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Metabolites
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Reviews and Advances in Microbial Metabolomics
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Reviews and Advances in Microbial Metabolomics

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

Deadline for manuscript submissions: closed (20 December 2021) | Viewed by 28049

Special Issue Editor

Dr. Silas G. Villas-Boas

E-Mail Website
Guest Editor
Luxembourg Institute of Science and Technology (LIST), L-4940 Hautcharage, Luxembourg
Interests: mass spectrometry; metabolic engineering; microbial metabolomics; central carbon metabolism; microbial physiology; secondary metabolites; metabolic pathway analysis; gas chromatography; metabolic flux analysis; sample preparation for metabolome analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Metabolomics is a fast-moving field that has gained enormous popularity in recent years. This new concept of unbiased and nontargeted analysis of cell metabolites in a system-wide hypothesis-driven approach has dramatically changed methodological strategies in life sciences. Within a system-wide approach, microbial systems have advantages over higher organisms. Microbes are less complex systems to be studied and exploited; the majority of genomes sequenced to date are from microorganisms, and we know much more about gene regulation, metabolic networks, and physiology of microbial cells than of higher eukaryote systems. In addition, microorganisms are widely used in industrial applications, mainly for the production of foodstuffs and high-value-added bioproducts such as vitamins, amino acids, enzymes, recombinant proteins, bulk chemicals, antibiotics, biopolymers, biofuels, and biopharmaceuticals.

This Special Issue of Metabolites, “Reviews and Advances in Microbial Metabolomics” will be dedicated not only to in-depth applications of metabolomic techniques to study microbial systems, microbial production, fermentation processes, antibiotic resistence, pathogenesis, but also to reporting innovative technology development to characterize microbial metabolism and metabolites. Manuscripts presenting critical reviews on challenging aspects of microbial metabolomics are also highly desired.

Dr. Silas G. Villas-Boas
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. 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

  • microorganism
  • microbe
  • microbial metabolomics
  • bioactive metabolites
  • antibiotic resistance
  • pathogenesis
  • fermentation
  • pathogens
  • industrial microbiology
  • metabolism

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Published Papers (6 papers)

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Research

Jump to: Review

13 pages, 630 KiB  
Article
Identification of New Natural Sources of Flavour and Aroma Metabolites from Solid-State Fermentation of Agro-Industrial By-Products
by Melodie A. Lindsay, Ninna Granucci, David R. Greenwood and Silas G. Villas-Boas
Metabolites 2022, 12(2), 157; https://doi.org/10.3390/metabo12020157 - 8 Feb 2022
Cited by 14 | Viewed by 3045
Abstract
Increasing consumer demand for natural flavours and fragrances has driven up prices and increased pressure on natural resources. A shift in consumer preference towards more sustainable and economical sources of these natural additives and away from synthetic production has encouraged research into alternative [...] Read more.
Increasing consumer demand for natural flavours and fragrances has driven up prices and increased pressure on natural resources. A shift in consumer preference towards more sustainable and economical sources of these natural additives and away from synthetic production has encouraged research into alternative supplies of these valuable compounds. Solid-state fermentation processes support the natural production of secondary metabolites, which represents most flavour and aroma compounds, while agro-industrial by-products are a low-value waste stream with a high potential for adding value. Accordingly, four filamentous fungi species with a history of use in the production of fermented foods and food additives were tested to ferment nine different agro-industrial by-products. Hundreds of volatile compounds were produced and identified using headspace (HS) solid-phase microextraction (SPME) coupled to gas chromatography–mass spectrometry (GC–MS). Four compounds of interest, phenylacetaldehyde, methyl benzoate, 1-octen-3-ol, and phenylethyl alcohol, were extracted and quantified. Preliminary yields were encouraging compared to traditional sources. This, combined with the low-cost substrates and the high-value natural flavours and aromas produced, presents a compelling case for further optimisation of the process. Full article
(This article belongs to the Special Issue Reviews and Advances in Microbial Metabolomics)
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13 pages, 2129 KiB  
Article
Sound Stimulation Can Affect Saccharomyces cerevisiae Growth and Production of Volatile Metabolites in Liquid Medium
by Alastair Harris, Melodie A. Lindsay, Austen R. D. Ganley, Andrew Jeffs and Silas G. Villas-Boas
Metabolites 2021, 11(9), 605; https://doi.org/10.3390/metabo11090605 - 7 Sep 2021
Cited by 9 | Viewed by 4431
Abstract
The biological effect of sound on microorganisms has been a field of interest for many years, with studies mostly focusing on ultrasonic and infrasonic vibrations. In the audible range (20 Hz to 20 kHz), sound has been shown to both increase colony formation [...] Read more.
The biological effect of sound on microorganisms has been a field of interest for many years, with studies mostly focusing on ultrasonic and infrasonic vibrations. In the audible range (20 Hz to 20 kHz), sound has been shown to both increase colony formation and disrupt microbial growth, depending upon the organism and frequency of sound used. In the brewer’s yeast Saccharomyces cerevisiae, sound has been shown to significantly alter growth, increase alcohol production, and affect the metabolite profile. In this study, S. cerevisiae was exposed to a continuous 90 dB @ 20 μPa tone at different frequencies (0.1 kHz, 10 kHz, and silence). Fermentation characteristics were monitored over a 50-h fermentation in liquid malt extract, with a focus on growth rate and biomass yield. The profile of volatile metabolites at the subsequent stationary phase of the ferment was characterised by headspace gas chromatography–mass spectrometry. Sound treatments resulted in a 23% increase in growth rate compared to that of silence. Subsequent analysis showed significant differences in the volatilomes between all experimental conditions. Specifically, aroma compounds associated with citrus notes were upregulated with the application of sound. Furthermore, there was a pronounced difference in the metabolites produced in high- versus low-frequency sounds. This suggests industrial processes, such as beer brewing, could be modulated by the application of audible sound at specific frequencies during growth. Full article
(This article belongs to the Special Issue Reviews and Advances in Microbial Metabolomics)
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12 pages, 1037 KiB  
Communication
Extracellular Vesicle Analysis by Paper Spray Ionization Mass Spectrometry
by Casey A. Chamberlain, Marguerite Hatch and Timothy J. Garrett
Metabolites 2021, 11(5), 308; https://doi.org/10.3390/metabo11050308 - 11 May 2021
Cited by 12 | Viewed by 3804
Abstract
Paper spray ionization mass spectrometry (PSI-MS) is a direct MS analysis technique with several reported bacterial metabolomics applications. As with most MS-based bacterial studies, all currently reported PSI-MS bacterial analyses have focused on the chemical signatures of the cellular unit. One dimension of [...] Read more.
Paper spray ionization mass spectrometry (PSI-MS) is a direct MS analysis technique with several reported bacterial metabolomics applications. As with most MS-based bacterial studies, all currently reported PSI-MS bacterial analyses have focused on the chemical signatures of the cellular unit. One dimension of the bacterial metabolome that is often lost in such analyses is the exometabolome (extracellular metabolome), including secreted metabolites, lipids, and peptides. A key component of the bacterial exometabolome that is gaining increased attention in the microbiology and biomedical communities is extracellular vesicles (EVs). These excreted structures, produced by cells in all domains of life, contain a variety of biomolecules responsible for a wide array of cellular functions, thus representing a core component of the bacterial secreted metabolome. Although previously examined using other MS approaches, no reports currently exist for a PSI-MS analysis of bacterial EVs, nor EVs from any other organism (exosomes, ectosomes, etc.). PSI-MS holds unique analytical strengths over other commonly used MS platforms and could thus provide an advantageous approach to EV metabolomics. To address this, we report a novel application representing, to our knowledge, the first PSI-MS analysis of EVs from any organism (using the human gut resident Oxalobacter formigenes as the experimental model, a bacterium whose EVs were never previously investigated). In this report, we show how we isolated and purified EVs from bacterial culture supernatant by EV-specific affinity chromatography, confirmed and characterized these vesicles by nanoparticle tracking analysis, analyzed the EV isolate by PSI-MS, and identified a panel of EV-derived metabolites, lipids, and peptides. This work serves as a pioneering study in the field of MS-based EV analysis and provides a new, rapid, sensitive, and economical approach to EV metabolomics. Full article
(This article belongs to the Special Issue Reviews and Advances in Microbial Metabolomics)
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8 pages, 405 KiB  
Communication
The Peptide Chain Release Factor Methyltransferase PrmC Influences the Pseudomonas aeruginosa PA14 Endo- and Exometabolome
by Tobias Depke, Susanne Häussler and Mark Brönstrup
Metabolites 2020, 10(10), 417; https://doi.org/10.3390/metabo10100417 - 18 Oct 2020
Viewed by 2477
Abstract
Pseudomonas aeruginosa is one of the most important nosocomial pathogens and understanding its virulence is the key to effective control of P. aeruginosa infections. The regulatory network governing virulence factor production in P. aeruginosa is exceptionally complex. Previous studies have shown that the [...] Read more.
Pseudomonas aeruginosa is one of the most important nosocomial pathogens and understanding its virulence is the key to effective control of P. aeruginosa infections. The regulatory network governing virulence factor production in P. aeruginosa is exceptionally complex. Previous studies have shown that the peptide chain release factor methyltransferase PrmC plays an important role in bacterial pathogenicity. Yet, the underlying molecular mechanism is incompletely understood. In this study, we used untargeted liquid and gas chromatography coupled to mass spectrometry to characterise the metabolome of a prmC defective P. aeruginosa PA14 strain in comparison with the corresponding strain complemented with prmC in trans. The comprehensive metabolomics data provided new insight into the influence of prmC on virulence and metabolism. prmC deficiency had broad effects on the endo- and exometabolome of P. aeruginosa PA14, with a marked decrease of the levels of aromatic compounds accompanied by reduced precursor supply from the shikimate pathway. Furthermore, a pronounced decrease of phenazine production was observed as well as lower abundance of alkylquinolones. Unexpectedly, the metabolomics data showed no prmC-dependent effect on rhamnolipid production and an increase in pyochelin levels. A putative virulence biomarker identified in a previous study was significantly less abundant in the prmC deficient strain. Full article
(This article belongs to the Special Issue Reviews and Advances in Microbial Metabolomics)
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Review

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12 pages, 690 KiB  
Review
Metabolomics-Microbiome Crosstalk in the Breast Cancer Microenvironment
by Mysoon M. Al-Ansari, Reem H. AlMalki, Lina A. Dahabiyeh and Anas M. Abdel Rahman
Metabolites 2021, 11(11), 758; https://doi.org/10.3390/metabo11110758 - 4 Nov 2021
Cited by 15 | Viewed by 4636
Abstract
Breast cancer, the most frequent cancer diagnosed among females, is associated with a high mortality rate worldwide. Alterations in the microbiota have been linked with breast cancer development, suggesting the possibility of discovering disease biomarkers. Metabolomics has emerged as an advanced promising analytical [...] Read more.
Breast cancer, the most frequent cancer diagnosed among females, is associated with a high mortality rate worldwide. Alterations in the microbiota have been linked with breast cancer development, suggesting the possibility of discovering disease biomarkers. Metabolomics has emerged as an advanced promising analytical approach for profiling metabolic features associated with breast cancer subtypes, disease progression, and response to treatment. The microenvironment compromises non-cancerous cells such as fibroblasts and influences cancer progression with apparent phenotypes. This review discusses the role of metabolomics in studying metabolic dysregulation in breast cancer caused by the effect of the tumor microenvironment on multiple cells such as immune cells, fibroblasts, adipocytes, etc. Breast tumor cells have a unique metabolic profile through the elevation of glycolysis and the tricarboxylic acid cycle metabolism. This metabolic profile is highly sensitive to microbiota activity in the breast tissue microenvironment. Metabolomics shows great potential as a tool for monitoring metabolic dysregulation in tissue and associating the findings with microbiome expression. Full article
(This article belongs to the Special Issue Reviews and Advances in Microbial Metabolomics)
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37 pages, 1443 KiB  
Review
What We Know So Far about the Metabolite-Mediated Microbiota-Intestinal Immunity Dialogue and How to Hear the Sound of This Crosstalk
by Clément Caffaratti, Caroline Plazy, Geoffroy Mery, Abdoul-Razak Tidjani, Federica Fiorini, Sarah Thiroux, Bertrand Toussaint, Dalil Hannani and Audrey Le Gouellec
Metabolites 2021, 11(6), 406; https://doi.org/10.3390/metabo11060406 - 21 Jun 2021
Cited by 19 | Viewed by 8616
Abstract
Trillions of microorganisms, termed the “microbiota”, reside in the mammalian gastrointestinal tract, and collectively participate in regulating the host phenotype. It is now clear that the gut microbiota, metabolites, and intestinal immune function are correlated, and that alterations of the complex and dynamic [...] Read more.
Trillions of microorganisms, termed the “microbiota”, reside in the mammalian gastrointestinal tract, and collectively participate in regulating the host phenotype. It is now clear that the gut microbiota, metabolites, and intestinal immune function are correlated, and that alterations of the complex and dynamic host-microbiota interactions can have deep consequences for host health. However, the mechanisms by which the immune system regulates the microbiota and by which the microbiota shapes host immunity are still not fully understood. This article discusses the contribution of metabolites in the crosstalk between gut microbiota and immune cells. The identification of key metabolites having a causal effect on immune responses and of the mechanisms involved can contribute to a deeper insight into host-microorganism relationships. This will allow a better understanding of the correlation between dysbiosis, microbial-based dysmetabolism, and pathogenesis, thus creating opportunities to develop microbiota-based therapeutics to improve human health. In particular, we systematically review the role of soluble and membrane-bound microbial metabolites in modulating host immunity in the gut, and of immune cells-derived metabolites affecting the microbiota, while discussing evidence of the bidirectional impact of this crosstalk. Furthermore, we discuss the potential strategies to hear the sound of such metabolite-mediated crosstalk. Full article
(This article belongs to the Special Issue Reviews and Advances in Microbial Metabolomics)
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