A database on microbial lignin catabolism
eLignin is a database that collects scientific knowledge of lignin-degrading and aromatic-compound-metabolizing microorganisms. It aims to showcase the biological diversity and specificity of microbes within this ecological niche.
The current version of the dataset includes references published up until year 2022.
Citation
If you have used eLignin in your research, we would be grateful if you would cite the following publication:
- Brink, D.P., Ravi, K., Lidén, G. and Gorwa-Grauslund, M. F. (2019). Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database. Applied Microbiology and Biotechnology (DOI: 10.1007/s00253-019-09692-4)
We would also like to point users toward the original literature review that eventually led to the creation of the eLignin database:
- Abdelaziz, O. Y., Brink, D. P., Prothmann, J., Ravi, K., Sun, M., García-Hidalgo, J., Sandahl, M., Hulteberg, C. P., Turner, C., Lidén, G. and Gorwa-Grauslund, M. F. (2016). Biological valorization of low molecular weight lignin. Biotechnology Advances, 34 (8), 1318–1346 (DOI: 10.1016/j.biotechadv.2016.10.001)
What is lignin?
Lignin is an aromatic biopolymer and one of the major components of lignocellulosic biomass (e.g. wood and agricultural waste). Due to its high recalcitrance and heterogeneity, lignin has proven challenging to depolymerize, which is a prerequisite for using it as a renewable feedstock for the sustainable production of platform chemicals.
In nature, lignin is degraded by microbes in a symbiotic relationship between rot-type fungi and prokaryotes: the fungi degrade the polymer to aromatic compounds, which in turn are metabolized by fungi and prokaryotes. A diverse set of metabolic pathways has evolved to enable efficient utilization of the heterogeneous aromatic products that result from lignin depolymerization. This database was built to map these microbes and their pathways.
How to use the eLignin microbial database?
Start by browsing the categories in the top navigation bar (Organisms, Substrates, etc.) or by using the free-text search bar in the header.
Each category has list and detail pages. A list page shows all available entries in that category and allows the user to filter on specific values. A detail page presents the data for an individual entry, such as a microbial strain, chemical compound, or metabolic pathway. The search bar produces a page of potential matches that link to their respective detail pages.
The data in eLignin comes from empirical observations reported in scientific publications. The database labels these observations as empirical, but also uses them to infer relationships that were not explicitly reported in the primary sources. For example, a microbial strain reported to metabolise vanillin is likely to have the canonical pathways and enzymes for vanillin metabolism even if those components were not reported as empirical observations. eLignin attempts to infer such relationships. See the Data Assumptions page for details on how eLignin distinguishes empirical data from inferred connections.
At the moment, eLignin does not include microbial strains that have been genetically engineered to alter their capacity to metabolize aromatic compounds.
About
The eLignin database was originally developed during a research project on lignin valorisation at Lund University, funded by the Swedish Foundation for Strategic Research (2015–2020). The original eLignin version was deployed from 2016 through 2023 as a closed-source LAMP application.
The current version of eLignin was refactored into an open-source, single-container web application in 2026. It was designed to be compatible with deployment at SciLifeLab Serve.
eLignin uses the BioPAX Level 3 ontology for representing metabolic pathways and reactions. See the ontology reference for details.
Metabolic pathways are visualized with Cytoscape.js.