Marnix H. Medema

Systematic mass-spectrometry-guided metabolic fingerprinting elucidates diversity of specialized metabolites across the Brassicaceae

The paper uses mass-spectrometry to systematically profile specialized metabolites across Brassicaceae species, identifying unique profiles and substructure motifs.

Elucidating biosynthetic pathways related to the synthesis of small halogenated peptidic natural products in marine sponge microbiomes

The paper identifies novel biosynthetic gene clusters in marine sponge microbiomes associated with brominated alkaloids.

PlantMetWiki: a FAIR knowledge graph for plant metabolic pathway cross-species representation and integration

PlantMetWiki integrates plant metabolic pathway data across species to enable cross-species analysis and hypothesis generation.

Distinct taxonomic groups of sponge symbionts have the biosynthetic capacity for the production of ether lipids

This study identifies distinct taxonomic groups of sponge symbionts with biosynthetic capacity for ether lipid production, supported by metagenomic analysis and lipidome confirmation.

RetroMol: Parsing a shared encoding from natural products and their biosynthetic gene clusters

RetroMol converts natural product structures and biosynthetic gene clusters into shared primary sequences to enable biosynthetic similarity comparisons.

A global regulatory atlas of Streptomyces reveals conserved and diversified transcriptional networks across actinomycetes

The paper constructs a regulatory atlas of Streptomyces and related actinomycetes using DAP-seq and ChIP-seq, revealing conserved and divergent transcriptional networks.

Charting the biosynthetic landscape of hybrid polyketide-nonribosomal peptide-specialized lipids

The paper identifies and characterizes new hybrid peptide-polyketide-specialized lipid biosynthesis pathways in bacteria, revealing novel metabolites with functional properties.

Multi-omics reveals mechanisms behind pathogen inhibition by a microalgal microbiome

This study uses multi-omics to show that a microalgal microbiome inhibits Vibrio anguillarum through iron sequestration via siderophore production.

SynCom101: A web-based platform for the standardized design of functionally tailored synthetic microbial communities

SynCom101 is a web-based platform that enables standardized, hypothesis-driven design of synthetic microbial communities using genomic and phenotypic data.

Metabolic fingerprinting of 17 Brassicaceae species across three tissues

The paper collects and standardizes metabolic fingerprints of 17 Brassicaceae species across three tissues using LC-MS/MS, enabling integration with genomic and transcriptomic data for natural product discovery.

A global metagenomic atlas uncovers ubiquitous biosynthetic potential linked to adaptation in extreme environments

The paper constructs a global metagenomic atlas of extremophilic microbes, revealing habitat-specific biosynthetic potential linked to adaptation in extreme environments.

Hidden molecular relationships are revealed by bootstrap resampling of mass spectral pairs with SpecReBoot

SpecReBoot improves molecular network analysis by quantifying confidence in MS/MS similarity scores, revealing hidden chemical relationships.

Reconstructing plant beneficial bacterial consortia by integrating dilution-to-extinction microbiome perturbation with genome-resolved synthetic ecology

This study reconstructs microbial consortia responsible for disease suppression in plants by combining dilution-to-extinction experiments with genome-resolved synthetic ecology.

PARAS: high-accuracy machine-learning of substrate specificities in nonribosomal peptide synthetases

Random forest predictors PARAS and PARASECT, trained on 3,653 curated adenylation domains, outperform earlier NRPS substrate predictors and correctly assigned L-Trp to an unusual tryptopeptin synthetase domain.

plantiSMASH 2.0: improvements to detection, annotation, and prioritization of plant biosynthetic gene clusters

plantiSMASH 2.0 improves detection, annotation, and prioritization of plant biosynthetic gene clusters by expanding BGC types and adding substrate prediction and regulatory analysis.

Automated genome mining predicts structural diversity and taxonomic distribution of peptide metallophores across bacteria

The paper introduces an automated method to detect non-ribosomal peptide metallophore biosynthesis gene clusters in bacterial genomes, revealing widespread metallophore production and chemical diversity.

BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters

The paper introduces updated versions of BiG-SCAPE and BiG-SLiCE for improved analysis of metabolic gene clusters, showing they provide consistent estimates of gene cluster diversity.

Using cross-species co-expression to predict metabolic interactions in microbiomes.

This paper predicts microbial metabolic interactions using cross-species co-expression analysis of RNA-sequencing data from microbiome datasets.

Substrate utilization and cross-feeding synergistically determine microbiome resistance to pathogen invasion

This study uses genome-scale models and synthetic communities to show that substrate utilization and cross-feeding synergistically determine microbiome resistance to pathogen invasion.

Predicting Rhizosphere Competence Related Catabolic Gene Clusters in plant-associated bacteria with RhizoSMASH

The paper develops RhizoSMASH, a tool to annotate catabolic gene clusters in plant-associated bacteria, revealing niche specialization and predicting rhizosphere competence.

MEANtools: multi-omics integration towards metabolite anticipation and biosynthetic pathway prediction

MEANtools predicts metabolic pathways de novo by integrating transcriptomic and metabolomic data using reaction rules and enzyme families.

BGC Atlas: A Web Resource for Exploring the Global Chemical Diversity Encoded in Bacterial Genomes

The paper introduces the BGC Atlas, a web resource that explores BGC diversity in metagenomes, identifying nearly 1.8 million BGCs and showing RiPPs as the most abundant compound class.

Prediction of gene cluster function based on transcriptional regulatory networks uncovers a novel locus required for desferrioxamine B biosynthesis

LogoMotif: a comprehensive database of transcription factor binding site profiles in Actinobacteria

LogoMotif provides a database of transcription factor binding sites in Actinobacteria, including position weight matrices and predicted interactions, to aid in gene regulation and compound discovery.

CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters

CAGECAT enables rapid homology searches and visualization of gene clusters across genomes, aiding in the discovery of novel metabolites through comparative analysis.

iPRESTO: automated discovery of biosynthetic sub-clusters linked to specific natural product substructures

iPRESTO detects sub-clusters in biosynthetic gene clusters to link natural product substructures to their genetic origins, improving annotation and discovery.

FERMO: a Dashboard for Automated Prioritization of Molecular Features from Mass Spectral Data

FERMO is a dashboard that automates the prioritization of molecular features from mass spectral data to link molecules to phenotypes.

Automated genome mining predicts combinatorial diversity and taxonomic distribution of peptide metallophore structures

The paper introduces an automated method to identify non-ribosomal peptide metallophore biosynthesis gene clusters in bacterial genomes, revealing widespread occurrence and untapped diversity.

TbasCO: Trait-based Comparative 'Omics Identifies Ecosystem-Level and Niche-Differentiating Adaptations of an Engineered Microbiome

The paper introduces TbasCO, a trait-based comparative omics approach that identifies ecosystem-level and niche-differentiating adaptations in microbial communities using genome-resolved time-series metatranscriptomics.

Whokaryote: distinguishing eukaryotic and prokaryotic contigs in metagenomes based on gene structure

Whokaryote classifies metagenomic contigs as eukaryotic or prokaryotic using gene structure features, outperforming existing methods and enabling better gene prediction in microbial communities.