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Marine Drugs
Special Issues
Omics Technologies and Marine Microbial Natural Product Discovery
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Omics Technologies and Marine Microbial Natural Product Discovery

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: 31 July 2025 | Viewed by 902

Special Issue Editor

Prof. Dr. Huayue Li

E-Mail Website
Guest Editor
Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
Interests: marine microorganisms; genome mining; biosynthesis

Special Issue Information

Dear Colleagues,

Marine ecosystems provide unique and advantageous environmental conditions for microbial diversity and specialized bioactivities. However, the discovery process of new microbial natural products is still time-consuming, labor-intensive, and unpredictable. The rapid development of “-omics” technologies, including but not limited to genomics and metabolomics, led to revolutionary changes in natural product research, which provides a comprehensive view of the biosynthetic capacity and production of microbial secondary metabolites that helps to prioritize the acquisition of structurally novel natural products.

The focus of this Special Issue is to highlight the potential use of omics technologies in the discovery of new marine microbial natural products. The application of single- or multi-omics, including genomics, metabolomics, proteomics, transcriptomics, and microbiomics, to discover structurally novel compounds from marine microbes is encouraged. Studies on the biosynthesis and bioactivities of new/known marine natural products are also welcome.

Prof. Dr. Huayue Li
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

  • marine
  • microbial natural products
  • omics
  • genomics
  • metabolomics
  • biosynthetic
  • multi-omics
  • metabolomics
  • proteomics
  • transcriptomics
  • microbiomics
  • microorganism

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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Research

18 pages, 2407 KiB  
Article
Genome-Wide Mining of Chitinase Diversity in the Marine Diatom Thalassiosira weissflogii and Functional Characterization of a Novel GH19 Enzyme
by Mengzhen Cheng, Shuang Li, Jiahui Wang, Xiaoqi Yang, Delin Duan and Zhanru Shao
Mar. Drugs 2025, 23(4), 144; https://doi.org/10.3390/md23040144 - 26 Mar 2025
Viewed by 234
Abstract
Chitin represents a globally abundant marine polymer with significant ecological and biotechnological value. β-chitin is an important carbon fixation product of diatoms and has a greater range of applications than α- and γ-chitin. However, there has been a paucity of research on the [...] Read more.
Chitin represents a globally abundant marine polymer with significant ecological and biotechnological value. β-chitin is an important carbon fixation product of diatoms and has a greater range of applications than α- and γ-chitin. However, there has been a paucity of research on the characterization of chitin-related enzymes from β-chitin producers. In this study, we performed a genome-wide identification of 38 putative chitinase genes in Thalassiosira weissflogii, a key producer of β-chitin. Through comprehensive analyses of phylogenetic relationships, conserved motifs, structural domains, and subcellular localization predictions, we revealed that T. weissflogii possesses evolutionarily distinct GH18 and GH19 chitinase families exhibiting unique motif and domain configurations. Subcellular localization predictions showed that most TwChis were presumed to be located in the chloroplast, with a few being present in the nucleus and extracellular. The enzymatic activity of TwChi2, a GH19 chitinase, showed that TwChi2 was a member of exochitinase (EC 3.2.1.201) with strong thermal stability (40 °C) and broad substrate adaptability of hydrolyzing bipolymer, 1% and 5% colloidal chitin, α-chitin and β-chitin. Altogether, we analyzed the chitinase gene family and characterized a highly active exochitinase from T. weissflogii, which can catalyze the degradation of both chitin polymers and chitin oligosaccharides. The relevant results lay a foundation for the internal regulation mechanism of chitin metabolism in diatoms and provide a candidate enzyme for the green industrial preparation of high-value chitin oligosaccharides. Full article
(This article belongs to the Special Issue Omics Technologies and Marine Microbial Natural Product Discovery)
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11 pages, 1412 KiB  
Article
Structure Elucidation, Biosynthetic Gene Cluster Distribution, and Biological Activities of Ketomemicin Analogs in Salinispora
by Gabriel Castro-Falcón, Dulce G. Guillén-Matus, Elany Barbosa Da Silva, Wentao Guo, Alicia Ross, Mateus Sá Magalhães Serafim, Thaís Helena Maciel Fernandes, Dean J. Tantillo, Anthony J. O’Donoghue and Paul R. Jensen
Mar. Drugs 2025, 23(3), 126; https://doi.org/10.3390/md23030126 - 14 Mar 2025
Viewed by 523
Abstract
Pseudopeptides are attractive agents for protease inhibition due to their structural similarities to the natural substrates of these enzymes, as well as their enhanced stability and resistance to enzymatic degradation. We report three new ketomemicin pseudopeptides (1–3) from extracts [...] Read more.
Pseudopeptides are attractive agents for protease inhibition due to their structural similarities to the natural substrates of these enzymes, as well as their enhanced stability and resistance to enzymatic degradation. We report three new ketomemicin pseudopeptides (1–3) from extracts of the marine actinomycete Salinispora pacifica strain CNY-498. Their constitution and relative configuration were elucidated using NMR, mass spectrometry, and quantum chemical calculations. Using GNPS molecular networking and publicly available Salinispora LCMS datasets, five additional ketomemicin analogs (4–8) were identified with ketomemicin production detected broadly across Salinispora species. The ketomemicin biosynthetic gene cluster (ktm) is highly conserved in Salinispora, occurring in 79 of 118 public genome sequences, including eight of the nine named species. Outside Salinispora, ktm homologs were detected in various genera of the phylum Actinomycetota that might encode novel ketomemicin analogs. Ketomemicins 1–3 were tested against a panel of eleven proteases, with 2 displaying moderate inhibitory activity. This study describes the first report of ketomemicin production by Salinispora cultures, the distribution of the corresponding biosynthetic gene cluster, and the protease inhibitory activity of new ketomemicin derivatives. Full article
(This article belongs to the Special Issue Omics Technologies and Marine Microbial Natural Product Discovery)
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