Department Environmental Chemistry

CyanoMetDB

A comprehensive public database of secondary metabolites from cyanobacteria

One major challenge associated with studying cyanobacterial secondary metabolites is access to a comprehensive publicly available list of known metabolites including information of their chemical structures. It was our motivation to create a comprehensive database to facilitate dereplication studies and chemical profiling. The result is CyanoMetDB, a highly curated, flat-file, openly-accessible database of cyanobacterial secondary metabolites. Our efforts have nearly doubled the number of entries with complete literature metadata and structural composition information compared to previously available open access databases. While information from commercial databases of secondary metabolites is only accessible to paying customers, several open access databases exist but were limited in terms of the number of cyanobacterial metabolites or parameters listed.

The work on CyanoMetDB was initiated at the 11th International Conference of Toxic Cyanobacteria (ICTC, 2019, Krakow, Poland) with the desire to have one comprehensive list of cyanobacterial metabolites to promote effective analysis and interchange of information. Publication trends in the field suggest that the discovery of cyanobacterial metabolites is still on the rise with up to 100 new compounds identified every year. For each compound, we include the primary literature metadata, sample type and whether nuclear resonance spectroscopy was used. The metabolites span over a wide range of molecular weights, between 118 and 2708 Da. We generated structural identifiers to represent the 2D molecules and recommend to use the simplified molecular input line entry system (SMILES) strings. Particularly the structural codes were often missing, incomplete or not standardized in previous sources and needed manual curation. One strong recommendation we like to make to the authors of future publications is to always publish a SMILES together with new structures that allows to import this information efficiently and with less chances of error.

 


CyanoMetDB can enhance the frequency with which compound annotations are assigned and facilitates communication, comparison and interpretation of results. Our intention is that CyanoMetDB aids the cyanobacteria community to improve identification of known and novel cyanobacterial metabolites and biosynthesis pathways and to study their ecological role and behaviour in environmental and engineered systems. The current and future versions of CyanoMetDB are and will be available on Zenodo and the NORMAN Suspect List Exchange (No S075). We recommend citing the repository on Zenodo (Doi:10.5281/zenodo.7922070) along with the Water Research article (Jones 2021, OI: 10.1016/j.watres.2021.117017) when CyanoMetDB content is used. CyanoMetDB is available as a database in MetFrag making in silico predicted fragmentation mass spectra available for these metabolites (https://msbi.ipb-halle.de/MetFragBeta/). We collaborated with The Natural Products Atlas team to include CyanoMetDB in their content as well as PubChem, who also added annotation content such as natural product taxonomy and chemical classes from CyanoMetDB.

Moving forward, we continue the curation of CyanoMetDB and we envision that CyanoMetDB serves as a framework for connecting and collating various data sources associated with cyanobacterial metabolites, e.g., their tandem mass spectrometry product ion spectra, toxicity data, biosynthesis pathways, etc. Our team welcomes participation of the cyanobacteria research community for future editions of CyanoMetDB.

Publications

CyanoMetDB, a comprehensive public database of secondary metabolites from cyanobacteria

Harmful cyanobacterial blooms, which frequently contain toxic secondary metabolites, are reported in aquatic environments around the world. More than two thousand cyanobacterial secondary metabolites have been reported from diverse sources over the past fifty years. A comprehensive, publically-accessible database detailing these secondary metabolites would facilitate research into their occurrence, functions and toxicological risks. To address this need we created CyanoMetDB, a highly curated, flat-file, openly-accessible database of cyanobacterial secondary metabolites collated from 850 peer-reviewed articles published between 1967 and 2020. CyanoMetDB contains 2010 cyanobacterial metabolites and 99 structurally related compounds. This has nearly doubled the number of entries with complete literature metadata and structural composition information compared to previously available open access databases. The dataset includes microcytsins, cyanopeptolins, other depsipeptides, anabaenopeptins, microginins, aeruginosins, cyclamides, cryptophycins, saxitoxins, spumigins, microviridins, and anatoxins among other metabolite classes. A comprehensive database dedicated to cyanobacterial secondary metabolites facilitates: (1) the detection and dereplication of known cyanobacterial toxins and secondary metabolites; (2) the identification of novel natural products from cyanobacteria; (3) research on biosynthesis of cyanobacterial secondary metabolites, including substructure searches; and (4) the investigation of their abundance, persistence, and toxicity in natural environments.
Jones, M. R.; Pinto, E.; Torres, M. A.; Dörr, F.; Mazur-Marzec, H.; Szubert, K.; Tartaglione, L.; Dell'Aversano, C.; Miles, C. O.; Beach, D. G.; McCarron, P.; Sivonen, K.; Fewer, D. P.; Jokela, J.; Janssen, E. M. -L. (2021) CyanoMetDB, a comprehensive public database of secondary metabolites from cyanobacteria, Water Research, 196, 117017 (12 pp.), doi:10.1016/j.watres.2021.117017, Institutional Repository

Deposition of database (current and future versions)

Zenodo – LINK

Janssen, E.M.-L.; Jones, M.R., Pinto E; Dörr, F.; Rios Jacinavicius, F.; Mazur-Marzec, H.; Szubert, K.; Konkel, R.; Tartaglione, L.; Dell'Aversano, C.; Miglione, A.; Beach, D.G.; McCarron, P.; Miles, C.O.; Sivonen, K.; Fewer, D.P.; Jokela, J.; Wahlsten, M.; Niedermeyer, T.; Schanbacher, F.; Leão, P.; Preto, M.; D’Agostino, P.M.; Baunach, M., Dittmann, E.;   Miguel-Gordo, M., Reher, R. Sieber, S., 2024. Dataset | CyanoMetDB | Comprehensive database of secondary metabolites from cyanobacteria, Zenodo, S75. DIO 10.5281/zenodo.13854577.