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
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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
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Journal ArticleDOI
Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides.
Alexander M. Kloosterman,Peter Cimermancic,Somayah S. Elsayed,Chao Du,Michalis Hadjithomas,Mohamed S. Donia,Michael A. Fischbach,Gilles P. van Wezel,Marnix H. Medema +8 more
TL;DR: DecRiPPter as discussed by the authors combines a Support Vector Machine (SVM) that identifies candidate RiPP precursors with pan-genomic analyses to identify which of these are encoded within operonlike structures that are part of the accessory genome of a genus.
Journal ArticleDOI
Sequencing rare marine actinomycete genomes reveals high density of unique natural product biosynthetic gene clusters.
Michelle Schorn,Mohammad Alanjary,Kristen Aguinaldo,Anton Korobeynikov,Sheila Podell,Nastassia V. Patin,Tommie Lincecum,Paul R. Jensen,Nadine Ziemert,Bradley S. Moore,Bradley S. Moore +10 more
TL;DR: It was found that genome size and phylogeny were good predictors of biosynthetic gene cluster diversity, with larger genomes rivalling the well-known marine producers in the Streptomyces and Salinispora genera.
Journal ArticleDOI
Competition among Nasal Bacteria Suggests a Role for Siderophore-Mediated Interactions in Shaping the Human Nasal Microbiota.
Reed M. Stubbendieck,Daniel S. May,Marc G. Chevrette,Mia I. Temkin,Evelyn Wendt-Pienkowski,Julian Cagnazzo,Caitlin M Carlson,James E. Gern,Cameron R. Currie +8 more
TL;DR: The results suggest that bacteria produce siderophores to compete for limited available iron in the nasal cavity and improve their fitness.
Journal ArticleDOI
GISMO--gene identification using a support vector machine for ORF classification
TL;DR: Using GISMO, the novel prokaryotic gene finder, several thousand new predictions for the published genomes that are supported by extrinsic evidence are found, which strongly suggest that these are very likely biologically active genes.
Posted ContentDOI
BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters
TL;DR: BiG-SLiCE is introduced, a tool designed to cluster massive numbers of BGCs that provides a "query mode" that can efficiently place newly sequenced B GCs into previously computed GCFs, plus a powerful output visualization engine that facilitates user-friendly data exploration.
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