Gut Microbiome and Host Metabolism

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

Deadline for manuscript submissions: 15 July 2025 | Viewed by 990

Special Issue Editors


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Guest Editor
Faculty of Kinesiology, University of Calgary, Calgary, AB T2N 1N4, Canada
Interests: host–microbiome interaction; carbohydrate and amino acids metabolism; multi-omics; metabolic diseases

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Guest Editor
Genome Center, University of California, Davis, CA 95616, USA
Interests: metabolomics; oxylipins; neurodegenerative diseases; antifungals

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Guest Editor
Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
Interests: gut microbiome; gut-brain axis; host-microbiome interaction

Special Issue Information

Dear Colleagues,

Disruptions in gut microbiome and host metabolism, especially in the metabolism of carbohydrates, lipids, and amino acid, play pivotal roles in the development of metabolic disorders such as obesity, diabetes, and related conditions. Understanding these co-metabolic processes at both the community and molecular levels is essential for devising effective preventive and therapeutic strategies to improve metabolic health. Recent advances in metagenomics, metabolomics, and (meta)transcriptomics, coupled with machine learning-based multi-omics integration, are significantly accelerating our ability to unravel these complex interactions across different axes and compartments. These innovations are shedding new light on metabolic regulation, disease mechanisms, and precision interventions.

This Special Issue of Metabolites, entitled "Gut Microbiome and Host Metabolism", invites submissions that explore the profound impact of the host–microbiome co-metabolism of carbohydrates, lipids, and amino acids on the onset and prevention of metabolic diseases. We welcome novel insights derived from clinical studies, animal models, and in vitro studies, particularly those employing multi-omics approaches or developing novel methodology to unravel these complex interactions.

Dr. Weilan Wang
Dr. Nuanyi Liang
Dr. Chunlong Mu
Guest Editors

Manuscript Submission Information

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Keywords

  • host–microbiome interactions
  • metabolic diseases
  • carbohydrate metabolism
  • amino acids metabo-lism
  • lipids metabolism
  • metagenomics
  • (meta)transcriptomics
  • metabolomics
  • multi-omics

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Published Papers (1 paper)

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Review

19 pages, 1710 KiB  
Review
Metatranscriptomics for Understanding the Microbiome in Food and Nutrition Science
by Christina F. Butowski, Yash Dixit, Marlon M. Reis and Chunlong Mu
Metabolites 2025, 15(3), 185; https://doi.org/10.3390/metabo15030185 - 10 Mar 2025
Viewed by 773
Abstract
Microbiome science has greatly expanded our understanding of the diverse composition and function of gut microorganisms over the past decades. With its rich microbial composition, the microbiome hosts numerous functionalities essential for metabolizing food ingredients and nutrients, resulting in the production of active [...] Read more.
Microbiome science has greatly expanded our understanding of the diverse composition and function of gut microorganisms over the past decades. With its rich microbial composition, the microbiome hosts numerous functionalities essential for metabolizing food ingredients and nutrients, resulting in the production of active metabolites that affect food fermentation or gut health. Most of these processes are mediated by microbial enzymes such as carbohydrate-active enzymes and amino acid metabolism enzymes. Metatranscriptomics enables the capture of active transcripts within the microbiome, providing invaluable functional insights into metabolic activities. Given the inter-kingdom complexity of the microbiome, metatranscriptomics could further elucidate the activities of fungi, archaea, and bacteriophages in the microbial ecosystem. Despite its potential, the application of metatranscriptomics in food and nutrition sciences remains limited but is growing. This review highlights the latest advances in food science (e.g., flavour formation and food enzymology) and nutrition science (e.g., dietary fibres, proteins, minerals, and probiotics), emphasizing the integration of metatranscriptomics with other technologies to address key research questions. Ultimately, metatranscriptomics represents a powerful tool for uncovering the microbiome activity, particularly in relation to active metabolic processes. Full article
(This article belongs to the Special Issue Gut Microbiome and Host Metabolism)
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