Journal ArticleDOI
The confluence of big data and evolutionary genome mining for the discovery of natural products.
Marc G. Chevrette,Athina Gavrilidou,Shrikant Mantri,Nelly Selem-Mojica,Nadine Ziemert,Francisco Barona-Gómez +5 more
TLDR
This review covers literature between 2003-2021 and highlights examples where Big Data and evolutionary analyses have been combined to provide bioinformatic resources and tools for the discovery of novel natural products and their biosynthetic enzymes.About:
This article is published in Natural Product Reports.The article was published on 2021-11-17. It has received 21 citations till now.read more
Citations
More filters
A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis - eScholarship
Andrej Sali,Michael A. Fischbach,Marnix H. Medema,Peter Cimermancic,Eriko Takano,MA Fischbach +5 more
TL;DR: By performing a systematic computational analysis of BGC evolution, this work derives evidence for three findings that shed light on the ways in which, despite these constraints, nature successfully invents new molecules.
Journal ArticleDOI
Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes
Athina Gavriilidou,Satria A. Kautsar,Nestor Zaburannyi,Daniel Krug,Rolf Müller,Marnix H. Medema,Nadine Ziemert +6 more
TL;DR: The authors analyzed ~170,000 bacterial genomes and ~47,000 metagenome assembled genomes using a modified BiG-SLiCE and the new clust-o-matic algorithm.
Journal ArticleDOI
Microbiome composition modulates secondary metabolism in a multispecies bacterial community
Marc G. Chevrette,Chris S. Thomas,Amanda Hurley,Natalia Rosario-Meléndez,Krishnan P. Sankaran,Yixing Tu,Austin W. Hall,S.B. Magesh,Jo Handelsman +8 more
TL;DR: Results from this model community show that bacterial BGC expression and chemical output depend on the identity and biosynthetic capacity of coculture partners, suggesting community composition and microbiome interactions may shape the regulation of secondary metabolism in nature.
Journal ArticleDOI
Targeted Large-Scale Genome Mining and Candidate Prioritization for Natural Product Discovery
TL;DR: Genomics-based approaches for prioritizing candidate BGCs extracted from large-scale genomic data are discussed, by highlighting studies that have successfully produced compounds with high chemical novelty, novel biosynthesis pathway, and potent bioactivities.
Journal ArticleDOI
Integrated Metabolomic–Genomic Workflows Accelerate Microbial Natural Product Discovery
TL;DR: This work considers innovative approaches which have led to prioritization of strain targets and have mitigated rediscovery rates, and discusses integration of principles of comparative evolutionary studies and retrobiosynthetic predictions to better understand biosynthetic mechanistic details and link genome sequence to structure.
References
More filters
Posted ContentDOI
ActDES- a Curated Actinobacterial Database for Evolutionary Studies
Jana K. Schniete,Nelly Selem-Mojica,Anna S. Birke,Pablo Cruz-Morales,Iain S. Hunter,Francisco Barona-Gómez,Paul A. Hoskisson +6 more
TL;DR: A curated, taxa-specific, non-redundant database of 612 high-quality actinobacterial genomes from 80 genera, chosen to represent a broad phylogenetic group with equivalent genome reannotation to aid detailed comparative analysis of Actinobacteria.
Journal ArticleDOI
ActDES – a curated actinobacterial database for evolutionary studies
Jana K. Schniete,Nelly Selem-Mojica,Anna S. Birke,Pablo Cruz-Morales,Iain S. Hunter,Francisco Barona-Gómez,Paul A. Hoskisson +6 more
TL;DR: A curated database of 612 high-quality actinobacterial genomes from 80 genera, chosen to represent a broad phylogenetic group with equivalent genome re-annotation, is presented in this paper.
Journal ArticleDOI
The Journal of Molecular Evolution Turns 50.
Related Papers (5)
Identifying key questions in the ecology and evolution of cancer.
Antoine M. Dujon,Antoine M. Dujon,Athena Aktipis,Catherine Alix-Panabières,Sarah R. Amend,Amy M. Boddy,Joel S. Brown,Jean Pascal Capp,James DeGregori,Paul W. Ewald,Robert A. Gatenby,Marco Gerlinger,Mathieu Giraudeau,Mathieu Giraudeau,Rodrigo Hamede,Elsa Hansen,Irina Kareva,Carlo C. Maley,Andriy Marusyk,Nicholas McGranahan,Nicholas McGranahan,Michael J. Metzger,Aurora M. Nedelcu,Robert Noble,Robert Noble,Leonard Nunney,Kenneth J. Pienta,Kornelia Polyak,Pascal Pujol,Andrew F. Read,Benjamin Roche,Benjamin Roche,Susanne Sebens,Eric Solary,Eric Solary,Kateřina Staňková,Kateřina Staňková,Holly A. Swain Ewald,Frédéric Thomas,Beata Ujvari +39 more