BacDive in 2025: the core database for prokaryotic strain data.

In 2025, the bacterial diversity database BacDive is the leading database for strain-level bacterial and archaeal information. It has been selected as an ELIXIR Core Data Resource as well as a Global Core Biodata Resource. Since its initial release more than ten years ago, BacDive (https://bacdive.

PhageDive: the comprehensive strain database of prokaryotic viral diversity.

Prokaryotic viruses represent the most diverse and abundant biological entities on Earth. So far, data on bacteriophages are not standardized, not readily available for comparative analyses and cannot be linked to the rapidly growing (meta)genomic data. We developed PhageDive (https://phagedive.

Systems Biology of Aromatic Compound Catabolism in Facultative Anaerobic EbN1.

Members of the genus thrive in diverse habitats and use a broad range of recalcitrant organic molecules coupled to denitrification or O respiration. To gain a holistic understanding of the model organism EbN1, we studied its catabolic network dynamics in response to 3-(4-hydroxyphenyl)propanoate, phenylalanine, 3-hydroxybenzoate, benzoate, and acetate utilized under nitrate-reducing versus oxic conditions. Integrated multi-omics (transcriptome, proteome, and metabolome) covered most of the catabolic network (199 genes) and allowed for the refining of knowledge of the degradation modules studied.

MediaDive: the expert-curated cultivation media database.

We present MediaDive (https://mediadive.dsmz.de), a comprehensive and expert-curated cultivation media database, which comprises recipes, instructions and molecular compositions of >3200 standardized cultivation media for >40 000 microbial strains from all domains of life.

DSMZCellDive: Diving into high-throughput cell line data.

Human and animal cell lines serve as model systems in a wide range of life sciences such as cancer and infection research or drug screening. Reproducible data are highly dependent on authenticated, contaminant-free cell lines, no better delivered than by the official and certified biorepositories. Offering a web portal to high-throughput information on these model systems will facilitate working with and comparing to these references by data otherwise dispersed at different sources.

BacDive in 2022: the knowledge base for standardized bacterial and archaeal data.

The bacterial metadatabase BacDive (https://bacdive.dsmz.de) has developed into a leading database for standardized prokaryotic data on strain level.

The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases.

Genome-scale metabolic models are of high interest in a number of different research fields. Flux balance analysis (FBA) and other mathematical methods allow the prediction of the steady-state behavior of metabolic networks under different environmental conditions. However, many existing applications for flux optimizations do not provide a metabolite-centric view on fluxes.

Utilization of Phenol as Carbon Source by the Thermoacidophilic Archaeon P2 Is Limited by Oxygen Supply and the Cellular Stress Response.

Present in many industrial effluents and as common degradation product of organic matter, phenol is a widespread compound which may cause serious environmental problems, due to its toxicity to animals and humans. Degradation of phenol from the environment by mesophilic bacteria has been studied extensively over the past decades, but only little is known about phenol biodegradation at high temperatures or low pH. In this work we studied phenol degradation in the thermoacidophilic archaeon P2 (basonym: ) under extreme conditions (80°C, pH 3.

BRENDA, the ELIXIR core data resource in 2021: new developments and updates.

The BRENDA enzyme database (https://www.brenda-enzymes.org), established in 1987, has evolved into the main collection of functional enzyme and metabolism data.

MetaboMAPS: Pathway sharing and multi-omics data visualization in metabolic context.

Metabolic pathways are an important part of systems biology research since they illustrate complex interactions between metabolites, enzymes, and regulators. Pathway maps are drawn to elucidate metabolism or to set data in a metabolic context. We present MetaboMAPS, a web-based platform to visualize numerical data on individual metabolic pathway maps.