Biosynthetic novelty index reveals the metabolic potential of rare actinobacteria isolated from highly oligotrophic sediments

Abstract

Calculations predict that testing of 5 000–10 000 molecules and >1 billion US dollars (£0.8 billion, £1=$1.2) are required for one single drug to come to the market. A solution to this problem is to establish more efficient protocols that reduce the high rate of re-isolation and continuous rediscovery of natural products during early stages of the drug development process. The study of ‘rare actinobacteria’ has emerged as a possible approach for increasing the discovery rate of drug leads from natural sources. Here, we define a simple genomic metric, defined as biosynthetic novelty index (BiNI), that can be used to rapidly rank strains according to the novelty of the subset of encoding biosynthetic clusters. By comparing a subset of high-quality genomes from strains of different taxonomic and ecological backgrounds, we used the BiNI score to support the notion that rare actinobacteria encode more biosynthetic gene cluster (BGC) novelty. In addition, we present the isolation and genomic characterization, focused on specialized metabolites and phenotypic screening, of two isolates belonging to genera Lentzea and Actinokineospora from a highly oligotrophic environment. Our results show that both strains harbour a unique subset of BGCs compared to other members of the genera Lentzea and Actinokineospora . These BGCs are responsible for potent antimicrobial and cytotoxic bioactivity. The experimental data and analysis presented in this study contribute to the knowledge of genome mining analysis in rare actinobacteria and, most importantly, can serve to direct sampling efforts to accelerate early stages of the drug discovery pipeline.

Lentzea sokolovensis sp. nov., Lentzea kristufekii sp. nov. and Lentzea miocenica sp. nov., rare actinobacteria from Miocene lacustrine sediment of the Sokolov Coal Basin, Czech Republic

“…Melanoid pigment production was determined on peptone-yeast extract agar ISP 6 (DSM 1269) and tyrosine agar ISP 7 (DSM 1619), prepared as described by [12,12]. The optimal growth conditions regarding temperature (4,10,17,20,25,28,35,37,42, and 45 °C) and pH growth range (pH 4-13 with increments of 1 pH unit) were tested on GYM Streptomyces medium (DSMZ 65 [13]) in duplicate. The pH values were adjusted using NaOH or HCl and all pH values of the prepared media were checked after autoclaving and adjusted if necessary.…”

“…The genus Lentzea has recently attracted a great deal interest due to its underestimated genetic diversity [ 3 4 ], including its genetic potential for biosynthesis of natural products that are in high demand in the pharmaceutical field [ 5 ]. For instance, lentzeosides with anti-HIV-1 integrase activity were isolated from the extremotolerant Lentzea sp.…”

“…Later, petrichorins A and B, produced by Lentzea flaviverrucosa DSM 44664 T , were shown to exhibit antitumor activity in vitro [ 7 ]. In general, the genus Lentzea shows the third highest biosynthetic novelty index among rare actinobacteria genera [ 4 ], suggesting that isolates of Lentzea sp. from various oligotrophic or extreme environments could be a good source of novel natural products.…”

Actinomycetota bioprospecting from ore-forming environments

“…Interestingly, our BGC network revealed only 18 significant relationships, comprising 12 different NPs, with 152 singletons representing novel BGCs (). To further ascertain the novelty of the biosynthetic potential encoded by each strain, we determined their BiNI scores [57]. BiNI scores are calculated by comparing BGCs found in actinobacteria in public databases, with higher scores indicating greater diversity.…”

Diversity and taxonomic distribution of bacterial biosynthetic gene clusters predicted to produce compounds with therapeutically relevant bioactivities

“…One of the major challenges in natural product discovery is rediscovery of known compounds, especially when isolating compounds from historically popular sources of natural products, such as Streptomyces (Kong et al, 2011 ). Previous studies have surveyed biosynthetic diversity across the bacterial taxonomy and found that there are many families of biosynthetic gene clusters (BGCs) with no known product, even in well-mined genera such as Streptomyces and other actinomycetes (Jensen et al, 2014 ; Schorn et al, 2016 ; Chevrette and Handelsman, 2021 ; Gavriilidou et al, 2022 ; Gonzalez-Salazar et al, 2023 ). A study of the chemical diversity throughout the history of natural product discovery showed similar results—while the average novelty of structures discovered has decreased over time there remains a slow and steady discovery of novel scaffolds (Pye et al, 2017 ).…”