENOMES
    • CONNECTING GCFs TO MOLECULES
    • CONNECTING MICROBES TO PLANT AND HUMAN HOSTS
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
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KEYWORDS

bioinformatics
biosynthetic gene cluster
microbiome
natural products
specialized metabolism

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