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
Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae
TL;DR: Comparative genomics analysis provided insight into the genomic basis of its endophytic lifestyle and antifungal activity, and Synteny analysis of polyketide synthases, non-ribosomal peptide synthetases, and hybrid (PKS-NRPS) gene clusters between S. brachiariae and S. oryzae revealed that just 37.5% of tested clusters have good synteny, while 63.
Journal ArticleDOI
Microevolution in the pansecondary metabolome of Aspergillus flavus and its potential macroevolutionary implications for filamentous fungi.
Milton T. Drott,Tomás Allen Rush,Tatum R. Satterlee,Richard J. Giannone,Paul E. Abraham,Claudio Greco,Nandhitha Venkatesh,Jeffrey M. Skerker,N. Louise Glass,N. Louise Glass,Jesse L. Labbé,Michael G. Milgroom,Nancy P. Keller +12 more
TL;DR: In this paper, the authors used 94 isolates of Aspergillus flavus, a cosmopolitan model fungus, sampled from seven states in the United States, and used ultra-high-performance high-resolution mass spectrometry to confirm that these genetic differences in BGCs also result in chemotypic differences in secondary metabolites production in different populations, which could mediate ecological interactions and be acted on by selection.
Journal ArticleDOI
Comparative Genomics and Metabolomics Analyses of Clavulanic Acid-Producing Streptomyces Species Provides Insight Into Specialized Metabolism.
Nader F. AbuSara,Brandon M. Piercey,Marcus A. Moore,Arshad Ali Shaikh,Louis-Félix Nothias,Santosh Kumar Srivastava,Pablo Cruz-Morales,Pieter C. Dorrestein,Francisco Barona-Gómez,Kapil Tahlan +9 more
TL;DR: The core set of genes responsible for producing clavulanic acid are proposed, based on analyses of the biosynthetic gene cluster content of the three Streptomyces species, by matching them with the specialized metabolites detected in the current study.
Journal ArticleDOI
A Machine Learning Bioinformatics Method to Predict Biological Activity from Biosynthetic Gene Clusters.
Allison S. Walker,Jon Clardy +1 more
TL;DR: In this article, a machine learning bioinformatics method for predicting a natural product's antibiotic activity directly from the sequence of its biosynthetic gene cluster was developed, which can attain accuracies as high as 80% and that have enabled the identification of enzymes and their corresponding molecular features associated with antibiotic activity.
Journal ArticleDOI
Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics.
Vittorio Tracanna,Adam Ossowicki,Marloes L. C. Petrus,Sam Overduin,Barbara R. Terlouw,George Lund,Serina L. Robinson,Sven Warris,Elio Schijlen,Gilles P. van Wezel,Jos M. Raaijmakers,Paolina Garbeva,Marnix H. Medema +12 more
TL;DR: In this paper, the authors applied functional amplicon sequencing of nonribosomal peptide synthetases-associated adenylation domains (A domains) to a collection of eight soils that are suppressive or nonsuppressive (i.e., conducive) to Fusarium culmorum, a fungal root pathogen of wheat.
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