Advances in Gut Microbiome Metabolomics

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Endocrinology and Clinical Metabolic Research".

Deadline for manuscript submissions: 15 May 2025 | Viewed by 1186

Special Issue Editors


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Guest Editor
Department of Molecular Systems Biology, Helmholtz Zentrum für Umweltforschung, 15, 04318 Leipzig, Germany
Interests: metabolomics (targeted/untargeted); human biomonitoring; microbiome research; mass spectrometry
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Helmholtz Zentrum für Umweltforschung, 15, 04318 Leipzig, Germany
Interests: targeted and untargeted metabolomics; LC-MS/MS-based methodology development; biomarkers
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Helmholtz Zentrum für Umweltforschung, 15, 04318 Leipzig, Germany
Interests: intestinal microbiome; multi-omics; metabolomics (targeted/untargeted); metaproteomics; 16S rRNA gene sequencing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The gut microbiome, a complex ecosystem of microorganisms residing in the human gastrointestinal tract, plays a crucial role in maintaining host health. Recent advances in metabolomics—a powerful tool for the comprehensive analysis of small molecules—have revolutionized our understanding of the functional outputs of the gut microbiome. This Special Issue explores the latest developments in gut microbiome metabolomics, highlighting novel methodologies, analytical techniques, and bioinformatics approaches that have enabled deeper insights into microbial metabolism and its impact on human health.

Key areas of focus include the identification of microbial-derived metabolites, their biochemical pathways, and their interactions with host systems. The integration of multi-omics data, advanced mass spectrometry, and nuclear magnetic resonance (NMR) technologies has facilitated the characterization of complex metabolite profiles, uncovering previously unknown links between the gut microbiome and various diseases, such as metabolic disorders, cancer, and neurodegenerative conditions. Additionally, this issue addresses the challenges of standardizing metabolomic analyses and the potential of personalized medicine approaches based on individual microbiome signatures.

Overall, the articles within this issue underscore the importance of gut microbiome metabolomics in advancing our understanding of microbiome-host interactions, paving the way for novel therapeutic strategies and diagnostic tools in precision medicine.

Dr. Ulrike E. Rolle-Kampczyk
Dr. Beatrice Engelmann
Dr. Sven-Bastiaan Haange
Guest Editors

Manuscript Submission Information

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Keywords

  • gut microbiome–host interaction
  • cross talk
  • metabolomics
  • omics- technologies
  • microbiome signatures
  • new diagnostic tools
  • novel therapeutic strategies

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Published Papers (1 paper)

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Research

14 pages, 3484 KiB  
Article
Bacillus megaterium DSM 32963 Enhances Specialized Pro-Resolving Mediator Production from an n-3 PUFA Salt in a Dynamic Model of the Human Intestine
by Bodo Speckmann, Paul M. Jordan, Oliver Werz, Robert K. Hofstetter, Ellen Ehring, Marie-Luise Vogel and Koen Venema
Metabolites 2025, 15(2), 105; https://doi.org/10.3390/metabo15020105 - 7 Feb 2025
Cited by 1 | Viewed by 851
Abstract
Background: Omega-3 polyunsaturated fatty acids (n-3 PUFA) have been used in the treatment of inflammatory bowel diseases (IBD) and irritable bowel syndrome (IBS), and their effects are potentiated upon conversion to specialized pro-resolving mediators (SPM). Recent studies indicated that the probiotic [...] Read more.
Background: Omega-3 polyunsaturated fatty acids (n-3 PUFA) have been used in the treatment of inflammatory bowel diseases (IBD) and irritable bowel syndrome (IBS), and their effects are potentiated upon conversion to specialized pro-resolving mediators (SPM). Recent studies indicated that the probiotic bacterial strain Bacillus megaterium DSM 32963 can be used to enhance the production of SPM and its precursors in vivo. Methods: Here, we explored the contribution of Bacillus megaterium DSM 32963 to SPM production in a validated, dynamic model of the upper and lower intestine. The TIM-1 and TIM-2 models were applied, with the TIM-2 model inoculated with the fecal microbiota of healthy individuals and probed with an n-3 PUFA lysine salt with and without Bacillus megaterium DSM 32963 or an SPM-enriched fish oil or placebo. Kinetics of SPM production were assessed by metabololipidomics analysis, and survival and engraftment of the Bacillus megaterium strain was monitored by plate counting and by strain-specific qPCR. Results: Bacillus megaterium DSM 32963 poorly survived TIM-1 conditions but propagated in the TIM-2 model, where it enabled the metabolism of n-3 PUFA to SPM (resolvin E2 and protectin DX) and SPM precursors (e.g., 5-hydroxyeicosapentaenoic acid (5-HEPE), 15-HEPE, 18-HEPE, 4-hydroxydocosahexaenoic acid (4-HDHA), 10-HDHA, and 17-HDHA, among other EPA- and DHA-derived metabolites) with significantly higher levels of lipid mediator production compared to the n-3 PUFA lysine salt alone; esterified n-3 PUFA were hardly converted by the microbiota. Conclusions: These findings reinforce that Bacillus megaterium DSM 32963 facilitates SPM production in situ from bioavailable n-3 PUFA in the large intestine, highlighting its use to complement eukaryotic SPM biosynthesis by the host and its possible therapeutic use for, e.g., IBD and IBS. Full article
(This article belongs to the Special Issue Advances in Gut Microbiome Metabolomics)
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