Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Jan 7;50(D1):D1317-D1323.
doi: 10.1093/nar/gkab941.

The Natural Products Atlas 2.0: a database of microbially-derived natural products

Jeffrey A van Santen  1 , Ella F Poynton  1 , Dasha Iskakova  1 , Emily McMann  1 , Tyler A Alsup  2 , Trevor N Clark  1 , Claire H Fergusson  1 , David P Fewer  3 , Alison H Hughes  4 , Caitlin A McCadden  2 , Jonathan Parra  4 , Sylvia Soldatou  5 , Jeffrey D Rudolf  2 , Elisabeth M-L Janssen  6 , Katherine R Duncan  4 , Roger G Linington  1
Affiliations

The Natural Products Atlas 2.0: a database of microbially-derived natural products

Jeffrey A van Santen et al. Nucleic Acids Res. .

Abstract

Within the natural products field there is an increasing emphasis on the study of compounds from microbial sources. This has been fuelled by interest in the central role that microorganisms play in mediating both interspecies interactions and host-microbe relationships. To support the study of natural products chemistry produced by microorganisms we released the Natural Products Atlas, a database of known microbial natural products structures, in 2019. This paper reports the release of a new version of the database which includes a full RESTful application programming interface (API), a new website framework, and an expanded database that includes 8128 new compounds, bringing the total to 32 552. In addition to these structural and content changes we have added full taxonomic descriptions for all microbial taxa and have added chemical ontology terms from both NP Classifier and ClassyFire. We have also performed manual curation to review all entries with incomplete configurational assignments and have integrated data from external resources, including CyanoMetDB. Finally, we have improved the user experience by updating the Overview dashboard and creating a dashboard for taxonomic origin. The database can be accessed via the new interactive website at https://www.npatlas.org.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
(A) Taxonomy dashboard screenshot. Each entry in the visualization may be clicked to view more detailed information about compound distributions within that taxonomic rank. (B) Visualization for all compounds of the bacterial class ‘Actinobacteria’.
Figure 2.
Figure 2.
(A) Rates of compound discovery from bacterial (blue) and fungal (red) sources over the period 2011–2020. (B) Rates of ‘novel’ compound discovery from bacterial (blue) and fungal (red) sources over the period 2011–2020.
Figure 3.
Figure 3.
Percentage of compounds in each NP Classifier pathway separated by taxonomic class.
See this image and copyright information in PMC

References

    1. Sorokina M., Merseburger P., Rajan K., Yirik M.A., Steinbeck C.. COCONUT online: Collection of Open Natural Products database. J. Cheminform. 2021; 13:1–13. - PMC - PubMed
    1. Rutz A., Sorokina M., Galgonek J., Mietchen D., Willighagen E., Gaudry A., Graham J.G., Stephan R., Page R., Vondrášek J.et al. .. The LOTUS initiative for open natural products research: knowledge management through Wikidata. 2021; bioRxiv doi:28 May 2021, preprint: not peer reviewed10.1101/2021.02.28.433265. - DOI - PMC - PubMed
    1. Zdouc M.M., Iorio M., Vind K., Simone M., Serina S., Brunati C., Monciardini P., Tocchetti A., Zarazúa G.S., Crüsemann M.et al. .. Effective approaches to discover new microbial metabolites in a large strain library. J. Ind. Microbiol. Biotechnol. 2021; 48:1–8. - PMC - PubMed
    1. Reher R., Kim H.W., Zhang C., Mao H.H., Wang M., Nothias L.F., Caraballo-Rodriguez A.M., Glukhov E., Teke B., Leao T.et al. .. A convolutional neural network-based approach for the rapid annotation of molecularly diverse natural products. J. Am. Chem. Soc. 2020; 142:4114–4120. - PMC - PubMed
    1. Kim H.W., Wang M., Leber C.A., Nothias L., Reher R., Kang K.B., van der Hooft J.J.J., Dorrestein P.C., Gerwick W.H., Cottrell G.W.et al. .. NPClassifier: deep neural structural classification tool for natural products. J. Nat. Prod. 2021; 10.26434/chemrxiv.12885494.v1. - DOI - PMC - PubMed

Publication types

Substances