M. H. Medema

Taxonomic and metabolic diversity of Actinobacteria isolated from faeces of a 28,000-year-old mammoth

The paper isolates and characterizes Actinobacteria from a 28,000-year-old mammoth's feces, revealing phylogenetic and metabolic differences from modern strains.

Comparative metagenomic analysis of biosynthetic diversity across sponge microbiomes highlights metabolic novelty, conservation and diversification

This study compares metagenomic data from sponge microbiomes to identify novel biosynthetic gene clusters and their conservation across species.

Disentangling the genetic basis of rhizosphere microbiome assembly in tomato

This study identifies genetic factors influencing rhizosphere microbiome assembly in tomato by linking plant QTLs to microbial gene functions.

Generation of lineage-resolved complete metagenome-assembled genomes by precision phasing

The paper generates lineage-resolved complete MAGs using HiFi reads from sheep fecal samples, achieving high-resolution deconvolution of microbial communities.

A biaryl-linked tripeptide from Planomonospora leads to widespread class of minimal RiPP gene clusters

The paper identifies a novel biaryl-linked tripeptide from Planomonospora and proposes a new family of RiPPs based on its biosynthetic pathway.

Integration of machine learning and pan-genomics expands the biosynthetic landscape of RiPP natural products

The paper introduces decRiPPter, a machine learning and pan-genomic approach to discover novel RiPP classes, identifying 42 new candidate families from Streptomyces genomes.

Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia

The paper uses machine learning to predict adenylate-forming enzyme function and substrate specificity, revealing a β-lactone biosynthesis pathway in Nocardia.

Extracting the GEMs: Genotype, Environment and Microbiome interactions shaping host phenotypes

The paper expands the traditional GE model to include microbiome interactions (GEM) and demonstrates its application in disentangling contributions to host phenotypes.

A metabolic pathway for bile acid dehydroxylation by the gut microbiome

This paper completes the metabolic pathway for bile acid dehydroxylation by the gut microbiome and demonstrates its heterologous expression in a non-producing commensal.

MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools

MolNetEnhancer integrates metabolomics tools to improve chemical annotation and structural insight from mass spectrometry data.

Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae

The paper introduces a workflow for large-scale metabolite annotation in Rhamnaceae plants, revealing metabolic diversity and identifying clade-specific biosynthetic pathways.

Did a plant-herbivore arms race drive chemical diversity in Euphorbia?

The study examines how geographic separation influenced chemical diversity in Euphorbia, finding reduced diterpenoid diversity in American species compared to Eurasian and African ones, suggesting adaptation to herbivory pressure.