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Metabolites
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Marine Microbes Related Metabolic Studies
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Marine Microbes Related Metabolic Studies

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Microbiology and Ecological Metabolomics".

Deadline for manuscript submissions: closed (31 August 2023) | Viewed by 9108

Special Issue Editors

Prof. Dr. Fan Zhang

E-Mail Website
Guest Editor
School of Pharmaceutical Sciences, Wuhan University, Wuhan 430072, China
Interests: microbial natural products; antibiotics discovery; untargeted metabolomics; genome mining; biosynthesis; MDR pathogens
Prof. Dr. Fei Gan

E-Mail Website
Guest Editor
College of Life Science, Wuhan University, Wuhan 430072, China
Interests: microbial synthetic biology; genetic code expansion; photosynthesis

Special Issue Information

Dear Colleagues,

Oceans cover over 70% of the earth. The largely unexplored marine world that presumably harbors the most biodiversity may be the vastest resource to discover secondary metabolites, exhibiting a wide range of pharmaceutically relevant bioactivities. Among the marine organisms, marine bacteria and fungi have shown to produce novel natural products with unique and diverse chemical structures. Therefore, the marine-microbe-related natural products can crucially develop novel drugs or drug leads. Recently, the application of new interdisciplinary approaches, such as bioinformatics and genome mining, MS-based metabolomics, ribosome engineering, and heterologous expression, have a significant boost on the exploration of novel functional biomolecules from these microbes and the huge chemical potential of marine sources.

This Special Issue of Metabolites welcomes both fundamental research papers and critical review works covering the lastest develpments of marine microbes related metabolic studies, including on the discovery, the structure elucidation, and the in vitro and in vivo bioactivity evaluation of biosynthetic pathways and pharmaceutical mechanisms, as well as the metabolic engineering of marine natural products. In addition, manuscripts describing innovative methodological approaches for the screening and discovery of marine-microbe-related compounds are highly welcome. This Special Issue intends collect groundbreaking contributions in this field.

Prof. Dr. Fan Zhang
Prof. Dr. Fei Gan
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. Metabolites 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 2700 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 bacteria
  • marine fungi
  • natural products
  • biological activities
  • omics approaches

Published Papers (5 papers)

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Research

46 pages, 20973 KiB  
Article
The Metabolite Profiling of Aspergillus fumigatus KMM4631 and Its Co-Cultures with Other Marine Fungi
by Anton N. Yurchenko, Liliana E. Nesterenko, Roman S. Popov, Natalya N. Kirichuk, Viktoria E. Chausova, Ekaterina A. Chingizova, Marina P. Isaeva and Ekaterina A. Yurchenko
Metabolites 2023, 13(11), 1138; https://doi.org/10.3390/metabo13111138 - 08 Nov 2023
Viewed by 1443
Abstract
An Aspergillus fumigatus KMM 4631 strain was previously isolated from a Pacific soft coral Sinularia sp. sample and was found to be a source of a number of bioactive secondary metabolites. The aims of this work are the confirmation of this strain’ identification [...] Read more.
An Aspergillus fumigatus KMM 4631 strain was previously isolated from a Pacific soft coral Sinularia sp. sample and was found to be a source of a number of bioactive secondary metabolites. The aims of this work are the confirmation of this strain’ identification based on ITS, BenA, CaM, and RPB2 regions/gene sequences and the investigation of secondary metabolite profiles of Aspergillus fumigatus KMM 4631 culture and its co-cultures with Penicillium hispanicum KMM 4689, Amphichorda sp. KMM 4639, Penicillium sp. KMM 4672, and Asteromyces cruciatus KMM 4696 from the Collection of Marine Microorganisms (PIBOC FEB RAS, Vladivostok, Russia). Moreover, the DPPH-radical scavenging activity, urease inhibition, and cytotoxicity of joint fungal cultures’ extracts on HepG2 cells were tested. The detailed UPLC MS qTOF investigation resulted in the identification and annotation of indolediketopiperazine, quinazoline, and tryptoquivaline-related alkaloids as well as a number of polyketides (totally 20 compounds) in the extract of Aspergillus fumigatus KMM 4631. The metabolite profiles of the co-cultures of A. fumigatus with Penicillium hispanicum, Penicillium sp., and Amphichorda sp. were similar to those of Penicillium hispanicum, Penicillium sp., and Amphichorda sp. monocultures. The metabolite profile of the co-culture of A. fumigatus with Asteromyces cruciatus differed from that of each monoculture and may be more promising for the isolation of new compounds. Full article
(This article belongs to the Special Issue Marine Microbes Related Metabolic Studies)
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15 pages, 2783 KiB  
Article
Elemental Composition of Plankton Exometabolites (Mucous Macroaggregates): Control by Biogenic and Lithogenic Components
by Nives Kovač, Jérôme Viers, Jadran Faganeli, Oliver Bajt and Oleg S. Pokrovsky
Metabolites 2023, 13(6), 726; https://doi.org/10.3390/metabo13060726 - 05 Jun 2023
Viewed by 852
Abstract
Among the various exometabolitic effects of marine microorganisms, massive mucilage events in the coastal zones of temperate and tropical seas are the most spectacular and environmentally important. Abundant mucilage material in the form of aggregates appears in late spring/early summer in the water [...] Read more.
Among the various exometabolitic effects of marine microorganisms, massive mucilage events in the coastal zones of temperate and tropical seas are the most spectacular and environmentally important. Abundant mucilage material in the form of aggregates appears in late spring/early summer in the water column of the Adriatic Sea. These macroaggregate biopolymers originate mainly from plankton exometabolites, with both autochthonous and allochthonous components, and strongly impact the tourism, fisheries, and economy of coastal countries. In contrast to extensive studies on the structural and chemical nature of macroaggregates performed over past decades, the full elemental composition of these substances remains poorly known, which does not allow for a complete understanding of their origin, evolution, and necessary remediation measures. Here, we report the results of comprehensive analyses of 55 major and trace elements in the composition of macro aggregates collected at the surface and in the water column during massive mucilage events. Through normalization of the elemental chemical composition of the upper earth crust (UCC), river suspended material (RSM), mean oceanic plankton, and mean oceanic particulate suspended material, we demonstrate that the water column macroaggregates reflect a superposition of the signal from plankton and marine particulate matter. The surface macroaggregates were preferentially enriched in lithogenic component, and carried the signature of planktonic material. The rare earth element (REE) signal was strongly dominated by plankton and, to a lesser degree, by oceanic particulate matter, while at the same time being strongly (>80 times) impoverished compared with UCC and RSM. Taken together, the elemental composition of macroaggregates allows for distinguishing the lithogenic and biogenic impacts on the occurrence of these unique large-scale mucilage events, linked to the exometabolism of marine plankton combined with the input of allochthonous inorganic material. Full article
(This article belongs to the Special Issue Marine Microbes Related Metabolic Studies)
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11 pages, 1488 KiB  
Article
Application of 1H HR-MAS NMR-Based Metabolite Fingerprinting of Marine Microalgae
by Carolina da Silva Canielles Caprara, Tatiane Ksyvickas Mathias, Maria de Fátima C. Santos, Marcelo G. M. D’Oca, Caroline Da R. M. D’Oca, Fabio Roselet, Paulo Cesar Abreu and Daniela Fernandes Ramos
Metabolites 2023, 13(2), 202; https://doi.org/10.3390/metabo13020202 - 30 Jan 2023
Cited by 1 | Viewed by 1619
Abstract
Natural products from the marine environment as well as microalgae, have been known for the complexity of the metabolites they produce due to their adaptability to different environmental conditions, which has been an inexhaustible source of several bioactive properties, such as antioxidant, anti-tumor, [...] Read more.
Natural products from the marine environment as well as microalgae, have been known for the complexity of the metabolites they produce due to their adaptability to different environmental conditions, which has been an inexhaustible source of several bioactive properties, such as antioxidant, anti-tumor, and antimicrobial. This study aims to characterize the main metabolites of three species of microalgae (Nannochloropsis oceanica, Chaetoceros muelleri, and Conticribra weissflogii), which have important applications in the biofuel and nutrition industries, by 1H High-resolution magic angle spinning nuclear magnetic resonance (1H HR-MAS NMR), a method which is non-destructive, is highly reproducible, and requires minimal sample preparation. Even though the three species were found in the same ecosystem and a superior production of lipid compounds was observed, important differences were identified in relation to the production of specialized metabolites. These distinct properties favor the use of these compounds as leaders in the development of new bioactive compounds, especially against environmental, human, and animal pathogens (One Health), and demonstrate their potential in the development of alternatives for aquaculture. Full article
(This article belongs to the Special Issue Marine Microbes Related Metabolic Studies)
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10 pages, 2174 KiB  
Article
ConCISE: Consensus Annotation Propagation of Ion Features in Untargeted Tandem Mass Spectrometry Combining Molecular Networking and In Silico Metabolite Structure Prediction
by Zachary A. Quinlan, Irina Koester, Allegra T. Aron, Daniel Petras, Lihini I. Aluwihare, Pieter C. Dorrestein, Craig E. Nelson and Linda Wegley Kelly
Metabolites 2022, 12(12), 1275; https://doi.org/10.3390/metabo12121275 - 16 Dec 2022
Cited by 9 | Viewed by 2247
Abstract
Recent developments in molecular networking have expanded our ability to characterize the metabolome of diverse samples that contain a significant proportion of ion features with no mass spectral match to known compounds. Manual and tool-assisted natural annotation propagation is readily used to classify [...] Read more.
Recent developments in molecular networking have expanded our ability to characterize the metabolome of diverse samples that contain a significant proportion of ion features with no mass spectral match to known compounds. Manual and tool-assisted natural annotation propagation is readily used to classify molecular networks; however, currently no annotation propagation tools leverage consensus confidence strategies enabled by hierarchical chemical ontologies or enable the use of new in silico tools without significant modification. Herein we present ConCISE (Consensus Classifications of In Silico Elucidations) which is the first tool to fuse molecular networking, spectral library matching and in silico class predictions to establish accurate putative classifications for entire subnetworks. By limiting annotation propagation to only structural classes which are identical for the majority of ion features within a subnetwork, ConCISE maintains a true positive rate greater than 95% across all levels of the ChemOnt hierarchical ontology used by the ClassyFire annotation software (superclass, class, subclass). The ConCISE framework expanded the proportion of reliable and consistent ion feature annotation up to 76%, allowing for improved assessment of the chemo-diversity of dissolved organic matter pools from three complex marine metabolomics datasets comprising dominant reef primary producers, five species of the diatom genus Pseudo-nitzchia, and stromatolite sediment samples. Full article
(This article belongs to the Special Issue Marine Microbes Related Metabolic Studies)
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29 pages, 6778 KiB  
Article
Spirulina platensis Suppressed iNOS and Proinflammatory Cytokines in Lipopolysaccharide-Induced BV2 Microglia
by Ee-Ling Ngu, Cheng-Yau Tan, Nicole Jean-Yean Lai, Kah-Hui Wong, Siew-Huah Lim, Long Chiau Ming, Kuan-Onn Tan, Siew-Moi Phang and Yoon-Yen Yow
Metabolites 2022, 12(11), 1147; https://doi.org/10.3390/metabo12111147 - 20 Nov 2022
Cited by 2 | Viewed by 1969
Abstract
The disease burden of neurodegenerative diseases is on the rise due to the aging population, and neuroinflammation is one of the underlying causes. Spirulina platensis is a well-known superfood with numerous reported bioactivities. However, the effect of S. platensis Universiti Malaya Algae Culture [...] Read more.
The disease burden of neurodegenerative diseases is on the rise due to the aging population, and neuroinflammation is one of the underlying causes. Spirulina platensis is a well-known superfood with numerous reported bioactivities. However, the effect of S. platensis Universiti Malaya Algae Culture Collection 159 (UMACC 159) (a strain isolated from Israel) on proinflammatory mediators and cytokines remains unknown. In this study, we aimed to determine the anti-neuroinflammatory activity of S. platensis extracts and identify the potential bioactive compounds. S. platensis extracts (hexane, ethyl acetate, ethanol, and aqueous) were screened for phytochemical content and antioxidant activity. Ethanol extract was studied for its effect on proinflammatory mediators and cytokines in lipopolysaccharide (LPS)-induced BV2 microglia. The potential bioactive compounds were identified using liquid chromatography-mass spectrometric (LC-MS) analysis. Ethanol extract had the highest flavonoid content and antioxidant and nitric oxide (NO) inhibitory activity. Ethanol extract completely inhibited the production of NO via the downregulation of inducible NO synthase (iNOS) and significantly reduced the production of tumor necrosis factor (TNF)-α and interleukin (IL)-6. Emmotin A, palmitic amide, and 1-monopalmitin, which might play an important role in cell signaling, have been identified. In conclusion, S. platensis ethanol extract inhibited neuroinflammation through the downregulation of NO, TNF-α and IL-6. This preliminary study provided insight into compound(s) isolation, which could contribute to the development of precision nutrition for disease management. Full article
(This article belongs to the Special Issue Marine Microbes Related Metabolic Studies)
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