Special Issue "Microbiome and Metabolome"

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Environmental Science".

Deadline for manuscript submissions: closed (31 July 2021).

Special Issue Editors

Dr. Laura-Isobel McCall
E-Mail Website
Guest Editor
University of Oklahoma, Department of Chemistry and Biochemistry
Interests: metabolomics; chemical cartography; host–microbe interactions; LC–MS; microbiome
Dr. Hosein Mohimani
E-Mail Website
Guest Editor
Computational Biology Department, School of Computer Science, Carnegie Mellon University, PA, USA
Interests: computational metabolomics and metagenomics; natural product discovery; microbiome analysis
Special Issues and Collections in MDPI journals
Dr. Andrés Mauricio Caraballo-Rodríguez
E-Mail Website
Guest Editor
Skaggs School of Pharmacy & Pharmaceutical Sciences, San Diego, United States
Interests: natural products; small molecules; metabolomics; mass spectrometry; chemical ecology
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues,

The microbiota, the community of microorganisms living on or in a given environment, is now widely acknowledged as a key determinant of health, disease, and organismal and ecosystem function. However, the mechanisms by which it does so remain poorly understood. Several small-molecule signals have been identified as mediators of this interaction, including short-chain fatty acids, secondary bile acids, amino acid metabolites, etc., but additional signals are clearly involved. Metabolomics is thus uniquely poised to define the chemical signals through which host and microbiota interact. Likewise, community living requires significant metabolic adaptations within microorganisms and considerable collaborative and competitive metabolic interactions between microbiota members in the environment and in hosts. This Special Issue of Metabolites, “Microbiome and Metabolome”, is dedicated to studies using metabolomics approaches to address these issues, and on novel data analysis approaches used to generate insight into these interactions. Multi-omics approaches integrating metabolomics with metagenomics, metatranscriptomics, or metaproteomics are of particular interest.

Dr. Laura-Isobel McCall

Dr. Hosein Mohimani

Dr. Andrés Mauricio Caraballo-Rodríguez
Guest Editors

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 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

  • metabolomics
  • microbiome
  • microbiota
  • multi-omics
  • environmental microbiota
  • host-associated microbiota
  • cross-species communication
  • microbial community metabolism
  • metabolic adaptation
  • secondary metabolites

Published Papers (6 papers)

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Research

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Article
Antibiotic-Induced Dysbiosis of Microbiota Promotes Chicken Lipogenesis by Altering Metabolomics in the Cecum
Metabolites 2021, 11(8), 487; https://doi.org/10.3390/metabo11080487 - 28 Jul 2021
Viewed by 184
Abstract
Elucidation of the mechanism of lipogenesis and fat deposition is essential for controlling excessive fat deposition in chicken. Studies have shown that gut microbiota plays an important role in regulating host lipogenesis and lipid metabolism. However, the function of gut microbiota in the [...] Read more.
Elucidation of the mechanism of lipogenesis and fat deposition is essential for controlling excessive fat deposition in chicken. Studies have shown that gut microbiota plays an important role in regulating host lipogenesis and lipid metabolism. However, the function of gut microbiota in the lipogenesis of chicken and their relevant mechanisms are poorly understood. In the present study, the gut microbiota of chicken was depleted by oral antibiotics. Changes in cecal microbiota and metabolomics were detected by 16S rRNA sequencing and ultra-high performance liquid chromatography coupled with MS/MS (UHPLC–MS/MS) analysis. The correlation between antibiotic-induced dysbiosis of gut microbiota and metabolites and lipogenesis were analysed. We found that oral antibiotics significantly promoted the lipogenesis of chicken. 16S rRNA sequencing indicated that oral antibiotics significantly reduced the diversity and richness and caused dysbiosis of gut microbiota. Specifically, the abundance of Proteobacteria was increased considerably while the abundances of Bacteroidetes and Firmicutes were significantly decreased. At the genus level, the abundances of genera Escherichia-Shigella and Klebsiella were significantly increased while the abundances of 12 genera were significantly decreased, including Bacteroides. UHPLC-MS/MS analysis showed that antibiotic-induced dysbiosis of gut microbiota significantly altered cecal metabolomics and caused declines in abundance of 799 metabolites and increases in abundance of 945 metabolites. Microbiota-metabolite network revealed significant correlations between 4 differential phyla and 244 differential metabolites as well as 15 differential genera and 304 differential metabolites. Three metabolites of l-glutamic acid, pantothenate acid and N-acetyl-l-aspartic acid were identified as potential metabolites that link gut microbiota and lipogenesis in chicken. In conclusion, our results showed that antibiotic-induced dysbiosis of gut microbiota promotes lipogenesis of chicken by altering relevant metabolomics. The efforts in this study laid a basis for further study of the mechanisms that gut microbiota regulates lipogenesis and fat deposition of chicken. Full article
(This article belongs to the Special Issue Microbiome and Metabolome)
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Article
Influence of Extraction Solvent on Nontargeted Metabolomics Analysis of Enrichment Reactor Cultures Performing Enhanced Biological Phosphorus Removal (EBPR)
Metabolites 2021, 11(5), 269; https://doi.org/10.3390/metabo11050269 - 26 Apr 2021
Viewed by 673
Abstract
Metabolome profiling is becoming more commonly used in the study of complex microbial communities and microbiomes; however, to date, little information is available concerning appropriate extraction procedures. We studied the influence of different extraction solvent mixtures on untargeted metabolomics analysis of two continuous [...] Read more.
Metabolome profiling is becoming more commonly used in the study of complex microbial communities and microbiomes; however, to date, little information is available concerning appropriate extraction procedures. We studied the influence of different extraction solvent mixtures on untargeted metabolomics analysis of two continuous culture enrichment communities performing enhanced biological phosphate removal (EBPR), with each enrichment targeting distinct populations of polyphosphate-accumulating organisms (PAOs). We employed one non-polar solvent and up to four polar solvents for extracting metabolites from biomass. In one of the reactor microbial communities, we surveyed both intracellular and extracellular metabolites using the same set of solvents. All samples were analysed using ultra-performance liquid chromatography mass spectrometry (UPLC-MS). UPLC-MS data obtained from polar and non-polar solvents were analysed separately and evaluated using extent of repeatability, overall extraction capacity and the extent of differential abundance between physiological states. Despite both reactors demonstrating the same bioprocess phenotype, the most appropriate extraction method was biomass specific, with methanol: water (50:50 v/v) and methanol: chloroform: water (40:40:20 v/v/v) being chosen as the most appropriate for each of the two different bioreactors, respectively. Our approach provides new data on the influence of solvent choice on the untargeted surveys of the metabolome of PAO enriched EBPR communities and suggests that metabolome extraction methods need to be carefully tailored to the specific complex microbial community under study. Full article
(This article belongs to the Special Issue Microbiome and Metabolome)
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Article
Host-Microbiome Interactions Mediated by Phenolic Metabolites in Chronically Critically Ill Patients
Metabolites 2021, 11(2), 122; https://doi.org/10.3390/metabo11020122 - 20 Feb 2021
Cited by 1 | Viewed by 1266
Abstract
The community structure and metabolic potential of gut microbiome is not well investigated, especially in chronically critically ill patients with prolonged dependence on support systems after severe brain disorders. Microbial phenolic metabolites can target the brain function by the direct and indirect modulation [...] Read more.
The community structure and metabolic potential of gut microbiome is not well investigated, especially in chronically critically ill patients with prolonged dependence on support systems after severe brain disorders. Microbial phenolic metabolites can target the brain function by the direct and indirect modulation of inflammation. The aim of this study was to investigate the features of the gut microbiota and profile of certain metabolites in the progression and reversibility of neurological disorders in chronically critically ill patients. Fecal samples were collected in dynamics from such patients (n = 44) and analyzed using 16S rRNA sequencing. Serum microbial and mitochondrial metabolites were measured by GC-MS and compared with the biomarkers and clinical neurological scores. The identified associations between specific bacterial taxa in fecal samples, neurological status and serum levels of metabolites suggest that impacts on specific members of the gut microbiota and their metabolism might be a promising tool for regulating brain function in future. Full article
(This article belongs to the Special Issue Microbiome and Metabolome)
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Article
Chemical Elicitors Induce Rare Bioactive Secondary Metabolites in Deep-Sea Bacteria under Laboratory Conditions
Metabolites 2021, 11(2), 107; https://doi.org/10.3390/metabo11020107 - 12 Feb 2021
Viewed by 876
Abstract
Bacterial genome sequencing has revealed a vast number of novel biosynthetic gene clusters (BGC) with potential to produce bioactive natural products. However, the biosynthesis of secondary metabolites by bacteria is often silenced under laboratory conditions, limiting the controlled expression of natural products. Here [...] Read more.
Bacterial genome sequencing has revealed a vast number of novel biosynthetic gene clusters (BGC) with potential to produce bioactive natural products. However, the biosynthesis of secondary metabolites by bacteria is often silenced under laboratory conditions, limiting the controlled expression of natural products. Here we describe an integrated methodology for the construction and screening of an elicited and pre-fractionated library of marine bacteria. In this pilot study, chemical elicitors were evaluated to mimic the natural environment and to induce the expression of cryptic BGCs in deep-sea bacteria. By integrating high-resolution untargeted metabolomics with cheminformatics analyses, it was possible to visualize, mine, identify and map the chemical and biological space of the elicited bacterial metabolites. The results show that elicited bacterial metabolites correspond to ~45% of the compounds produced under laboratory conditions. In addition, the elicited chemical space is novel (~70% of the elicited compounds) or concentrated in the chemical space of drugs. Fractionation of the crude extracts further evidenced minor compounds (~90% of the collection) and the detection of biological activity. This pilot work pinpoints strategies for constructing and evaluating chemically diverse bacterial natural product libraries towards the identification of novel bacterial metabolites in natural product-based drug discovery pipelines. Full article
(This article belongs to the Special Issue Microbiome and Metabolome)
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Article
Metabolites from Microbes Isolated from the Skin of the Panamanian Rocket Frog Colostethus panamansis (Anura: Dendrobatidae)
Metabolites 2020, 10(10), 406; https://doi.org/10.3390/metabo10100406 - 13 Oct 2020
Cited by 2 | Viewed by 1030
Abstract
The Panamanian rocket frog Colostethus panamansis (family Dendrobatidae) has been affected by chytridiomycosis, a deadly disease caused by the fungus Batrachochytrium dendrobatidis (Bd). While there are still uninfected frogs, we set out to isolate microbes from anatomically distinct regions in an [...] Read more.
The Panamanian rocket frog Colostethus panamansis (family Dendrobatidae) has been affected by chytridiomycosis, a deadly disease caused by the fungus Batrachochytrium dendrobatidis (Bd). While there are still uninfected frogs, we set out to isolate microbes from anatomically distinct regions in an effort to create a cultivable resource within Panama for potential drug/agricultural/ecological applications that perhaps could also be used as part of a strategy to protect frogs from infections. To understand if there are specific anatomies that should be explored in future applications of this resource, we mapped skin-associated bacteria of C. panamansis and their metabolite production potential by mass spectrometry on a 3D model. Our results indicate that five bacterial families (Enterobacteriaceae, Comamonadaceae, Aeromonadaceae, Staphylococcaceae and Pseudomonadaceae) dominate the cultivable microbes from the skin of C. panamansis. The combination of microbial classification and molecular analysis in relation to the anti-Bd inhibitory databases reveals the resource has future potential for amphibian conservation. Full article
(This article belongs to the Special Issue Microbiome and Metabolome)
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Review

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Review
Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations
Metabolites 2021, 11(1), 55; https://doi.org/10.3390/metabo11010055 - 15 Jan 2021
Cited by 2 | Viewed by 2240
Abstract
Various studies aiming to elucidate the role of the gut microbiome-metabolome co-axis in health and disease have primarily focused on water-soluble polar metabolites, whilst non-polar microbial lipids have received less attention. The concept of microbiota-dependent lipid biotransformation is over a century old. However, [...] Read more.
Various studies aiming to elucidate the role of the gut microbiome-metabolome co-axis in health and disease have primarily focused on water-soluble polar metabolites, whilst non-polar microbial lipids have received less attention. The concept of microbiota-dependent lipid biotransformation is over a century old. However, only recently, several studies have shown how microbial lipids alter intestinal and circulating lipid concentrations in the host, thus impacting human lipid homeostasis. There is emerging evidence that gut microbial communities play a particularly significant role in the regulation of host cholesterol and sphingolipid homeostasis. Here, we review and discuss recent research focusing on microbe-host-lipid co-metabolism. We also discuss the interplay of human gut microbiota and molecular lipids entering host systemic circulation, and its role in health and disease. Full article
(This article belongs to the Special Issue Microbiome and Metabolome)
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