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Biosynthetic potential of the global ocean microbiome

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Item Type:Article
Title:Biosynthetic potential of the global ocean microbiome
Creators Name:Paoli, L. and Ruscheweyh, H.J. and Forneris, C.C. and Hubrich, F. and Kautsar, S. and Bhushan, A. and Lotti, A. and Clayssen, Q. and Salazar, G. and Milanese, A. and Carlström, C.I. and Papadopoulou, C. and Gehrig, D. and Karasikov, M. and Mustafa, H. and Larralde, M. and Carroll, L.M. and Sánchez, P. and Zayed, A.A. and Cronin, D.R. and Acinas, S.G. and Bork, P. and Bowler, C. and Delmont, T.O. and Gasol, J.M. and Gossert, A.D. and Kahles, A. and Sullivan, M.B. and Wincker, P. and Zeller, G. and Robinson, S.L. and Piel, J. and Sunagawa, S.
Abstract:Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups, this diversity encompasses a rich discovery potential for ecologically and biotechnologically relevant enzymes and biochemical compounds. However, studying this diversity to identify genomic pathways for the synthesis of such compounds and assigning them to their respective hosts remains challenging. The biosynthetic potential of microorganisms in the open ocean remains largely uncharted owing to limitations in the analysis of genome-resolved data at the global scale. Here we investigated the diversity and novelty of biosynthetic gene clusters in the ocean by integrating around 10,000 microbial genomes from cultivated and single cells with more than 25,000 newly reconstructed draft genomes from more than 1,000 seawater samples. These efforts revealed approximately 40,000 putative mostly new biosynthetic gene clusters, several of which were found in previously unsuspected phylogenetic groups. Among these groups, we identified a lineage rich in biosynthetic gene clusters ('Candidatus Eudoremicrobiaceae') that belongs to an uncultivated bacterial phylum and includes some of the most biosynthetically diverse microorganisms in this environment. From these, we characterized the phospeptin and pythonamide pathways, revealing cases of unusual bioactive compound structure and enzymology, respectively. Together, this research demonstrates how microbiomics-driven strategies can enable the investigation of previously undescribed enzymes and natural products in underexplored microbial groups and environments.
Keywords:Computational Biology and Bioinformatics, Environmental Microbiology
Source:Nature
ISSN:0028-0836
Publisher:Nature Publishing Group
Volume:607
Number:7917
Page Range:111–118
Date:7 July 2022
Official Publication:https://doi.org/10.1038/s41586-022-04862-3
PubMed:View item in PubMed

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