Mining Indonesian Microbial Biodiversity for Novel Natural Compounds by a Combined Genome Mining and Molecular Networking Approach

Abstract

Indonesia is one of the most biodiverse countries in the world and a promising resource for novel natural compound producers. Actinomycetes produce about two thirds of all clinically used antibiotics. Thus, exploiting Indonesia’s microbial diversity for actinomycetes may lead to the discovery of novel antibiotics. A total of 422 actinomycete strains were isolated from three different unique areas in Indonesia and tested for their antimicrobial activity. Nine potent bioactive strains were prioritized for further drug screening approaches. The nine strains were cultivated in different solid and liquid media, and a combination of genome mining analysis and mass spectrometry (MS)-based molecular networking was employed to identify potential novel compounds. By correlating secondary metabolite gene cluster data with MS-based molecular networking results, we identified several gene cluster-encoded biosynthetic products from the nine strains, including naphthyridinomycin, amicetin, echinomycin, tirandamycin, antimycin, and desferrioxamine B. Moreover, 16 putative ion clusters and numerous gene clusters were detected that could not be associated with any known compound, indicating that the strains can produce novel secondary metabolites. Our results demonstrate that sampling of actinomycetes from unique and biodiversity-rich habitats, such as Indonesia, along with a combination of gene cluster networking and molecular networking approaches, accelerates natural product identification.

Applications and Restrictions of Integrated Genomic and Metabolomic Screening: An Accelerator for Drug Discovery from Actinomycetes?

“…The listed examples demonstrate that integrated genomic and metabolomic screening has already been successfully applied for various purposes: The strategy has proven useful for comparative genomic and metabolomic studies as to explore the full biosynthetic potential of known or newly isolated Actinomyces strains and to detect similarities in the production profile of distinct strains [ 23 , 40 , 53 ]. This way, new producers of known compounds could be found [ 24 , 54 ].…”

“…Handayani et al [ 53 ] aimed to explore the biosynthetic capabilities of Streptomyces isolates from rarely explored habitats in Indonesian terrestrial and marine environments. Firstly, 422 isolates were prioritized according to their bioactivity against a board of test microbes.…”

“…Two more unidentifiable ion clusters were detected, for which a number of BGCs could code so that matching was not yet possible. The detected substances’ structures have not been elucidated yet [ 53 ].…”

Integrated Metabolomic–Genomic Workflows Accelerate Microbial Natural Product Discovery

“…and promote the discovery of novel natural products. 26 Each of these research teams utilized the Biosynthetic Gene Similarity Clustering and Prospecting engine (BiG-SCAPE) 18 which groups BGCs into gene cluster families based on sequence similarity networks. This software tool is now paired with the CORe Analysis of Syntenic Orthologues to prioritize Natural Product Gene Clusters (CORASON), 18 a tool that defines phylogenetic relationships within gene cluster families.…”

ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria

“…Together, these techniques are complemented by pages that detail site-specific phage recombinase targets and external resources such as ‘The Actinobacteriophage Database’. Metabolomics techniques [58] and recent efforts to integrate them with genomic data [59–64] are also absent from Practical Streptomyces Genetics and this is an area we plan to incorporate into ActinoBase. Many of these sections are still a work in progress or have yet to be written.…”