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Recent Advances in Natural Products Chemistry Related to Metabolites and Microbiomes

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

Deadline for manuscript submissions: closed (9 December 2019) | Viewed by 42095

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Dr. Francesco Vinale

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1. Dipartimento di Agraria, Università degli Studi di Napoli Federico II, 80055 Portici (NA), Italy
2. Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche (IPSP-CNR), 80055 Portici (NA), Italy
Interests: biological control; Trichoderma; secondary metabolites; metabolite characterization; plant pathogens
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Maria Luisa Balestrieri

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Department of Biochemistry, Biophysics and General Pathology, School of Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
Interests: aging; oxidative stress; nitric oxide; endothelial cells; endothelial progenitor cells; angiogenesis; inflammation; cell senescence; apoptosis; atherosclerosis; diabetes, endothelial dysfunction, sirtuins and cardiovascular disease; natural products; betaines; health; bioactive compounds; free radicals; antioxidants; ergothioneine; cell cycle; cancer-related biochemical pathways; cell proliferation; senescence; cancer cell death; epigenetic regulation; sirtuins and cancer
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The microbiome is generally referred to as the collective microbial genome found in a particular habitat, while the microbiota is the set of microorganisms living in a specific environment. However, some authors use the term “microbiome” also to indicate the microbes that co-exist within complex communities. In this Special Issue, the term “metabolites” refers only to the small molecules showing important functions in biological processes, with particular emphasis on secondary metabolites. The set of low-molecular-weight metabolites that are produced by organisms is defined as the “metabolome”. The components of the metabolome represent the end products of gene expression and define the biochemical status of an organism.

In the present Special Issue, the following topics will be covered:

isolation of novel microbial compounds using metabolomic approaches;
molecules and metabolomes related to agricultural applications (crop and animal productions);
microbiomes and related natural products with beneficial effects in agriculture;
plant metabolites with bioactive properties;
influence of beneficial microbes and/or their metabolites on plant metabolomes;
microbial metabolites involved in plant or animal interactions;
influence of production technologies on animal metabolomes and microbiomes.

Full research papers, reviews, short communications reporting the finding and the characterization of molecules, metabolomes, and related microbiomes and showing their potential for agricultural applications both directly (e.g., increased nutritional value of crops) and indirectly (e.g., effects on the environment, agricultural practices, etc.), as well as their effects on health are invited for this editorial project.

Dr. Francesco Vinale
Prof. Maria Luisa Balestrieri
Guest Editors

Manuscript Submission Information

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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 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

secondary metabolites
microbial metabolites
microbiome
metabolome
agriculture
health benefits

Published Papers (10 papers)

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Research

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32 pages, 8428 KiB

Open AccessArticle

Enhancement of Versatile Extracellular Cellulolytic and Hemicellulolytic Enzyme Productions by Lactobacillus plantarum RI 11 Isolated from Malaysian Food Using Renewable Natural Polymers

by Nursyafiqah A. Mohamad Zabidi, Hooi Ling Foo, Teck Chwen Loh, Rosfarizan Mohamad and Raha Abdul Rahim

Molecules 2020, 25(11), 2607; https://doi.org/10.3390/molecules25112607 - 03 Jun 2020

Cited by 19 | Viewed by 3430

Abstract

Lactobacillus plantarum RI 11 was reported recently to be a potential lignocellulosic biomass degrader since it has the capability of producing versatile extracellular cellulolytic and hemicellulolytic enzymes. Thus, this study was conducted to evaluate further the effects of various renewable natural polymers on the growth and production of extracellular cellulolytic and hemicellulolytic enzymes by this novel isolate. Basal medium supplemented with molasses and yeast extract produced the highest cell biomass (log 10.51 CFU/mL) and extracellular endoglucanase (11.70 µg/min/mg), exoglucanase (9.99 µg/min/mg), β-glucosidase (10.43 nmol/min/mg), and mannanase (8.03 µg/min/mg), respectively. Subsequently, a statistical optimization approach was employed for the enhancement of cell biomass, and cellulolytic and hemicellulolytic enzyme productions. Basal medium that supplemented with glucose, molasses and soybean pulp (F5 medium) or with rice straw, yeast extract and soybean pulp (F6 medium) produced the highest cell population of log 11.76 CFU/mL, respectively. However, formulated F12 medium supplemented with glucose, molasses and palm kernel cake enhanced extracellular endoglucanase (4 folds), exoglucanase (2.6 folds) and mannanase (2.6 folds) specific activities significantly, indicating that the F12 medium could induce the highest production of extracellular cellulolytic and hemicellulolytic enzymes concomitantly. In conclusion, L. plantarum RI 11 is a promising and versatile bio-transformation agent for lignocellulolytic biomass. Full article

(This article belongs to the Special Issue Recent Advances in Natural Products Chemistry Related to Metabolites and Microbiomes)

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27 pages, 2771 KiB

Open AccessArticle

Rapid Evaluation and Optimization of Medium Components Governing Tryptophan Production by Pediococcus acidilactici TP-6 Isolated from Malaysian Food via Statistical Approaches

by Ye Heng Lim, Hooi Ling Foo, Teck Chwen Loh, Rosfarizan Mohamad and Raha Abdul Rahim

Molecules 2020, 25(4), 779; https://doi.org/10.3390/molecules25040779 - 11 Feb 2020

Cited by 9 | Viewed by 3203

Abstract

Tryptophan is one of the most extensively used amino acids in livestock industry owing to its effectiveness in enhancing the growth performance of animals. Conventionally, the production of tryptophan relies heavily on genetically modified Escherichia coli but its pathogenicity is a great concern. Our recent study demonstrated that a lactic acid bacterium (LAB), Pediococcus acidilactici TP-6 that isolated from Malaysian food was a promising tryptophan producer. However, the tryptophan production must enhance further for viable industrial application. Hence, the current study evaluated the effects of medium components and optimized the medium composition for tryptophan production by P. acidilactici TP-6 statistically using Plackett-Burman Design, and Central Composite Design. The optimized medium containing molasses (14.06 g/L), meat extract (23.68 g/L), urea (5.56 g/L) and FeSO₄ (0.024 g/L) significantly enhanced the tryptophan production by 150% as compared to the control de Man, Rogosa and Sharpe medium. The findings obtained in this study revealed that rapid evaluation and effective optimization of medium composition governing tryptophan production by P. acidilactici TP-6 were feasible via statistical approaches. Additionally, the current findings reveal the potential of utilizing LAB as a safer alternative tryptophan producer and provides insight for future exploitation of various amino acid productions by LAB. Full article

(This article belongs to the Special Issue Recent Advances in Natural Products Chemistry Related to Metabolites and Microbiomes)

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11 pages, 1203 KiB

Open AccessArticle

A Preliminary Study on Metabolome Profiles of Buffalo Milk and Corresponding Mozzarella Cheese: Safeguarding the Authenticity and Traceability of Protected Status Buffalo Dairy Products

by Angela Salzano, Gelsomina Manganiello, Gianluca Neglia, Francesco Vinale, Donato De Nicola, Michael D’Occhio and Giuseppe Campanile

Molecules 2020, 25(2), 304; https://doi.org/10.3390/molecules25020304 - 12 Jan 2020

Cited by 21 | Viewed by 3869

Abstract

The aim of this study is to combine advanced GC-MS and metabolite identification in a robust and repeatable technology platform to characterize the metabolome of buffalo milk and mozzarella cheese. The study utilized eleven dairies located in a protected designation of origin (PDO) region and nine dairies located in non-PDO region in Italy. Samples of raw milk (100 mL) and mozzarella cheese (100 g) were obtained from each dairy. A total of 185 metabolites were consistently detected in both milk and mozzarella cheese. The PLS-DA score plots clearly differentiated PDO and non-PDO milk and mozzarella samples. For milk samples, it was possible to divide metabolites into two classes according to region: those with lower concentrations in PDO samples (galactopyranoside, hydroxybuthyric acid, allose, citric acid) and those with lower concentrations in non-PDO samples (talopyranose, pantothenic acid, mannobiose, etc.,). The same was observed for mozzarella samples with the proportion of some metabolites (talopyranose, 2, 3-dihydroxypropyl icosanoate, etc.,) higher in PDO samples while others (tagatose, lactic acid dimer, ribitol, etc.,) higher in non-PDO samples. The findings establish the utility of GC-MS together with mass spectral libraries as a powerful technology platform to determine the authenticity, and create market protection, for “Mozzarella di Bufala Campana.” Full article

(This article belongs to the Special Issue Recent Advances in Natural Products Chemistry Related to Metabolites and Microbiomes)

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16 pages, 3495 KiB

Open AccessArticle

The Trichoderma atroviride Strains P1 and IMI 206040 Differ in Their Light-Response and VOC Production

by Verena Speckbacher, Veronika Ruzsanyi, Modestus Wigger and Susanne Zeilinger

Molecules 2020, 25(1), 208; https://doi.org/10.3390/molecules25010208 - 03 Jan 2020

Cited by 16 | Viewed by 5060

Abstract

Trichoderma atroviride is a strong necrotrophic mycoparasite antagonizing and feeding on a broad range of fungal phytopathogens. It further beneficially acts on plants by enhancing growth in root and shoot and inducing systemic resistance. Volatile organic compounds (VOCs) are playing a major role in all those processes. Light is an important modulator of secondary metabolite biosynthesis, but its influence has often been neglected in research on fungal volatiles. To date, T. atroviride IMI 206040 and T. atroviride P1 are among the most frequently studied T. atroviride strains and hence are used as model organisms to study mycoparasitism and photoconidiation. However, there are no studies available, which systematically and comparatively analyzed putative differences between these strains regarding their light-dependent behavior and VOC biosynthesis. We therefore explored the influence of light on conidiation and the mycoparasitic interaction as well as the light-dependent production of VOCs in both strains. Our data show that in contrast to T. atroviride IMI 206040 conidiation in strain P1 is independent of light. Furthermore, significant strain- and light-dependent differences in the production of several VOCs between the two strains became evident, indicating that T. atroviride P1 could be a better candidate for plant protection than IMI 206040. Full article

(This article belongs to the Special Issue Recent Advances in Natural Products Chemistry Related to Metabolites and Microbiomes)

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19 pages, 2222 KiB

Open AccessArticle

The Ancient Neapolitan Sweet Lime and the Calabrian Lemoncetta Locrese Belong to the Same Citrus Species

by Domenico Cautela, Maria Luisa Balestrieri, Sara Savini, Anna Sannino, Giovanna Ferrari, Luigi Servillo, Luigi De Masi, Annalisa Pastore and Domenico Castaldo

Molecules 2020, 25(1), 113; https://doi.org/10.3390/molecules25010113 - 27 Dec 2019

Cited by 5 | Viewed by 3572

Abstract

“Neapolitan limmo” is an ancient and rare sweet Mediterranean lime, now almost extinct but used until a few decades ago for the production of a fragrant liqueur called the “four citrus fruits”. The objective of this work was to compare, through the use of chemical (flavonoids, volatile organic compounds, and chiral compounds) and molecular (DNA fingerprint based on RAPD-PCR) markers, the residual population of Neapolitan limmo with other populations of sweet limes, identified in Calabria and known as “lemoncetta Locrese”. We report for the first time specific botanical characteristics of the two fruits and unequivocally show that the ancient sweet Mediterranean limes Neapolitan limmo and lemoncetta Locrese are synonyms of the same Citrus species. Owing to the biodiversity conserved in their places of origin, it will now be possible to recover, enhance and implement the use of this ancient sweet lime for agro-industrial purposes. Full article

(This article belongs to the Special Issue Recent Advances in Natural Products Chemistry Related to Metabolites and Microbiomes)

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13 pages, 2212 KiB

Open AccessArticle

Exploring the Phytochemical Landscape of the Early-Diverging Flowering Plant Amborella trichopoda Baill.

by Sheng Wu, Alexander E. Wilson, Lijing Chang and Li Tian

Molecules 2019, 24(21), 3814; https://doi.org/10.3390/molecules24213814 - 23 Oct 2019

Cited by 7 | Viewed by 2985

Abstract

Although the evolutionary significance of the early-diverging flowering plant Amborella (Amborella trichopoda Baill.) is widely recognized, its metabolic landscape, particularly specialized metabolites, is currently underexplored. In this work, we analyzed the metabolomes of Amborella tissues using liquid chromatography high-resolution electrospray ionization mass spectrometry (LC-HR-ESI-MS). By matching the mass spectra of Amborella metabolites with those of authentic phytochemical standards in the publicly accessible libraries, 63, 39, and 21 compounds were tentatively identified in leaves, stems, and roots, respectively. Free amino acids, organic acids, simple sugars, cofactors, as well as abundant glycosylated and/or methylated phenolic specialized metabolites were observed in Amborella leaves. Diverse metabolites were also detected in stems and roots, including those that were not identified in leaves. To understand the biosynthesis of specialized metabolites with glycosyl and methyl modifications, families of small molecule UDP-dependent glycosyltransferases (UGTs) and O-methyltransferases (OMTs) were identified in the Amborella genome and the InterPro database based on conserved functional domains. Of the 17 phylogenetic groups of plant UGTs (A–Q) defined to date, Amborella UGTs are absent from groups B, N, and P, but they are highly abundant in group L. Among the 25 Amborella OMTs, 7 cluster with caffeoyl-coenzyme A (CCoA) OMTs involved in lignin and phenolic metabolism, whereas 18 form a clade with plant OMTs that methylate hydroxycinnamic acids, flavonoids, or alkaloids. Overall, this first report of metabolomes and candidate metabolic genes in Amborella provides a starting point to a better understanding of specialized metabolites and biosynthetic enzymes in this basal lineage of flowering plants. Full article

(This article belongs to the Special Issue Recent Advances in Natural Products Chemistry Related to Metabolites and Microbiomes)

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12 pages, 849 KiB

Open AccessArticle

Chemical Analysis of Lepidium meyenii (Maca) and Its Effects on Redox Status and on Reproductive Biology in Stallions

by Simona Tafuri, Natascia Cocchia, Domenico Carotenuto, Anastasia Vassetti, Alessia Staropoli, Vincenzo Mastellone, Vincenzo Peretti, Francesca Ciotola, Sara Albarella, Chiara Del Prete, Veronica Palumbo, Luigi Esposito, Francesco Vinale and Francesca Ciani

Molecules 2019, 24(10), 1981; https://doi.org/10.3390/molecules24101981 - 23 May 2019

Cited by 37 | Viewed by 7025

Abstract

The present study was conducted to assess the chemical composition of Yellow Maca (Lepidium meyenii) and its biological activity on stallions following oral administration of hypocotyl powder. Maca was subjected to methanolic extraction and the chemical analysis was carried out by LC-MS-QTOF (liquid chromatography-mass spectrometry). Our results showed that Maca contains some effective antioxidants, a high percentage of glucosinolates, and other important components with a high antioxidant capacity. To evaluate the plant biological activity in stallions fed with Maca powder for 60 days, the redox status and some reproductive parameters were investigated. Blood and semen samples were collected at 0, 30, 60, and 90 days from the beginning of this study. Blood samples showed a decrease of the reactive oxygen metabolites, evaluated by d-ROMs test, and an increase of the antioxidant barrier in terms of biological antioxidant potential (BAP test), powerful oxidant capacity (OXY-Adsorbent test), and thiols evaluation (-SHp test). Furthermore, semen samples showed a positive trend during Maca administration in the following parameters: ejaculate volumes and sperm concentrations, total and progressive motility, and acrosome integrity. Full article

(This article belongs to the Special Issue Recent Advances in Natural Products Chemistry Related to Metabolites and Microbiomes)

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11 pages, 3065 KiB

Open AccessArticle

The Issue of Misidentification of Kojic Acid with Flufuran in Aspergillus flavus

by Marina DellaGreca, Gaetano De Tommaso, Maria Michela Salvatore, Rosario Nicoletti, Andrea Becchimanzi, Mauro Iuliano and Anna Andolfi

Molecules 2019, 24(9), 1709; https://doi.org/10.3390/molecules24091709 - 02 May 2019

Cited by 14 | Viewed by 3378

Abstract

In the course of investigations on the complex phenomenon of bee decline, Aspergillus flavus was isolated from the haemocoel of worker bees. Observations on the metabolomic profile of this strain showed kojic acid to be the dominant product in cultures on Czapek-Dox broth. However, an accurate review of papers documenting secondary metabolite production in A. flavus also showed that an isomer of kojic acid, identified as 5-(hydroxymethyl)-furan-3-carboxylic acid and named flufuran is reported from this species. The spectroscopic data of kojic acid were almost identical to those reported in the literature for flufuran. This motivated a comparative study of commercial kojic acid and 5-(hydroxymethyl)-furan-3-carboxylic acid, highlighting some differences, for example in the ¹³C-NMR and UV spectra for the two compounds, indicating that misidentification of the kojic acid as 5-(hydroxymethyl)-furan-3-carboxylic acid has occurred in the past. Full article

(This article belongs to the Special Issue Recent Advances in Natural Products Chemistry Related to Metabolites and Microbiomes)

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11 pages, 577 KiB

Open AccessArticle

Chlamyphilone, a Novel Pochonia chlamydosporia Metabolite with Insecticidal Activity

by Federica Lacatena, Roberta Marra, Pierluigi Mazzei, Alessandro Piccolo, Maria Cristina Digilio, Massimo Giorgini, Sheridan L. Woo, Pierpaolo Cavallo, Matteo Lorito and Francesco Vinale

Molecules 2019, 24(4), 750; https://doi.org/10.3390/molecules24040750 - 19 Feb 2019

Cited by 9 | Viewed by 3284

Abstract

Metabolites from a collection of selected fungal isolates have been screened for insecticidal activity against the aphid Acyrthosiphon pisum. Crude organic extracts of culture filtrates from six fungal isolates (Paecilomyces lilacinus, Pochonia chlamydosporia, Penicillium griseofulvum, Beauveria bassiana, Metarhizium anisopliae and Talaromyces pinophilus) caused mortality of aphids within 72 h after treatment. In this work, bioassay-guided fractionation has been used to characterize the main bioactive metabolites accumulated in fungal extracts. Leucinostatins A, B and D represent the bioactive compounds produced by P. lilacinus. From P. griseofulvum and B. bassiana extracts, griseofulvin and beauvericin have been isolated, respectively; 3-O-Methylfunicone and a mixture of destruxins have been found in the active fractions of T. pinophilum and M. anisopliae, respectively. A novel azaphilone compound, we named chlamyphilone, with significant insecticidal activity, has been isolated from the culture filtrate of P. chlamydosporia. Its structure has been determined using extensive spectroscopic methods and chemical derivatization. Full article

(This article belongs to the Special Issue Recent Advances in Natural Products Chemistry Related to Metabolites and Microbiomes)

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28 pages, 4839 KiB

Open AccessFeature PaperReview

Structures and Bioactive Properties of Myrtucommulones and Related Acylphloroglucinols from Myrtaceae

by Rosario Nicoletti, Maria Michela Salvatore, Pasquale Ferranti and Anna Andolfi

Molecules 2018, 23(12), 3370; https://doi.org/10.3390/molecules23123370 - 19 Dec 2018

Cited by 19 | Viewed by 5408

Abstract

Myrtaceae are a group of plants that include a number of renowned species used in ethnomedicine in many areas worldwide. Their valuable therapeutic properties have stimulated a fruitful research activity addressed to the identification of the bioactive components of their extracts yielding a great diversity of terpenes; polyphenols; and other exclusive products. Among the latter, starting with the discovery of myrtucommulone A from myrtle (Myrtus communis), a series of structurally-related acylphloroglucinol compounds have been characterized from several species that represent the basic active principles to be considered in view of possible drug development. Aspects concerning chemical and biological properties of these products are reviewed in the present paper. Full article

(This article belongs to the Special Issue Recent Advances in Natural Products Chemistry Related to Metabolites and Microbiomes)

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