Metabolomics and Marine Biotechnology: Coupling Metabolite Profiling and Organism Biology for the Discovery of New Compounds

Abstract

The high diversity of marine natural products represents promising opportunities for drug discovery, an important area in marine biotechnology. Within this context, high-throughput techniques such as metabolomics are extremely useful in unveiling unexplored chemical diversity at much faster rates than classical bioassay-guided approaches. Metabolomics approaches enable studying large sets of metabolites, even if they are produced at low concentrations. Although, metabolite identification remains the main metabolomics bottleneck, bioinformatic tools such as molecular networks can lead to the annotation of unknown metabolites and discovery of new compounds. A metabolomic approach in drug discovery has two major advantages: it enables analyses of multiple samples, allowing fast dereplication of already known compounds and provides a unique opportunity to relate metabolite profiles to organisms’ biology. Understanding the ecological and biological factors behind a certain metabolite production can be extremely useful in enhancing compound yields, optimizing compound extraction or in selecting bioactive compounds. Metazoan-associated microbiota are often responsible for metabolite synthesis, however, classical approaches only allow studying metabolites produced from cultivatable microbiota, which often differ from the compounds produced within the host. Therefore, coupling holobiome metabolomics with microbiome analysis can bring new insights to the role of microbiota in compound production. The ultimate potential of metabolomics is its coupling with other “omics” (i.e., transcriptomics and metagenomics). Although, such approaches are still challenging, especially in non-model species where genomes have not been annotated, this innovative approach is extremely valuable in elucidating gene clusters associated with biosynthetic pathways and will certainly become increasingly important in marine drug discovery.

Presence of Bromotyrosine Alkaloids in Marine Sponges Is Independent of Metabolomic and Microbiome Architectures

“…Interest in sponge-sourced natural products is sustained due to their pharmaceutical potential and their roles in shaping benthic marine community structure ( 1 , 2 ). Building upon spectroscopic and crystallographic descriptions of sponge-derived natural products, mass spectrometry (MS)-based metabolome mining strategies are beginning to reveal additional chemical diversity in sponge holobionts ( 3 , 4 ).…”

How Do the Players Play? A Post-Genomic Analysis Paradigm to Understand Aquatic Ecosystem Processes

“…Though many of the compounds remained unambiguously defined, integration of these approaches did reveal a network of interactive processes related to anaerobic activity and biodegradation in the presence of petroleum compounds (Bargiela et al, 2015). Overall, insights into microbial function and resilience in low-pH environments or complex hydrocarbon impacted zones have implications for predictive models of aquatic ecosystem health and sustainability, but also significant potential for resource management and biotechnological advancements such as the discovery of novel compounds (Reverter et al, 2020), as well as biomarker discovery (Pomfret et al, 2019).…”

“…In many fields, such as those discussed above, the call for a shift toward post-genomics or "multi-omics" approaches has been expressed for several years and in some cases have been embraced by at least segments of the research community (Anderson et al, 2012;Llewellyn et al, 2015;Cocolin et al, 2018;Reverter et al, 2020). While these studies tout the numerous advantages for applying them in "complex" circumstances, they are also unified in expressing concern for the equally "complex" technical challenges.…”

<p>From Primary Cell and Tissue Cultures to Aquatic Invertebrate Cell Lines: An Updated Overview</p> <p>&nbsp;</p>

“…Ample information has been gained on this issue in mammalian cell cultures ( Čuperlović-Culf et al 2010;Mohmad-Saberi et al 2013). Yet, the study of the secretome of aquatic invertebrates has seldomly been undertaken (Kocot et al 2016), but data on the metabolome of whole organisms in the context of marine natural product discoveries are becoming quite common (Reverter et al 2020). Furthermore, high-precision tool development specific to seawater are now available (Sogin et al 2019).…”