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Marine Drugs
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Marine Metabolomics 2023
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Marine Metabolomics 2023

A special issue of Marine Drugs (ISSN 1660-3397). This special issue belongs to the section "Marine Biotechnology Related to Drug Discovery or Production".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 20494

Special Issue Editor

Dr. Rob Keyzers

grade E-Mail Website1 Website2
Guest Editor
School of Chemical and Physical Sciences, and Center for Biodiscovery, Victoria University of Wellington, Wellington 6140, New Zealand
Interests: marine invertebrate natural products; bioactive natural products; structure determination of new metabolites; isolation and purification; chemical analysis; analytical chemistry of natural compounds and xenochemicals
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Marine resources continue to be a significant source of new and rare compounds, ranging from small molecules of only a few atoms, including unusual elements like arsenic, through to some of the largest non-proteinaceous chemicals ever observed. This chemical diversity is not restricted to any one kingdom or phylum, but rather extends across all organisms, from seaweed through both vertebrate and invertebrate animals, and onto microorganisms including bacteria and fungi.

As a tool, metabolomics seeks to characterize all the chemicals present in an organism at a given point in time. Metabolomics is in essence the ultimate -omics, being the result of the functioning of the source organism's genome and proteome. Quantifying the metabolites produced by an organism can give fundamental insight into understanding inter- and intra-species relationships and functions.

This Special Issue invites researchers engaged in the field of marine-derived chemistry to submit manuscripts related to metabolomics. Particular foci include applications of new methodologies for metabolomics, studies of distinctive molecular classes, or geographical-based studies. Both research articles and review manuscripts are welcome.

Dr. Rob Keyzers
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Marine Drugs is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • metabolomics
  • NMR
  • LCMS
  • GCMS
  • GNPS
  • chromatography
  • chemical ecology
  • bioactivity
  • chemical analysis primary metabolism
  • secondary metabolism

Related Special Issue

Published Papers (7 papers)

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41 pages, 37100 KiB  
Article
Screening of a Thraustochytrid Strain Collection for Carotenoid and Squalene Production Characterized by Cluster Analysis, Comparison of 18S rRNA Gene Sequences, Growth Behavior, and Morphology
by Inga K. Koopmann, Bettina A. Müller and Antje Labes
Mar. Drugs 2023, 21(4), 204; https://doi.org/10.3390/md21040204 - 24 Mar 2023
Cited by 1 | Viewed by 4278
Abstract
Carotenoids and squalene are important terpenes that are applied in a wide range of products in foods and cosmetics. Thraustochytrids might be used as alternative production organisms to improve production processes, but the taxon is rarely studied. A screening of 62 strains of [...] Read more.
Carotenoids and squalene are important terpenes that are applied in a wide range of products in foods and cosmetics. Thraustochytrids might be used as alternative production organisms to improve production processes, but the taxon is rarely studied. A screening of 62 strains of thraustochytrids sensu lato for their potential to produce carotenoids and squalene was performed. A phylogenetic tree was built based on 18S rRNA gene sequences for taxonomic classification, revealing eight different clades of thraustochytrids. Design of experiments (DoE) and growth models identified high amounts of glucose (up to 60 g/L) and yeast extract (up to 15 g/L) as important factors for most of the strains. Squalene and carotenoid production was studied by UHPLC-PDA-MS measurements. Cluster analysis of the carotenoid composition partially mirrored the phylogenetic results, indicating a possible use for chemotaxonomy. Strains in five clades produced carotenoids. Squalene was found in all analyzed strains. Carotenoid and squalene synthesis was dependent on the strain, medium composition and solidity. Strains related to Thraustochytrium aureum and Thraustochytriidae sp. are promising candidates for carotenoid synthesis. Strains closely related to Schizochytrium aggregatum might be suitable for squalene production. Thraustochytrium striatum might be a good compromise for the production of both molecule groups. Full article
(This article belongs to the Special Issue Marine Metabolomics 2023)
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19 pages, 3609 KiB  
Article
Bioactivity Profiling and Untargeted Metabolomics of Microbiota Associated with Mesopelagic Jellyfish Periphylla periphylla
by Ernest Oppong-Danquah, Martina Miranda, Martina Blümel and Deniz Tasdemir
Mar. Drugs 2023, 21(2), 129; https://doi.org/10.3390/md21020129 - 17 Feb 2023
Cited by 2 | Viewed by 2664
Abstract
The marine mesopelagic zone extends from water depths of 200 m to 1000 m and is home to a vast number and diversity of species. It is one of the least understood regions of the marine environment with untapped resources of pharmaceutical relevance. [...] Read more.
The marine mesopelagic zone extends from water depths of 200 m to 1000 m and is home to a vast number and diversity of species. It is one of the least understood regions of the marine environment with untapped resources of pharmaceutical relevance. The mesopelagic jellyfish Periphylla periphylla is a well-known and widely distributed species in the mesopelagic zone; however, the diversity or the pharmaceutical potential of its cultivable microbiota has not been explored. In this study, we isolated microorganisms associated with the inner and outer umbrella of P. periphylla collected in Irminger Sea by a culture-dependent approach, and profiled their chemical composition and biological activities. Sixteen mostly gram-negative bacterial isolates were selected and subjected to an OSMAC cultivation regime approach using liquid and solid marine broth (MB) and glucose–yeast–malt (GYM) media. Their ethyl acetate (EtOAc) extracts were assessed for cytotoxicity and antimicrobial activity against fish and human pathogens. All, except one extract, displayed diverse levels of antimicrobial activities. Based on low IC50 values, four most bioactive gram-negative strains; Polaribacter sp. SU124, Shewanella sp. SU126, Psychrobacter sp. SU143 and Psychrobacter sp. SU137, were prioritized for an in-depth comparative and untargeted metabolomics analysis using feature-based molecular networking. Various chemical classes such as diketopiperazines, polyhydroxybutyrates (PHBs), bile acids and other lipids were putatively annotated, highlighting the biotechnological potential in P. periphylla-associated microbiota as well as gram-negative bacteria. This is the first study providing an insight into the cultivable bacterial community associated with the mesopelagic jellyfish P. periphylla and, indeed, the first to mine the metabolome and antimicrobial activities of these microorganisms. Full article
(This article belongs to the Special Issue Marine Metabolomics 2023)
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14 pages, 1133 KiB  
Article
Neosuberitenone, a New Sesterterpenoid Carbon Skeleton; New Suberitenones; and Bioactivity against Respiratory Syncytial Virus, from the Antarctic Sponge Suberites sp.
by Joe Bracegirdle, Stine S. H. Olsen, Michael N. Teng, Kim C. Tran, Charles D. Amsler, James B. McClintock and Bill J. Baker
Mar. Drugs 2023, 21(2), 107; https://doi.org/10.3390/md21020107 - 01 Feb 2023
Viewed by 2613
Abstract
Respiratory syncytial virus (RSV) is a highly contagious human pathogen that poses a significant threat to children under the age of two, and there is a current need for new small molecule treatments. The Antarctic sponge Suberites sp. is a known source of [...] Read more.
Respiratory syncytial virus (RSV) is a highly contagious human pathogen that poses a significant threat to children under the age of two, and there is a current need for new small molecule treatments. The Antarctic sponge Suberites sp. is a known source of sesterterpenes, and following an NMR-guided fractionation procedure, it was found to produce several previously unreported metabolites. Neosuberitenone (1), with a new carbon scaffold herein termed the ‘neosuberitane’ backbone, six suberitenone derivatives (2–7), an ansellane-type terpenoid (8), and a highly degraded sesterterpene (9), as well as previously reported suberitenones A (10) and B (11), were characterized. The structures of all of the isolated metabolites including absolute configurations are proposed on the basis of NMR, HRESIMS, optical rotation, and XRD data. The biological activities of the metabolites were evaluated in a range of infectious disease assays. Suberitenones A, B, and F (3) were found to be active against RSV, though, along with other Suberites sp. metabolites, they were inactive in bacterial and fungal screens. None of the metabolites were cytotoxic for J774 macrophages or A549 adenocarcinoma cells. The selectivity of suberitenones A, B, and F for RSV among other infectious agents is noteworthy. Full article
(This article belongs to the Special Issue Marine Metabolomics 2023)
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23 pages, 2224 KiB  
Article
Bioactivity and Metabolome Mining of Deep-Sea Sediment-Derived Microorganisms Reveal New Hybrid PKS-NRPS Macrolactone from Aspergillus versicolor PS108-62
by Florent Magot, Gwendoline Van Soen, Larissa Buedenbender, Fengjie Li, Thomas Soltwedel, Laura Grauso, Alfonso Mangoni, Martina Blümel and Deniz Tasdemir
Mar. Drugs 2023, 21(2), 95; https://doi.org/10.3390/md21020095 - 28 Jan 2023
Cited by 4 | Viewed by 2804
Abstract
Despite low temperatures, poor nutrient levels and high pressure, microorganisms thrive in deep-sea environments of polar regions. The adaptability to such extreme environments renders deep-sea microorganisms an encouraging source of novel, bioactive secondary metabolites. In this study, we isolated 77 microorganisms collected by [...] Read more.
Despite low temperatures, poor nutrient levels and high pressure, microorganisms thrive in deep-sea environments of polar regions. The adaptability to such extreme environments renders deep-sea microorganisms an encouraging source of novel, bioactive secondary metabolites. In this study, we isolated 77 microorganisms collected by a remotely operated vehicle from the seafloor in the Fram Strait, Arctic Ocean (depth of 2454 m). Thirty-two bacteria and six fungal strains that represented the phylogenetic diversity of the isolates were cultured using an One-Strain-Many-Compounds (OSMAC) approach. The crude EtOAc extracts were tested for antimicrobial and anticancer activities. While antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) and Enterococcus faecium was common for many isolates, only two bacteria displayed anticancer activity, and two fungi inhibited the pathogenic yeast Candida albicans. Due to bioactivity against C. albicans and rich chemical diversity based on molecular network-based untargeted metabolomics, Aspergillus versicolor PS108-62 was selected for an in-depth chemical investigation. A chemical work-up of the SPE-fractions of its dichloromethane subextract led to the isolation of a new PKS-NRPS hybrid macrolactone, versicolide A (1), a new quinazoline (−)-isoversicomide A (3), as well as three known compounds, burnettramic acid A (2), cyclopenol (4) and cyclopenin (5). Their structures were elucidated by a combination of HRMS, NMR, [α]D, FT-IR spectroscopy and computational approaches. Due to the low amounts obtained, only compounds 2 and 4 could be tested for bioactivity, with 2 inhibiting the growth of C. albicans (IC50 7.2 µg/mL). These findings highlight, on the one hand, the vast potential of the genus Aspergillus to produce novel chemistry, particularly from underexplored ecological niches such as the Arctic deep sea, and on the other, the importance of untargeted metabolomics for selection of marine extracts for downstream chemical investigations. Full article
(This article belongs to the Special Issue Marine Metabolomics 2023)
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15 pages, 2993 KiB  
Article
Limited Metabolomic Overlap between Commensal Bacteria and Marine Sponge Holobionts Revealed by Large Scale Culturing and Mass Spectrometry-Based Metabolomics: An Undergraduate Laboratory Pedagogical Effort at Georgia Tech
by Jessica M. Deutsch, Madison O. Green, Priyanka Akavaram, Ashleigh C. Davis, Sarth S. Diskalkar, Isabelle A. Du Plessis, Hannah A. Fallon, Emma M. Grason, Emma G. Kauf, Zoe M. Kim, Jeffrey R. Miller II, Abby L. Neal, Tatiana Riera, Sofie-Ellen Stroeva, Jollin Tran, Vivi Tran, Azucena Velgara Coronado, Vanessa Velgara Coronado, Benjamin T. Wall, Chung mo Yang, Ipsita Mohanty, Nadine H. Abrahamse, Christopher J. Freeman, Cole G. Easson, Cara L. Fiore, Alison E. Onstine, Naima Djeddar, Shweta Biliya, Anton V. Bryksin, Neha Garg and Vinayak Agarwaladd Show full author list remove Hide full author list
Mar. Drugs 2023, 21(1), 53; https://doi.org/10.3390/md21010053 - 14 Jan 2023
Cited by 2 | Viewed by 3311
Abstract
Sponges are the richest source of bioactive organic small molecules, referred to as natural products, in the marine environment. It is well established that laboratory culturing-resistant symbiotic bacteria residing within the eukaryotic sponge host matrix often synthesize the natural products that are detected [...] Read more.
Sponges are the richest source of bioactive organic small molecules, referred to as natural products, in the marine environment. It is well established that laboratory culturing-resistant symbiotic bacteria residing within the eukaryotic sponge host matrix often synthesize the natural products that are detected in the sponge tissue extracts. However, the contributions of the culturing-amenable commensal bacteria that are also associated with the sponge host to the overall metabolome of the sponge holobiont are not well defined. In this study, we cultured a large library of bacteria from three marine sponges commonly found in the Florida Keys. Metabolomes of isolated bacterial strains and that of the sponge holobiont were compared using mass spectrometry to reveal minimal metabolomic overlap between commensal bacteria and the sponge hosts. We also find that the phylogenetic overlap between cultured commensal bacteria and that of the sponge microbiome is minimal. Despite these observations, the commensal bacteria were found to be a rich resource for novel natural product discovery. Mass spectrometry-based metabolomics provided structural insights into these cryptic natural products. Pedagogic innovation in the form of laboratory curricula development is described which provided undergraduate students with hands-on instruction in microbiology and natural product discovery using metabolomic data mining strategies. Full article
(This article belongs to the Special Issue Marine Metabolomics 2023)
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22 pages, 2920 KiB  
Article
A Metabolomics-Based Toolbox to Assess and Compare the Metabolic Potential of Unexplored, Difficult-to-Grow Bacteria
by Federica Fiorini, Felizitas Bajerski, Olga Jeske, Cendrella Lepleux, Jörg Overmann and Mark Brönstrup
Mar. Drugs 2022, 20(11), 713; https://doi.org/10.3390/md20110713 - 14 Nov 2022
Cited by 1 | Viewed by 2158
Abstract
Novel high-throughput cultivation techniques create a demand to pre-select strains for in-depth follow-up studies. We report a workflow to identify promising producers of novel natural products by systematically characterizing their metabolomes. For this purpose, 60 strains from four phyla (Proteobacteria, Bacteroidetes, Actinobacteria and [...] Read more.
Novel high-throughput cultivation techniques create a demand to pre-select strains for in-depth follow-up studies. We report a workflow to identify promising producers of novel natural products by systematically characterizing their metabolomes. For this purpose, 60 strains from four phyla (Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes) comprising 16 novel species and six novel genera were cultivated from marine and terrestrial sources. Their cellular metabolomes were recorded by LC-MS/MS; data analysis comprised databases MS/MS matching, in silico compound assignment, and GNPS-based molecular networking. Overall, 1052 different molecules were identified from 6418 features, among them were unusual metabolites such as 4-methoxychalcone. Only a minor portion of the 755 features were found in all phyla, while the majority occurred in a single phylogroup or even in a single strain. Metabolomic methods enabled the recognition of highly talented strains such as AEG42_45, which had 107 unique features, among which a family of 28 potentially novel and related compounds according to MS/MS similarities. In summary, we propose that high-throughput cultivation and isolation of bacteria in combination with the presented systematic and unbiased metabolome analysis workflow is a promising approach to capture and assess the enormous metabolic potential of previously uncultured bacteria. Full article
(This article belongs to the Special Issue Marine Metabolomics 2023)
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25 pages, 4526 KiB  
Perspective
Case Studies in Molecular Network-Guided Marine Biodiscovery
by Shamsunnahar Khushi, Angela A. Salim and Robert J. Capon
Mar. Drugs 2023, 21(7), 413; https://doi.org/10.3390/md21070413 - 20 Jul 2023
Viewed by 1584
Abstract
In reviewing a selection of recent case studies from our laboratory, we revealed some lessons learned and benefits accrued from the application of mass spectrometry (MS/MS) molecular networking in the field of marine sponge natural products. Molecular networking proved pivotal to our discovery [...] Read more.
In reviewing a selection of recent case studies from our laboratory, we revealed some lessons learned and benefits accrued from the application of mass spectrometry (MS/MS) molecular networking in the field of marine sponge natural products. Molecular networking proved pivotal to our discovery of many new natural products and even new classes of natural product, some of which were opaque to alternate dereplication and prioritization strategies. Case studies included the discovery of: (i) trachycladindoles, an exceptionally rare class of bioactive indole alkaloid previously only known from a single southern Australia sample of Trachycladus laevispirulifer; (ii) dysidealactams, an unprecedented class of sesquiterpene glycinyl-lactam and glycinyl-imide from a Dysidea sp., a sponge genera often discounted as having been exhaustively studied; (iii) cacolides, an unprecedented family of sesterterpene α-methyl-γ-hydroxybutenolides from a Cacospongia sp., all too easily mischaracterized and deprioritized during dereplication as a well-known class of sponge sesterterpene tetronic acids; and (iv) thorectandrins, a new class of indole alkaloid which revealed unexpected insights into the chemical and biological properties of the aplysinopsins, one of the earliest and more extensively reported class of sponge natural products. Full article
(This article belongs to the Special Issue Marine Metabolomics 2023)
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