Nadine Ziemert

BGC Atlas v2: biosynthetic gene clusters with taxonomic and environmental context at scale

BGC Atlas v2 expands the collection of predicted biosynthetic gene clusters to over 16 million, providing taxonomic and environmental context for natural product discovery.

Computational pipeline reveals nature's untapped reservoir of halogenating enzymes

The paper develops a computational pipeline and database to annotate halogenating enzymes in genomic and metagenomic data, revealing underexplored clusters and improving predictions of microbial halogenated natural products.

metaSMASH: Scalable Biosynthetic Gene Cluster Detection for Large Metagenomic Assemblies

metaSMASH improves BGC detection in large metagenomes by reducing computational cost while maintaining result accuracy.

PhyloNaP: a user-friendly database of Phylogeny for Natural Product-producing enzymes

PhyloNaP provides a database of phylogenetic trees for biosynthetic enzymes, enabling functional inference and community contributions.

Cooperative siderophore use stabilizes a protective leaf microbiome

The paper shows that cooperative siderophore exchange between Rhodotorula kratochvilovae and Pseudomonas species stabilizes the leaf microbiome and protects plants from pathogens.

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.

Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes

This study uses ultra-deep metagenomic sequencing to analyze soil microbes, revealing extensive microbial diversity and biosynthetic potential previously unexplored.

PanBGC: A Pangenome-inspired framework for comparative analysis of biosynthetic gene clusters

PanBGC provides a framework to analyze biosynthetic gene clusters across microbial genomes, classifying genes into core, accessory, and unique categories and quantifying diversity through openness metrics.

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.

Strong pairwise Interactions do not Drive Interactions in a Plant Leaf Associated Microbial Community

The paper investigates microbe-microbe interactions in a synthetic microbial community on Arabidopsis leaves, finding that in vitro pairwise interactions differ from in planta correlation networks, suggesting community-level synergism over competition.

Goldfinder: Unraveling Networks of Gene Co-occurrence and Avoidance in Bacterial Pangenomes

Goldfinder infers gene co-occurrence and co-avoidance in bacterial pangenomes by considering phylogenetic relationships, reducing spurious associations compared to existing tools.

Structural and evolutionary analyses support reclassification of glycopeptide antibiotics as xyclopeptides

The paper reclassifies glycopeptide antibiotics as xyclopeptides based on structural and evolutionary analyses of biosynthetic gene clusters.

Compendium of secondary metabolite biosynthetic diversity encoded in bacterial genomes

The paper analyzes bacterial genomes and metagenome assembled genomes to assess the diversity of secondary metabolite biosynthesis, finding that only 3% of potential natural products are experimentally characterized.