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natural products

  • Open Access
    RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery
    Research Article | Novel Systems Biology Techniques
    RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery

    Bioinformatics-powered discovery of novel ribosomal natural products (RiPPs) has historically been hindered by the lack of a common genetic feature across RiPP classes. Herein, we introduce RRE-Finder, a method for identifying RRE domains, which are present in a majority of prokaryotic RiPP biosynthetic gene clusters (BGCs). RRE-Finder identifies RRE domains 3,000 times faster than current methods, which rely on time-consuming secondary...

    Alexander M. Kloosterman, Kyle E. Shelton, Gilles P. van Wezel, Marnix H. Medema, Douglas A. Mitchell
  • Open Access
    Comparative Genomics and Metabolomics in the Genus <em>Nocardia</em>
    Research Article | Applied and Environmental Science
    Comparative Genomics and Metabolomics in the Genus Nocardia

    Our work emphasizes that Nocardia represent a prolific source for natural products rivaling better-characterized genera such as Streptomyces or Amycolatopsis. Furthermore, we showed that large-scale analysis of biosynthetic gene clusters using similarity networks with high stringency allows the distinction and prediction of natural product structural variations. This will facilitate future genomics-driven drug...

    Daniel Männle, Shaun M. K. McKinnie, Shrikant S. Mantri, Katharina Steinke, Zeyin Lu, Bradley S. Moore, Nadine Ziemert, Leonard Kaysser
  • Open Access
    A Metabolome- and Metagenome-Wide Association Network Reveals Microbial Natural Products and Microbial Biotransformation Products from the Human Microbiota
    Editor's Pick Research Article | Novel Systems Biology Techniques
    A Metabolome- and Metagenome-Wide Association Network Reveals Microbial Natural Products and Microbial Biotransformation Products from the Human Microbiota

    Experimental advances have enabled the acquisition of tandem mass spectrometry and metagenomics sequencing data from tens of thousands of environmental/host-oriented microbial communities. Each of these communities contains hundreds of microbial features (corresponding to microbial species) and thousands of molecular features (corresponding to microbial natural products). However, with the current technology, it is very difficult to...

    Liu Cao, Egor Shcherbin, Hosein Mohimani
  • Open Access
    Resistance Gene-Directed Genome Mining of 50 <em>Aspergillus</em> Species
    Research Article | Novel Systems Biology Techniques
    Resistance Gene-Directed Genome Mining of 50 Aspergillus Species

    Species belonging to the Aspergillus genus are known to produce a large number of secondary metabolites; some of these compounds are used as pharmaceuticals, such as penicillin, cyclosporine, and statin. With whole-genome sequencing, it became apparent that the genetic potential for secondary metabolite production is much larger than expected. As an increasing number of species are whole-genome sequenced, thousands of secondary...

    Inge Kjærbølling, Tammi Vesth, Mikael R. Andersen
  • Open Access
    A Phylogenetic and Functional Perspective on Volatile Organic Compound Production by <em>Actinobacteria</em>
    Editor's Pick Research Article | Applied and Environmental Science
    A Phylogenetic and Functional Perspective on Volatile Organic Compound Production by Actinobacteria

    Soil microbes produce a diverse array of natural products, including volatile organic compounds (VOCs). Volatile compounds are important molecules in soil habitats, where they mediate interactions between bacteria, fungi, insects, plants, and animals. We measured the VOCs produced by a broad diversity of soil- and dust-dwelling Actinobacteria in vitro. We detected a total of 126 unique volatile compounds, and each strain...

    Mallory Choudoir, Sam Rossabi, Matthew Gebert, Detlev Helmig, Noah Fierer
  • Open Access
    The Tripod for Bacterial Natural Product Discovery: Genome Mining, Silent Pathway Induction, and Mass Spectrometry-Based Molecular Networking
    Special Issue Perspective | Molecular Biology and Physiology
    The Tripod for Bacterial Natural Product Discovery: Genome Mining, Silent Pathway Induction, and Mass Spectrometry-Based Molecular Networking

    Natural products are the richest source of chemical compounds for drug discovery. Particularly, bacterial secondary metabolites are in the spotlight due to advances in genome sequencing and mining, as well as for the potential of biosynthetic pathway manipulation to awake silent (cryptic) gene clusters under laboratory cultivation.

    Daniela B. B. Trivella, Rafael de Felicio
  • Open Access
    Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology
    Special Issue Perspective | Novel Systems Biology Techniques
    Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology

    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.

    Marnix H. Medema
  • Open Access
    Increased Biosynthetic Gene Dosage in a Genome-Reduced Defensive Bacterial Symbiont
    Research Article | Host-Microbe Biology
    Increased Biosynthetic Gene Dosage in a Genome-Reduced Defensive Bacterial Symbiont

    Secondary metabolites, which are small-molecule organic compounds produced by living organisms, provide or inspire drugs for many different diseases. These natural products have evolved over millions of years to provide a survival benefit to the producing organism and often display potent biological activity with important therapeutic applications. For instance, defensive compounds in the environment may be cytotoxic to eukaryotic cells...

    Juan Lopera, Ian J. Miller, Kerry L. McPhail, Jason C. Kwan
  • Open Access
    Large-Scale Bioinformatics Analysis of <em>Bacillus</em> Genomes Uncovers Conserved Roles of Natural Products in Bacterial Physiology
    Research Article | Molecular Biology and Physiology
    Large-Scale Bioinformatics Analysis of Bacillus Genomes Uncovers Conserved Roles of Natural Products in Bacterial Physiology

    Bacilli are capable of producing a diverse array of specialized metabolites, many of which have gained attention for their roles as signals that affect bacterial physiology and development. Up to this point, however, the Bacillus genus’s metabolic capacity has been underexplored. We undertook a deep genomic analysis of 1,566 Bacillus genomes to understand the full spectrum of metabolites that this bacterial...

    Kirk J. Grubbs, Rachel M. Bleich, Kevin C. Santa Maria, Scott E. Allen, Sherif Farag, AgBiome Team, Elizabeth A. Shank, Albert A. Bowers
  • Open Access
    Spatial Molecular Architecture of the Microbial Community of a <em>Peltigera</em> Lichen
    Editor's Pick Research Article | Novel Systems Biology Techniques
    Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen

    Microbial communities have evolved over centuries to live symbiotically. The direct visualization of such communities at the chemical and functional level presents a challenge. Overcoming this challenge may allow one to visualize the spatial distributions of specific molecules involved in symbiosis and to define their functional roles in shaping the community structure. In this study, we examined the diversity of microbial genes and...

    Neha Garg, Yi Zeng, Anna Edlund, Alexey V. Melnik, Laura M. Sanchez, Hosein Mohimani, Alexey Gurevich, Vivian Miao, Stefan Schiffler, Yan Wei Lim, Tal Luzzatto-Knaan, Shengxin Cai, Forest Rohwer, Pavel A. Pevzner, Robert H. Cichewicz, Theodore Alexandrov, Pieter C. Dorrestein

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