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Cited by 22Advanced Proteomics Techniques and ApplicationsGut microbiota and healthGenomics and Phylogenetic Studies

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Metaproteomics in the One Health framework for unraveling microbial effectors in microbiomes

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Heyer, Robert, Wolf, Maximilian, Benndorf, Dirk, Uzzau, Sergio, Seifert, Jana, Grenga, Lucia, Pabst, Martin, Schmitt, Heike, Mesuere, Bart, Van Den Bossche, Tim, Haange, Sven-Bastiaan, Jehmlich, Nico, Di Luca, Mariagrazia, Ferrer, Manuel, Serrano-Villar, Sergio, Armengaud, Jean, Bode, Helge B., Hellwig, Patrick, Masselot, Catherine Robbe, Léonard, Renaud, Wilmes, Paul·2025·Microbiome
DOI 10.1186/s40168-025-02119-5PMC PMC12100821

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Abstract

One Health seeks to integrate and balance the health of humans, animals, and environmental systems, which are intricately linked through microbiomes. These microbial communities exchange microbes and genes, influencing not only human and animal health but also key environmental, agricultural, and biotechnological processes. Preventing the emergence of pathogens as well as monitoring and controlling the composition of microbiomes through microbial effectors including virulence factors, toxins, antibiotics, non-ribosomal peptides, and viruses holds transformative potential. However, the mechanisms by which these microbial effectors shape microbiomes and their broader functional consequences for host and ecosystem health remain poorly understood. Metaproteomics offers a novel methodological framework as it provides insights into microbial dynamics by quantifying microbial biomass composition, metabolic functions, and detecting effectors like viruses, antimicrobial resistance proteins, and non-ribosomal peptides. Here, we highlight the potential of metaproteomics in elucidating microbial effectors and their impact on microbiomes and discuss their potential for modulating microbiomes to foster desired functions. Graphical Abstract Word Cloud showing the abundance of keywords in combination with the “Microbiome” in PubMed NCBI. As abundance values, the rounded logarithm with the base of 2 hits were used and submitted to https://wordart.com/create . For microbiome, the number without any combination was used for calculation. The word cloud displays different aspects of microbiome research: (i.) sources of microbiomes (green), (ii.) interactions (purple), (iii.) involved taxa (red), (iv.) applied experimental approaches (blue), and (vi.) societal effects and recent or future applications (gray).

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Metadata

Authors
Heyer, R., Wolf, M., Benndorf, D., Uzzau, S., Seifert, J., Grenga, L., Pabst, M., Schmitt, H., Mesuere, B., Van Den Bossche, T., Haange, S.-B., Jehmlich, N., Di Luca, M., Ferrer, M., Serrano-Villar, S., Armengaud, J., Bode, H. B., Hellwig, P., Masselot, C. R., Léonard, R., & Wilmes, P.
Affiliations
  • Bielefeld University (DE)
  • Anhalt University of Applied Sciences (DE)
  • University of Sassari (IT)
  • University of Hohenheim (DE)
  • Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR)
  • Delft University of Technology (NL)
  • National Institute for Public Health and the Environment (NL)
  • Ghent University (BE)
  • Helmholtz Centre for Environmental Research (DE)
  • Consejo Superior de Investigaciones Científicas (ES)
  • Philipps University of Marburg (DE)
  • Max Planck Institute for Dynamics of Complex Technical Systems (DE)
  • Centre National de la Recherche Scientifique (FR)
  • University of Luxembourg (LU)
Corresponding author
Heyer, Robert
ORCID
Venue
Microbiome
Publisher
Springer Science and Business Media LLC
Published
2025-05-23
Volume
13
Issue
1
Pages
134-134
ISSN
2049-2618 (ISSN-L)
DOI
10.1186/s40168-025-02119-5
PMC
PMC12100821
OpenAlex
W4410621645
Cited by
22
References
6
Citations by year
2026: 16 · 2025: 6
FWCI
5.51
Type
journal article
Language
en
Open access
Licence
Locations
  • Microbiome (publishedVersion, cc-by)
  • ChemRxiv (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DIGITAL.CSIC (Spanish National Research Council (CSIC)) (acceptedVersion)
  • Ghent University Academic Bibliography (Ghent University) (submittedVersion, cc-by)
  • Open Repository and Bibliography (University of Luxembourg) (submittedVersion, cc-by)
  • MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
  • HAL (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • UnissResearch (Università degli Studi di Sassari) (submittedVersion)
  • Publikationen an der Universität Bielefeld (Universität Bielefeld) (submittedVersion)
Funders
  • Région Occitanie (ANR-20-CE34-0012)
  • Agence Nationale de la Recherche (ANR-24-INBS-0015)
  • Research Foundation Flanders (1286824N)
  • Agencia Estatal de Investigación (MICIU/AEI/10.13039/501100011033)
  • NextGenerationEU/PRTR (PID2023-153370OB-I00)
  • CSIC (INMUNOBIOTA)
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
metaproteomics, One Health, microbiome, virulence factors, toxins, antibiotics, nonribosomal peptides, viruses, microbial interactions, microbiota modulation
MeSH terms
One Health, Animals, Bacteria, Humans, Virulence Factors, Proteomics, Microbiota

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