StreptomeDB 3.0: an updated compendium of streptomycetes natural products

Abstract

Antimicrobial resistance is an emerging global health threat necessitating the rapid development of novel antimicrobials. Remarkably, the vast majority of currently available antibiotics are natural products (NPs) isolated from streptomycetes, soil-dwelling bacteria of the genus Streptomyces. However, there is still a huge reservoir of streptomycetes NPs which remains pharmaceutically untapped and a compendium thereof could serve as a source of inspiration for the rational design of novel antibiotics. Initially released in 2012, StreptomeDB (http://www.pharmbioinf.uni-freiburg.de/streptomedb) is the first and only public online database that enables the interactive phylogenetic exploration of streptomycetes and their isolated or mutasynthesized NPs. In this third release, there are substantial improvements over its forerunners, especially in terms of data content. For instance, about 2500 unique NPs were newly annotated through manual curation of about 1300 PubMed-indexed articles, published in the last five years since the second release. To increase interoperability, StreptomeDB entries were hyperlinked to several spectral, (bio)chemical and chemical vendor databases, and also to a genome-based NP prediction server. Moreover, predicted pharmacokinetic and toxicity profiles were added. Lastly, some recent real-world use cases of StreptomeDB are highlighted, to illustrate its applicability in life sciences.

Insights into the Variation in Bioactivities of Closely Related Streptomyces Strains from Marine Sediments of the Visayan Sea against ESKAPE and Ovarian Cancer

“…Bacteria belonging to the family Actinomycetaceae are important natural sources of antimicrobial drugs [ 4 , 5 , 6 ]. The species of terrestrial bacteria belonging to this family, particularly the genus Streptomyces, have been demonstrated to prolifically produce diverse bioactive compounds currently sold in the market and prescribed for clinical use [ 4 , 7 , 8 , 9 ]. These free-living, saprophytic microorganisms could be found in diverse environments such as rain forests, lake and ocean sediments, estuaries, as well as deep ocean trenches, lake mud, beach sands, and sponges [ 5 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 ].…”

SubTap, a Versatile 3D Printed Platform for Eavesdropping on Extracellular Interactions

“…To further investigate this data set, we identified the subset of 43 observed m / z features ( Table S4 ) matching compounds that are known to be produced by S. coelicolor present in StreptomeDB ( 27 ). Several of these m / z features were observed only in samples containing S. coelicolor ( Fig.…”

SeMPI 2.0—A Web Server for PKS and NRPS Predictions Combined with Metabolite Screening in Natural Product Databases

“…This option allows one to detect the putative BGC for a given streptomyces natural product. The streptomyces genomes included all complete genomes associated with compounds stored in the StreptomeDB v3 [ 54 ]. Whereas the database screening allows for the detection of putative SMs for a submitted BGC, the addition of preprocessed BGCs also enables reverse screening, thus allowing one to connect SMs with their putative BGCs.…”