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Marine Drugs
Special Issues
Genomics-Guided Drug Discovery from Ocean Microbiome
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Special Issue "Genomics-Guided Drug Discovery from Ocean Microbiome"

A special issue of Marine Drugs (ISSN 1660-3397).

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 7248

Special Issue Editors

Prof. Dr. Peiyuan Qian

E-Mail Website
Guest Editor
Division of Life Sciences, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hongkong, China
Interests: larval omics; marine molecular ecology; microbial ecology; marine natural products; biofouling and antifouling; marine invertebrates
Special Issues, Collections and Topics in MDPI journals
Dr. Yongxin Li

E-Mail Website
Guest Editor
Department of Chemistry, The University of Hong Kong, Pokfulam 999077, Hongkong, China
Interests: marine natural product; microbiome; biosynthesis; synthetic biology; genome mining

Special Issue Information

Dear Colleagues,

This ocean environment with extremely high biomass and biodiversity not only provides food for us, but also offers a vast untapped genetic pool with medicinal and biotechnical potential. Particularly, the ocean microbiome produces diverse natural products such as signal molecules and antibiotics that mediate communication and competition, and are a vast unexplored source for drug discovery. Recently advances in metabolomics and genomics, combined with emerging synthetic biology strategies, are rapidly changing the landscape of microbial natural product discovery. Recent metagenome mining of the ocean microbiome revealed the huge biosynthetic potential of natural products hidden in the uncultivated microbiomes, the vast majority of which are still “orphans”.

The ocean microbiome presents an untapped source for natural product discovery. Novel integrated approaches that combine genomics, metabolomics, and synthetic biology strategies are recently applied to harness the chemical potential of the microbiome for targeted natural product discovery. This Special Issue invites articles from both genomics- and synthetic biology-enabled studies on ocean microbiomes with a focus on natural product discovery and characterization. We particularly welcome articles that combine genomics, metabolomics, and synthetic biology approach for the discovery of marine bacterial natural products.

Prof. Dr. Peiyuan Qian
Dr. Yongxin Li
Guest Editors

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

  • ocean microbiome
  • drug discovery
  • natural products
  • secondary metabolites
  • omics
  • genome mining
  • metabolic analysis
  • synthetic biology
  • biosynthesis

Published Papers (3 papers)

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Research

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Article
Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates
by
Andrea Iselin Elvheim
,
Chun Li
and
Bjarne Landfald
Mar. Drugs 2023, 21(3), 165; https://doi.org/10.3390/md21030165 - 02 Mar 2023
Viewed by 882
Abstract
Marine invertebrate microbiomes have been a rich source of bioactive compounds and interesting genomic features. In cases where the achievable amounts of metagenomic DNA are too low for direct sequencing, multiple displacement amplification (MDA) can be used for whole genome amplification. However, MDA [...] Read more.
Marine invertebrate microbiomes have been a rich source of bioactive compounds and interesting genomic features. In cases where the achievable amounts of metagenomic DNA are too low for direct sequencing, multiple displacement amplification (MDA) can be used for whole genome amplification. However, MDA has known limitations which can affect the quality of the resulting genomes and metagenomes. In this study, we evaluated the conservation of biosynthetic gene clusters (BGCs) and enzymes in MDA products from low numbers of prokaryotic cells (estimated 2–850). Marine invertebrate microbiomes collected from Arctic and sub-Arctic areas served as source material. The cells were separated from the host tissue, lysed, and directly subjected to MDA. The MDA products were sequenced by Illumina sequencing. Corresponding numbers of bacteria from a set of three reference strains were treated the same way. The study demonstrated that useful information on taxonomic, BGC, and enzyme diversities was obtainable from such marginal quantities of metagenomic material. Although high levels of assembly fragmentation resulted in most BGCs being incomplete, we conclude that this genome mining approach has the potential to reveal interesting BGCs and genes from hard-to-reach biological sources. Full article
(This article belongs to the Special Issue Genomics-Guided Drug Discovery from Ocean Microbiome)
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Review

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Review
Marine Bacterial Ribosomal Peptides: Recent Genomics- and Synthetic Biology-Based Discoveries and Biosynthetic Studies
by
Linda Sukmarini
Mar. Drugs 2022, 20(9), 544; https://doi.org/10.3390/md20090544 - 24 Aug 2022
Viewed by 2690
Abstract
Marine biodiversity is represented by an exceptional and ample array of intriguing natural product chemistries. Due to their extensive post-translational modifications, ribosomal peptides—also known as ribosomally synthesized and post-translationally modified peptides (RiPPs)—exemplify a widely diverse class of natural products, endowing a broad range [...] Read more.
Marine biodiversity is represented by an exceptional and ample array of intriguing natural product chemistries. Due to their extensive post-translational modifications, ribosomal peptides—also known as ribosomally synthesized and post-translationally modified peptides (RiPPs)—exemplify a widely diverse class of natural products, endowing a broad range of pharmaceutically and biotechnologically relevant properties for therapeutic or industrial applications. Most RiPPs are of bacterial origin, yet their marine derivatives have been quite rarely investigated. Given the rapid advancement engaged in a more powerful genomics approach, more biosynthetic gene clusters and pathways for these ribosomal peptides continue to be increasingly characterized. Moreover, the genome-mining approach in integration with synthetic biology techniques has markedly led to a revolution of RiPP natural product discovery. Therefore, this present short review article focuses on the recent discovery of RiPPs from marine bacteria based on genome mining and synthetic biology approaches during the past decade. Their biosynthetic studies are discussed herein, particularly the organization of targeted biosynthetic gene clusters linked to the encoded RiPPs with potential bioactivities. Full article
(This article belongs to the Special Issue Genomics-Guided Drug Discovery from Ocean Microbiome)
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Review
Targeted Large-Scale Genome Mining and Candidate Prioritization for Natural Product Discovery
by
Jessie James Limlingan Malit
,
Hiu Yu Cherie Leung
and
Pei-Yuan Qian
Mar. Drugs 2022, 20(6), 398; https://doi.org/10.3390/md20060398 - 16 Jun 2022
Cited by 11 | Viewed by 3194
Abstract
Large-scale genome-mining analyses have identified an enormous number of cryptic biosynthetic gene clusters (BGCs) as a great source of novel bioactive natural products. Given the sheer number of natural product (NP) candidates, effective strategies and computational methods are keys to choosing appropriate BGCs [...] Read more.
Large-scale genome-mining analyses have identified an enormous number of cryptic biosynthetic gene clusters (BGCs) as a great source of novel bioactive natural products. Given the sheer number of natural product (NP) candidates, effective strategies and computational methods are keys to choosing appropriate BGCs for further NP characterization and production. This review discusses genomics-based approaches for prioritizing candidate BGCs extracted from large-scale genomic data, by highlighting studies that have successfully produced compounds with high chemical novelty, novel biosynthesis pathway, and potent bioactivities. We group these studies based on their BGC-prioritization logics: detecting presence of resistance genes, use of phylogenomics analysis as a guide, and targeting for specific chemical structures. We also briefly comment on the different bioinformatics tools used in the field and examine practical considerations when employing a large-scale genome mining study. Full article
(This article belongs to the Special Issue Genomics-Guided Drug Discovery from Ocean Microbiome)
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