Omics for Bioprospecting and Drug Discovery from Bacteria and Microalgae

Abstract

“Omics” represent a combinatorial approach to high-throughput analysis of biological entities for various purposes. It broadly encompasses genomics, transcriptomics, proteomics, lipidomics, and metabolomics. Bacteria and microalgae exhibit a wide range of genetic, biochemical and concomitantly, physiological variations owing to their exposure to biotic and abiotic dynamics in their ecosystem conditions. Consequently, optimal conditions for adequate growth and production of useful bacterial or microalgal metabolites are critically unpredictable. Traditional methods employ microbe isolation and ‘blind’-culture optimization with numerous chemical analyses making the bioprospecting process laborious, strenuous, and costly. Advances in the next generation sequencing (NGS) technologies have offered a platform for the pan-genomic analysis of microbes from community and strain downstream to the gene level. Changing conditions in nature or laboratory accompany epigenetic modulation, variation in gene expression, and subsequent biochemical profiles defining an organism’s inherent metabolic repertoire. Proteome and metabolome analysis could further our understanding of the molecular and biochemical attributes of the microbes under research. This review provides an overview of recent studies that have employed omics as a robust, broad-spectrum approach for screening bacteria and microalgae to exploit their potential as sources of drug leads by focusing on their genomes, secondary metabolite biosynthetic pathway genes, transcriptomes, and metabolomes. We also highlight how recent studies have combined molecular biology with analytical chemistry methods, which further underscore the need for advances in bioinformatics and chemoinformatics as vital instruments in the discovery of novel bacterial and microalgal strains as well as new drug leads.

Proteomic Profiling of Emiliania huxleyi Using a Three-Dimensional Separation Method Combined with Tandem Mass Spectrometry

“…Several studies have performed an integrated metabolomics-proteomics, which could show a better landscape of the marine plankton [81,82]. Integrating "-omics" studies (e.g., genomics, proteomics, transcriptomics, metabolomics, lipidomics, and glycomics) will enable the investigation of the impacts of ecological interactions on organism physiology as well as evaluation of physiological and biochemical properties relating to human health for future applications [83,84].…”

Evaluation of Apple Root-Associated Endophytic Streptomyces pulveraceus Strain ES16 by an OSMAC-Assisted Metabolomics Approach

“…For example, an increased abundance of environmental stress sensing genes, particularly in the rhizosphere microbiome of ARD soils compared to ARDunaffected soils, was recently unraveled by a metagenomics approach (Radl et al, 2019). Against this background, in the present study, we aimed to study apple root-associated endophytic S. pulveraceus ES16 by employing a chemical OSMAC approach (Romano et al, 2018;Pan et al, 2019;Maghembe et al, 2020) to induce high stress and sporulation in the organism. Earlier studies have substantiated that Streptomyces species are stressed and forced to sporulate by regulation of the pleiotropic transcriptional factors such as GlnR, MtrA, and PhoP, which can be achieved by manipulating the nature of carbon and nitrogen sources, their quantity (specifically the carbon/nitrogen ratio as well as their depletion), and phosphate availability in the medium (Karandikar et al, 1996;Martín and Liras, 2020).…”

“…In the present study, the phenotypic observations of endophytic S. pulveraceus ES16 under specific OSMAC parameters revealed an earthy soil odor release during this bacterium's prolific sporulation on PDA plates that induced stress to the organism. One important reason why we employed the six different defined media conditions to cultivate the organism was to study its secreted volatilome and metabolome expressed under the influence of stressful media conditions compared to nutrient-rich and optimum conditions (Romano et al, 2018;Pan et al, 2019;Maghembe et al, 2020). OSMAC-guided SPME-GC-MS analyses further revealed that the organism produces the volatile signal compound geosmin (compound 1, Figure 3; γ εω-"geo": earth, oσ µη-"osmi": smell) only under stressful conditions and during sporulation, and it is responsible for this scent.…”

“…Hence, it is necessary to understand the chemical-ecological interactions of endophytes on a case-by-case basis to fully exploit the potential of natural product biosynthesis and sustainable production for agriculture and industrial production of desired pharmaceutically relevant compounds, as well as to elucidate the intricate mesh of endophytic microbial chemoecological networks with coexisting organisms. A comprehensive and robust methodological approach employed to achieve this is called the One Strain Many Compounds (OSMAC) approach (Bode et al, 2002;Maghembe et al, 2020). The OSMAC approach enables establishing a comprehensive metabolic profile for each microorganism, revealing the compounds produced by the organism in its natural ecological niche (Romano et al, 2018;Pan et al, 2019;Maghembe et al, 2020).…”

“…A comprehensive and robust methodological approach employed to achieve this is called the One Strain Many Compounds (OSMAC) approach (Bode et al, 2002;Maghembe et al, 2020). The OSMAC approach enables establishing a comprehensive metabolic profile for each microorganism, revealing the compounds produced by the organism in its natural ecological niche (Romano et al, 2018;Pan et al, 2019;Maghembe et al, 2020). In vitro, culture-based OSMAC approach includes modulation of the physiochemical culture parameters, the addition of ecological niche-mimetic biotic and abiotic stress factors and triggers, and bioprocess optimization in a bid to selectively express cryptic gene clusters that are only expressed under particular conditions in the original natural habitat of the microorganism under study (Pan et al, 2019;Maghembe et al, 2020).…”