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Metabolites
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Biomarker Discovery through Microbiome Metabolism Analysis
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Biomarker Discovery through Microbiome Metabolism Analysis

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

Deadline for manuscript submissions: closed (28 February 2022) | Viewed by 14078

Special Issue Editor

Prof. Dr. Daniel Globisch

E-Mail Website
Guest Editor
Department of Medicinal Chemistry, Uppsala University, SE-75123 Uppsala, Sweden
Interests: metabolomics; microbiota; chemical biology; biomarker discovery; organic chemistry; phase II metabolism; medicinal chemistry; drug discovery
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear colleagues,

Metabolomics is the investigation of metabolites in any sample type and finds application in diverse areas including biomarker discovery, systems biology, and drug discovery. Within the past decade, it has become evident that microbiota produce a plethora of metabolites that can profoundly affect the human host by impacting physiology and disease development. These microbial communities inhabit the surface of the human body including the gastrointestinal tract and skin. The vastly expanded enzymatic repertoire and corresponding (bio)chemical capabilities of the microbiota compared to the human host increase the complexity of metabolomics studies. Microbiome dysbiosis has been linked to disease development but metabolic alterations still remain largely unknown.

This Special Issue highlights investigations of microbiome metabolism in the context of biomarker discovery for diseases, diet or toxicology using metabolomics techniques. We are seeking submissions describing the metabolic link between microbiota metabolism and human physiology, e.g. dietary intervention studies, fecal sample investigations, computational analysis, new analytical developments, and targeted or untargeted approaches.

Prof. Dr. Daniel Globisch
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

  • Metabolomics
  • Microbiome
  • Co-Metabolism
  • Fecal samples
  • Disease Development
  • Biomarker Discovery

Published Papers (5 papers)

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Research

12 pages, 1985 KiB  
Article
Evaluating Cefoperazone-Induced Gut Metabolic Functional Changes in MR1-Deficient Mice
by Jinchun Sun, Zhijun Cao, Ashley D. Smith, Paul E. Carlson Jr, Michael Coryell, Huizhong Chen and Richard D. Beger
Metabolites 2022, 12(5), 380; https://doi.org/10.3390/metabo12050380 - 22 Apr 2022
Cited by 1 | Viewed by 1876
Abstract
Mucosal-associated invariant T cells are activated following the recognition of bacterial antigens presented by the major histocompatibility complex class I-related molecule (MR1). Previous metagenomics data showed that MR1−/− knock-out (KO) mice had distinct microbiota and displayed a resistance to Clostridioides difficile (CDI) [...] Read more.
Mucosal-associated invariant T cells are activated following the recognition of bacterial antigens presented by the major histocompatibility complex class I-related molecule (MR1). Previous metagenomics data showed that MR1−/− knock-out (KO) mice had distinct microbiota and displayed a resistance to Clostridioides difficile (CDI) colonization vs. wild-type (WT) mice. In the present study, LC/MS-based untargeted metabolomics are applied to evaluate the changes in metabolic activities, in accordance with the changes in gut microbiota caused by cefoperazone (Cef) treatment. Adult C57Bl/6J WT and MR1−/− KO mice were given sterile drinking water or spiked with 0.5 mg/mL Cef ad libitum for five days. Fecal pellets were collected daily, and both small intestinal and cecal contents were harvested at sacrifice. The PLS-DA score plots of the metabolomic data indicate that the microbiota is relatively less disturbed by Cef treatment in KO mice, which is consistent with the metagenomics data. The most noticeable differences in the metabolome of KO and WT mice were the increases in carbohydrates in the WT mice, but not in the KO mice. Metabolic functional biomarkers were identified through the correlation analysis of gamma-aminobutyric acid (GABA) and riboflavin. These detected metabolic functional biomarkers could provide information complementary to metagenomics data. Full article
(This article belongs to the Special Issue Biomarker Discovery through Microbiome Metabolism Analysis)
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19 pages, 2609 KiB  
Article
NMR Metabolomics Reveal Urine Markers of Microbiome Diversity and Identify Benzoate Metabolism as a Mediator between High Microbial Alpha Diversity and Metabolic Health
by Johannes Hertel, Daniel Fässler, Almut Heinken, Frank U. Weiß, Malte Rühlemann, Corinna Bang, Andre Franke, Kathrin Budde, Ann-Kristin Henning, Astrid Petersmann, Uwe Völker, Henry Völzke, Ines Thiele, Hans-Jörgen Grabe, Markus M. Lerch, Matthias Nauck, Nele Friedrich and Fabian Frost
Metabolites 2022, 12(4), 308; https://doi.org/10.3390/metabo12040308 - 31 Mar 2022
Cited by 11 | Viewed by 3270
Abstract
Microbial metabolites measured using NMR may serve as markers for physiological or pathological host–microbe interactions and possibly mediate the beneficial effects of microbiome diversity. Yet, comprehensive analyses of gut microbiome data and the urine NMR metabolome from large general population cohorts are missing. [...] Read more.
Microbial metabolites measured using NMR may serve as markers for physiological or pathological host–microbe interactions and possibly mediate the beneficial effects of microbiome diversity. Yet, comprehensive analyses of gut microbiome data and the urine NMR metabolome from large general population cohorts are missing. Here, we report the associations between gut microbiota abundances or metrics of alpha diversity, quantified from stool samples using 16S rRNA gene sequencing, with targeted urine NMR metabolites measures from 951 participants of the Study of Health in Pomerania (SHIP). We detected significant genus–metabolite associations for hippurate, succinate, indoxyl sulfate, and formate. Moreover, while replicating the previously reported association between hippurate and measures of alpha diversity, we identified formate and 4-hydroxyphenylacetate as novel markers of gut microbiome alpha diversity. Next, we predicted the urinary concentrations of each metabolite using genus abundances via an elastic net regression methodology. We found profound associations of the microbiome-based hippurate prediction score with markers of liver injury, inflammation, and metabolic health. Moreover, the microbiome-based prediction score for hippurate completely mediated the clinical association pattern of microbial diversity, hinting at a role of benzoate metabolism underlying the positive associations between high alpha diversity and healthy states. In conclusion, large-scale NMR urine metabolomics delivered novel insights into metabolic host–microbiome interactions, identifying pathways of benzoate metabolism as relevant candidates mediating the beneficial health effects of high microbial alpha diversity. Full article
(This article belongs to the Special Issue Biomarker Discovery through Microbiome Metabolism Analysis)
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16 pages, 1615 KiB  
Article
High-Throughput UHPLC-MS to Screen Metabolites in Feces for Gut Metabolic Health
by Andressa de Zawadzki, Maja Thiele, Tommi Suvitaival, Asger Wretlind, Min Kim, Mina Ali, Annette F. Bjerre, Karin Stahr, Ismo Mattila, Torben Hansen, Aleksander Krag and Cristina Legido-Quigley
Metabolites 2022, 12(3), 211; https://doi.org/10.3390/metabo12030211 - 25 Feb 2022
Cited by 3 | Viewed by 3361
Abstract
Feces are the product of our diets and have been linked to diseases of the gut, including Chron’s disease and metabolic diseases such as diabetes. For screening metabolites in heterogeneous samples such as feces, it is necessary to use fast and reproducible analytical [...] Read more.
Feces are the product of our diets and have been linked to diseases of the gut, including Chron’s disease and metabolic diseases such as diabetes. For screening metabolites in heterogeneous samples such as feces, it is necessary to use fast and reproducible analytical methods that maximize metabolite detection. As sample preparation is crucial to obtain high quality data in MS-based clinical metabolomics, we developed a novel, efficient and robust method for preparing fecal samples for analysis with a focus in reducing aliquoting and detecting both polar and non-polar metabolites. Fecal samples (n = 475) from patients with alcohol-related liver disease and healthy controls were prepared according to the proposed method and analyzed in an UHPLC-QQQ targeted platform in order to obtain a quantitative profile of compounds that impact liver-gut axis metabolism. MS analyses of the prepared fecal samples have shown reproducibility and coverage of n = 28 metabolites, mostly comprising bile acids and amino acids. We report metabolite-wise relative standard deviation (RSD) in quality control samples, inter-day repeatability, LOD (limit of detection), LOQ (limit of quantification), range of linearity and method recovery. The average concentrations for 135 healthy participants are reported here for clinical applications. Our high-throughput method provides a novel tool for investigating gut-liver axis metabolism in liver-related diseases using a noninvasive collected sample. Full article
(This article belongs to the Special Issue Biomarker Discovery through Microbiome Metabolism Analysis)
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14 pages, 2348 KiB  
Article
Native Microbiome Members of C. elegans Act Synergistically in Biosynthesis of Pyridoxal 5′-Phosphate
by Orçun Haçariz, Charles Viau, Xue Gu and Jianguo Xia
Metabolites 2022, 12(2), 172; https://doi.org/10.3390/metabo12020172 - 11 Feb 2022
Cited by 2 | Viewed by 2120
Abstract
The roles of the healthy microbiome on the host and the relationships between members of the microbiome remain to be fully characterized. Due to the complexity of the interactions between the mammalian microbiome and its host, the use of model organisms such as [...] Read more.
The roles of the healthy microbiome on the host and the relationships between members of the microbiome remain to be fully characterized. Due to the complexity of the interactions between the mammalian microbiome and its host, the use of model organisms such as the nematode worm Caenorhabditis elegans is a promising strategy to study host-microbiome interactions in vivo, as well as bacterial crosstalk within the host. Previously it was found that native bacterial isolates of the worm, Chryseobacterium sp. CHNTR56 MYb120 and Comamonas sp. 12022 MYb131, possess genomic diversity in the biosynthesis of the active form of vitamin B6, pyridoxal 5′-phosphate (PLP), and contribute to host fitness and lifespan extension. However, the relative contribution of PLP from each isolate, as well as the existence of interbacterial relationships within the worm gut remain to be characterized. In the present work, we investigated the presence and measured the abundance of PLP in the isolates and in the worms grown with the isolates using ultraperformance liquid chromatography tandem-mass spectrometry (UPLC-MS/MS). Our analyses confirmed the presence of PLP in vitro and in vivo. The elevated abundance of PLP in the isolates (which reached statistically significant levels when the two isolates were combined), and within worms grown with the combination of bacterial isolates, compared to control, indicated synergism between the isolates in the production of PLP. Isotope labeling revealed that Comamonas sp. 12022 MYb131 was the main provider of PLP in worms grown with the combination of bacterial isolates. The dominance of this isolate inside the worm was further confirmed by a colonization assay. An untargeted metabolomics analysis of the bacteria showed that the pathways related to cell growth, protein synthesis and lipid synthesis/energy production were regulated in the combination group in comparison with Comamonas sp. 12022 MYb131 alone. Furthermore, glutamine, involved in the de novo synthesis of purine and pyrimidines, was specifically abundant in this group, indicating the potential role of this metabolite in initiating and sustaining bacterial growth. This bacterial crosstalk is suggested to promote the growth of Comamonas sp. 12022 MYb131 in vivo, and synthesis of bacterial metabolites such as PLP in the worm gut. Full article
(This article belongs to the Special Issue Biomarker Discovery through Microbiome Metabolism Analysis)
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15 pages, 2609 KiB  
Article
Integrative Analysis of Metabolome and Microbiome in Patients with Progressive Alcohol-Associated Liver Disease
by Bei Gao, Yixin Zhu, Nan Gao, Weishou Shen, Peter Stärkel and Bernd Schnabl
Metabolites 2021, 11(11), 766; https://doi.org/10.3390/metabo11110766 - 10 Nov 2021
Cited by 3 | Viewed by 2391
Abstract
Alcohol-associated liver disease is one of the most prevalent diseases around the world, with 10–20% of patients developing progressive liver disease. To identify the complex and correlated nature of metabolic and microbial data types in progressive liver disease, we performed an integrated analysis [...] Read more.
Alcohol-associated liver disease is one of the most prevalent diseases around the world, with 10–20% of patients developing progressive liver disease. To identify the complex and correlated nature of metabolic and microbial data types in progressive liver disease, we performed an integrated analysis of the fecal and serum metabolomes with the gut microbiome in a cohort of 38 subjects, including 15 patients with progressive liver disease, 16 patients with non-progressive liver disease, and 7 control subjects. We found that although patients were generally clustered in three groups according to disease status, metabolites showed better separation than microbial species. Furthermore, eight serum metabolites were correlated with two microbial species, among which seven metabolites were decreased in patients with progressive liver disease. Five fecal metabolites were correlated with three microbial species, among which four metabolites were decreased in patients with progressive liver disease. When predicting progressive liver disease from non-progressive liver disease using correlated metabolic and microbial signatures with the random forest model, correlated serum metabolites and microbial species showed great predictive power, with the area under the receiver operating characteristic curve achieving 0.91. The multi-omics signatures identified in this study are helpful for the early identification of patients with progressive alcohol-associated liver disease, which is a key step for therapeutic intervention. Full article
(This article belongs to the Special Issue Biomarker Discovery through Microbiome Metabolism Analysis)
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