Multilaboratory Untargeted Mass Spectrometry Metabolomics Collaboration to Identify Bottlenecks and Comprehensively Annotate A Single Dataset.

Annotation is the process of assigning features in mass spectrometry metabolomics data sets to putative chemical structures or "analytes." The purpose of this study was to identify challenges in the annotation of untargeted mass spectrometry metabolomics datasets and suggest strategies to overcome them. Toward this goal, we analyzed an extract of the plant ashwagandha () using liquid chromatography-mass spectrometry on two different platforms (an Orbitrap and Q-ToF) with various acquisition modes.

Olive mill solid waste induces beneficial mushroom-specialized metabolite diversity revealed by computational metabolomics strategies.

Introduction: Mushrooms contain besides proteins a diverse pallet of specialized metabolites bioactive in either beneficial or harmful manner. Therefore, mushrooms have been exploited by humans for centuries for dietary or medical purposes. For example, the edible and medicinal mushrooms Hericium erinaceus and Pleurotus eryngii are grown commercially around the world.

antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation.

Microorganisms synthesize small bioactive compounds through their secondary or specialized metabolism. Those compounds play an important role in microbial interactions and soil health, but are also crucial for the development of pharmaceuticals or agrochemicals. Over the past decades, advancements in genome sequencing have enabled the identification of large numbers of biosynthetic gene clusters directly from microbial genomes.

Non-targeted metabolomics-based molecular networking enables the chemical characterization of Rumex sanguineus, a wild edible plant.

Introduction And Objective: Rumex sanguineus, a traditional medicinal plant of the Polygonaceae family, is gaining popularity as an edible resource. However, despite its historical and nutritional significance, its chemical composition remains poorly understood. To deepen the understanding of the of Rumex sanguineus composition, an in-depth analysis using non-targeted, mass spectrometry-based metabolomics was performed.

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration.

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015.

Metabolome-guided genome mining of RiPP natural products.

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a chemically diverse class of metabolites. Many RiPPs show potent biological activities that make them attractive starting points for drug development. A promising approach for the discovery of new classes of RiPPs is genome mining.

Feature-Based Molecular Networking for the Targeted Identification of G-Inhibiting FR900359 Derivatives.

Both the soil bacterium and the bacterial endosymbiont Burkholderia crenata of the plant are producers of FR900359 (FR). This cyclic depsipeptide is a potent and selective G protein inhibitor used extensively to investigate the intracellular signaling of G protein coupled receptors (GPCRs). In this study, the metabolomes of both FR producers were investigated and compared using feature-based molecular networking (FBMN).

Blocks in the pseudouridimycin pathway unlock hidden metabolites in the Streptomyces producer strain.

We report a metabolomic analysis of Streptomyces sp. ID38640, a soil isolate that produces the bacterial RNA polymerase inhibitor pseudouridimycin. The analysis was performed on the wild type, on three newly constructed and seven previously reported mutant strains disabled in different genes required for pseudouridimycin biosynthesis.

Effective approaches to discover new microbial metabolites in a large strain library.

Natural products have provided many molecules to treat and prevent illnesses in humans, animals and plants. While only a small fraction of the existing microbial diversity has been explored for bioactive metabolites, tens of thousands of molecules have been reported in the literature over the past 80 years. Thus, the main challenge in microbial metabolite screening is to avoid the re-discovery of known metabolites in a cost-effective manner.

: A Metabolomics Perspective on an Underexplored Actinobacteria Genus.

Despite an excellent track record, microbial drug discovery suffers from high rates of rediscovery. Better workflows for the rapid investigation of complex extracts are needed to increase throughput and to allow early prioritization of samples. In addition, systematic characterization of poorly explored strains is seldomly performed.

A biaryl-linked tripeptide from Planomonospora reveals a widespread class of minimal RiPP gene clusters.

Microbial natural products impress by their bioactivity, structural diversity, and ingenious biosynthesis. While screening the less exploited actinobacterial genus Planomonospora, two cyclopeptides were discovered, featuring an unusual Tyr-His biaryl bridging across a tripeptide scaffold, with the sequences N-acetyl-Tyr-Tyr-His and N-acetyl-Tyr-Phe-His. Planomonospora genomes pointed toward a ribosomal synthesis of the cyclopeptide from a pentapeptide precursor encoded by 18-bp bytA, to our knowledge the smallest coding gene ever reported.