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Special Issue "Microbial Natural Products"

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Natural Products Chemistry".

Deadline for manuscript submissions: 31 August 2020.

Special Issue Editors

Dr. Francisco (Paco) Barona-Gomez
Website
Guest Editor
Unidad de Genómica Avanzada (Langebio), Mexico City, Mexico
Interests: evolution of metabolic diversity; bacterial genome dynamics and niche adaptation; enzyme evolution; genome-mining tools
Dr. Cuauhtemoc Licona-Cassani

Section Board Member
Centro de Biotecnología FEMSA, Tecnológico de Monterrey, NL, Mexico
Interests: industrial genomics; microbial physiology; actinobacteria; natural products; microbial natural products; genome mining; industrial microbiology
Dr. Corina Diana Ceapă
Website
Assistant Guest Editor
Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
Interests: comparative genomics, host–microbe interactions, novel antibiotics, biotechnological applications

Special Issue Information

Dear Colleagues,

The microbes and the metabolites that they produce have the potential to improve the world in which we live. In particular, the evolution of microbes in various and sometimes extreme environments leads to the apparition of novel functionalities and survival strategies. Natural products discovery has provided the majority of the drugs used in clinics and a large proportion of current industrial enzymes and antibacterials. Natural products, also referred to as secondary or specialized metabolites of bacteria and fungi, are enormously diverse. For instance, it is estimated that only 1% of the diversity inherent to endophytes has so far been explored. In light of the necessity for novel antibiotics, due to a worldwide increase in bacterial resistance, as well as a need for sustainable industrial applications, there remains a strong call for microbial natural products discovery and design. This Special Issue aims to identify and review the latest bioactive compounds that have been discovered and explore the evolutionary driving forces behind the diversification of natural products, as well as their medical, pharmacological, and industrial applications.

Dr. Francisco (Paco) Barona-Gomez
Dr. Cuauhtemoc Licona-Cassani
Dr. Corina Diana Ceapă

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 papers will be 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. Molecules is an international peer-reviewed open access semimonthly 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 2000 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

  • Novel Actinobacteria
  • Secondary metabolites
  • Protein evolution
  • Microbial natural products discovery

Published Papers (8 papers)

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Research

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Open AccessArticle
Identification of Secondary Metabolites from Aspergillus pachycristatus by Untargeted UPLC-ESI-HRMS/MS and Genome Mining
Molecules 2020, 25(4), 913; https://doi.org/10.3390/molecules25040913 - 18 Feb 2020
Abstract
Aspergillus pachycristatus is an industrially important fungus for the production of the antifungal echinocandin B and is closely related to model organism A. nidulans. Its secondary metabolism is largely unknown except for the production of echinocandin B and sterigmatocystin. We constructed mutants [...] Read more.
Aspergillus pachycristatus is an industrially important fungus for the production of the antifungal echinocandin B and is closely related to model organism A. nidulans. Its secondary metabolism is largely unknown except for the production of echinocandin B and sterigmatocystin. We constructed mutants for three genes that regulate secondary metabolism in A. pachycristatus NRRL 11440, and evaluated the secondary metabolites produced by wild type and mutants strains. The secondary metabolism was explored by metabolic networking of UPLC-HRMS/MS data. The genes and metabolites of A. pachycristatus were compared to those of A. nidulans FGSC A4 as a reference to identify compounds and link them to their encoding genes. Major differences in chromatographic profiles were observable among the mutants. At least 28 molecules were identified in crude extracts that corresponded to nine characterized gene clusters. Moreover, metabolic networking revealed the presence of a yet unexplored array of secondary metabolites, including several undescribed fellutamides derivatives. Comparative reference to its sister species, A. nidulans, was an efficient way to dereplicate known compounds, whereas metabolic networking provided information that allowed prioritization of unknown compounds for further metabolic exploration. The mutation of global regulator genes proved to be a useful tool for expanding the expression of metabolic diversity in A. pachycristatus. Full article
(This article belongs to the Special Issue Microbial Natural Products)
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Open AccessArticle
Interaction with Soil Bacteria Affects the Growth and Amino Acid Content of Piriformospora indica
Molecules 2020, 25(3), 572; https://doi.org/10.3390/molecules25030572 - 28 Jan 2020
Abstract
Exploration of the effect of soil bacteria on growth and metabolism of beneficial root endophytic fungi is relevant to promote favorable associations between microorganisms of the plant rhizosphere. Hence, the interaction between the plant-growth-promoting fungus Piriformospora indica and different soil bacteria was investigated. [...] Read more.
Exploration of the effect of soil bacteria on growth and metabolism of beneficial root endophytic fungi is relevant to promote favorable associations between microorganisms of the plant rhizosphere. Hence, the interaction between the plant-growth-promoting fungus Piriformospora indica and different soil bacteria was investigated. The parameters studied were fungal growth and its amino acid composition during the interaction. Fungus and bacteria were confronted in dual cultures in Petri dishes, either through agar or separated by a Perspex wall that only allowed the bacterial volatiles to be effective. Fungal growth was stimulated by Azotobacter chroococcum, whereas Streptomyces anulatus AcH 1003 inhibited it and Streptomyces sp. Nov AcH 505 had no effect. To analyze amino acid concentration data, targeted metabolomics was implemented under supervised analysis according to fungal-bacteria interaction and time. Orthogonal partial least squares-discriminant analysis (OPLS-DA) model clearly discriminated P. indicaA. chroococcum and P. indicaS. anulatus interactions, according to the respective score plot in comparison to the control. The most observable responses were in the glutamine and alanine size groups: While Streptomyces AcH 1003 increased the amount of glutamine, A. chroococcum decreased it. The fungal growth and the increase of alanine content might be associated with the assimilation of nitrogen in the presence of glucose as a carbon source. The N-fixing bacterium A. chroococcum should stimulate fungal amino acid metabolism via glutamine synthetase-glutamate synthase (GS-GOGAT). The data pointed to a stimulated glycolytic activity in the fungus observed by the accumulation of alanine, possibly via alanine aminotransferase. The responses toward the growth-inhibiting Streptomyces AcH 1003 suggest an (oxidative) stress response of the fungus. Full article
(This article belongs to the Special Issue Microbial Natural Products)
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Open AccessArticle
Chemical Composition and Biological Activities of Metabolites from the Marine Fungi Penicillium sp. Isolated from Sediments of Co To Island, Vietnam
Molecules 2019, 24(21), 3830; https://doi.org/10.3390/molecules24213830 - 24 Oct 2019
Abstract
Marine microorganisms are an invaluable source of novel active secondary metabolites possessing various biological activities. In this study, the extraction and isolation of the marine sediment Penicillium species collected in Vietnam yielded ten secondary metabolites, including sporogen AO-1 (1), 3-indolecarbaldehyde ( [...] Read more.
Marine microorganisms are an invaluable source of novel active secondary metabolites possessing various biological activities. In this study, the extraction and isolation of the marine sediment Penicillium species collected in Vietnam yielded ten secondary metabolites, including sporogen AO-1 (1), 3-indolecarbaldehyde (2), 2-[(5-methyl-1,4-dioxan-2-yl)methoxy]ethanol (3), 2-[(2R-hydroxypropanoyl)amino]benzamide (4), 4-hydroxybenzandehyde (5), chrysogine (6), 3-acetyl-4-hydroxycinnoline (7), acid 1H-indole-3-acetic (8), cyclo (Tyr-Trp) (9), and 2’,3’-dihydrosorbicillin (10). Their structures were identified by the analysis of 1D and 2D NMR data. Among the isolated compounds, 2-[(5-methyl-1,4-dioxan-2-yl)methoxy]ethanol (3) showed a strong inhibitory effect against Enterococcus faecalis with a minimum inhibitory concentration value of 32 µg/mL. Both 2-[(2R-hydroxypropanoyl)amino]benzamide (4) and 4-hydroxybenzandehyde (5) selectively inhibited E. coli with minimum inhibitory concentration values of 16 and 8 µg/mL, respectively. 2’,3’-Dihydrosorbicillin (10) potentially inhibited α-glucosidase activity at a concentration of 2.0 mM (66.31%). Full article
(This article belongs to the Special Issue Microbial Natural Products)
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Open AccessArticle
Chaetomadrasins A and B, Two New Cytotoxic Cytochalasans from Desert Soil-Derived Fungus Chaetomium madrasense 375
Molecules 2019, 24(18), 3240; https://doi.org/10.3390/molecules24183240 - 05 Sep 2019
Cited by 1
Abstract
Two new cytochalasans, Chaetomadrasins A (1) and B (2), along with six known analogues (38), were isolated from the solid-state fermented culture of desert soil-derived Chaetomium madrasense 375. Their structures were clarified by comprehensive spectroscopic [...] Read more.
Two new cytochalasans, Chaetomadrasins A (1) and B (2), along with six known analogues (38), were isolated from the solid-state fermented culture of desert soil-derived Chaetomium madrasense 375. Their structures were clarified by comprehensive spectroscopic analyses, and the absolute configurations of Compounds 1 and 2 were confirmed by electronic circular dichroism (ECD) and calculated ECD. For the first time, Chaetomadrasins A (1), which belongs to the chaetoglobosin family, is characterized by the presence of all oxygen atoms in the form of Carbonyl. Chaetomadrasin B (2) represents the first example of chaetoglobosin type cytochalasan characterized by a hydroxy unit and carbonyl group fused to the indole ring. Compounds 1 and 2 displayed moderate cytotoxicity against HepG2 human hepatocellular carcinoma cells. Full article
(This article belongs to the Special Issue Microbial Natural Products)
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Open AccessArticle
Broad-Spectrum Antiviral Natural Products from the Marine-Derived Penicillium sp. IMB17-046
Molecules 2019, 24(15), 2821; https://doi.org/10.3390/molecules24152821 - 02 Aug 2019
Cited by 1
Abstract
A new pyrazine derivative, trypilepyrazinol (1), a new α-pyrone polyketide, (+)-neocitreoviridin (2), and a new ergostane analogue, 3β-hydroxyergosta-8,14,24(28)-trien-7-one (3), were isolated and characterized along with five known compounds from the marine-derived fungus Penicillium sp. IMB17-046. The structures [...] Read more.
A new pyrazine derivative, trypilepyrazinol (1), a new α-pyrone polyketide, (+)-neocitreoviridin (2), and a new ergostane analogue, 3β-hydroxyergosta-8,14,24(28)-trien-7-one (3), were isolated and characterized along with five known compounds from the marine-derived fungus Penicillium sp. IMB17-046. The structures of these new compounds were determined using spectroscopic data analyses (HRESIMS, 1D- and 2D-NMR), X-ray crystallography analysis, and TDDFT ECD calculation. Compounds 1 and 3 exhibited broad-spectrum antiviral activities against different types of viruses, including human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza A virus (IAV), with IC50 values ranging from 0.5 to 7.7 μM. Compounds 1 and 2 showed antibacterial activities against Helicobacter pylori, a causative pathogen of various gastric diseases, with minimum inhibitory concentration (MIC) values of 1–16 μg/mL. Full article
(This article belongs to the Special Issue Microbial Natural Products)
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Open AccessArticle
New Butenolides and Cyclopentenones from Saline Soil-Derived Fungus Aspergillus Sclerotiorum
Molecules 2019, 24(14), 2642; https://doi.org/10.3390/molecules24142642 - 21 Jul 2019
Abstract
Three new γ-hydroxyl butenolides (13), a pair of new enantiomeric spiro-butenolides (4a and 4b), a pair of enantiomeric cyclopentenones (5a new and 5b new natural), and six known compounds (611), were [...] Read more.
Three new γ-hydroxyl butenolides (13), a pair of new enantiomeric spiro-butenolides (4a and 4b), a pair of enantiomeric cyclopentenones (5a new and 5b new natural), and six known compounds (611), were isolated from Aspergillus sclerotiorum. Their structures were established by spectroscopic data and electronic circular dichroism (ECD) spectra. Two pairs of enantiomers [(+)/(–)-6c and (+)/(–)-6d] obtained from the reaction of 6 with acetyl chloride (AcCl) confirmed that 6 was a mixture of two pairs of enantiomers. In addition, the X-ray data confirmed that 7 was also a racemate. The new metabolites (15) were evaluated for their inhibitory activity against cancer and non-cancer cell lines. As a result, compound 1 exhibited moderate cytotoxicity to HL60 and A549 with IC50 values of 6.5 and 8.9 µM, respectively, and weak potency to HL-7702 with IC50 values of 17.6 µM. Furthermore, compounds 19 were screened for their antimicrobial activity using the micro-broth dilution method. MIC values of 200 μg/mL were obtained for compounds 2 and 3 towards Staphylococcus aureus and Escherichia coli, while compound 8 exhibited a MIC of 50 μ/mL towards Candida albicans. Full article
(This article belongs to the Special Issue Microbial Natural Products)
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Open AccessArticle
Insights into Triterpene Acids in Fermented Mycelia of Edible Fungus Poria cocos by a Comparative Study
Molecules 2019, 24(7), 1331; https://doi.org/10.3390/molecules24071331 - 04 Apr 2019
Cited by 3
Abstract
As an edible sclerotia-forming fungus, Poria cocos is widely used as a food supplement and as a tonic in China. High-performance liquid chromatography-quadrupole/time-of-flight mass spectrometry (HPLC-QTOF-MS/MS) was applied to identify triterpene acids in fermented mycelia of P. cocos, as well as the [...] Read more.
As an edible sclerotia-forming fungus, Poria cocos is widely used as a food supplement and as a tonic in China. High-performance liquid chromatography-quadrupole/time-of-flight mass spectrometry (HPLC-QTOF-MS/MS) was applied to identify triterpene acids in fermented mycelia of P. cocos, as well as the epidermis and inner part of natural sclerotia. A total of 19 triterpene acids were identified in fermented mycelia, whereas 31 were identified in the epidermis and 24 in the inner part. Nine triterpene acids were quantitatively determined, and the concentrations of two valuable triterpenes, dehydropachymic acid and pachymic acid, reached 1.07 mg/g and 0.61 mg/g in the fermented mycelia part, respectively, and were both significantly higher than the concentration in the two natural parts. The fermented mycelia could be a good choice for producing some target triterpene compounds and functional foods through fermentation thanks to the high concentration of some triterpene acids. Full article
(This article belongs to the Special Issue Microbial Natural Products)
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Review

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Open AccessReview
Terrestrial Microorganisms: Cell Factories of Bioactive Molecules with Skin Protecting Applications
Molecules 2019, 24(9), 1836; https://doi.org/10.3390/molecules24091836 - 13 May 2019
Cited by 8
Abstract
It is well known that terrestrial environments host an immense microbial biodiversity. Exposed to different types of stress, such as UV radiation, temperature fluctuations, water availability and the inter- / intra-specific competition for resources, terrestrial microorganisms have been evolved to produce a large [...] Read more.
It is well known that terrestrial environments host an immense microbial biodiversity. Exposed to different types of stress, such as UV radiation, temperature fluctuations, water availability and the inter- / intra-specific competition for resources, terrestrial microorganisms have been evolved to produce a large spectrum of bioactive molecules. Bacteria, archaea, protists, fungi and algae have shown a high potential of producing biomolecules for pharmaceutical or other industrial purposes as they combine a sustainable, relatively low-cost and fast-production process. Herein, we provide an overview of the different bioactive molecules produced by terrestrial microorganisms with skin protecting applications. The high content in polyphenolic and carotenoid compounds produced by several strains, as well as the presence of exopolysaccharides, melanins, indole and pyrrole derivatives, mycosporines, carboxylic acids and other molecules, are discussed in the context of their antioxidant, photo-protective and skin-whitening activity. Relevant biotechnological tools developed for the enhanced production of high added value natural products, as well as the protecting effect of some antioxidant, hydrolytic and degrading enzymes are also discussed. Furthermore, we describe classes of microbial compounds that are used or have the potential to be used as antimicrobials, moisturizers, biosurfactants, pigments, flavorings and fragrances. Full article
(This article belongs to the Special Issue Microbial Natural Products)
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