The Metaproteomics Initiative: five years of community-driven progress

Tim Van Den Bossche; Lucia Grenga; Gelio Alves; Magnus Arntzen; Dirk Benndorf; Madita Brauer; Daniel Figeys; Celine Henry; Robert L. Hettich; Robert Heyer; Pratik D. Jagtap; Nico Jehmlich; Manuel Kleiner; Leyuan Li; Bart Mesuere; Martin Pabst; Jagroop Pandhal; Phillip B. Pope; Jana Seifert; Anke Trautwein-Schult; Pieter Verschaffelt; Paul Wilmes; Jean Armengaud; Benoit J. Kunath

doi:10.1186/s40168-026-02463-0

The Metaproteomics Initiative: five years of community-driven progress

Tim Van Den Bossche
, Lucia Grenga
, Gelio Alves
, Magnus Arntzen
, Dirk Benndorf
, Madita Brauer
, Daniel Figeys
, Celine Henry
, Robert L. Hettich
, Robert Heyer
, Pratik D. Jagtap
, Nico Jehmlich
, Manuel Kleiner
, Leyuan Li
, Bart Mesuere
, Martin Pabst
, Jagroop Pandhal
, Phillip B. Pope
, Jana Seifert
, Anke Trautwein-Schult

Pieter Verschaffelt, Paul Wilmes, Jean Armengaud, Benoit J. Kunath

Bioanalytical Mass Spectrometry

Research output: Contribution to journal › Comment/debate

Abstract

The Metaproteomics Initiative was officially launched in 2021 to strengthen collaboration, promote knowledge exchange, and support and lead standardization efforts within the growing metaproteomics community. Over the past 5 years, the Initiative has developed into a structured, global network of researchers. It has launched community-driven benchmark studies, helped shape emerging metadata and reporting standards, developed practical guidance and training materials, organized international symposia, and fostered connections across the microbiome research landscape (https://metaproteomics.org/). We outline the Initiative’s organization, activities, achievements, and ongoing efforts, and reflect on how sustained, community-led coordination has shaped the development of metaproteomics as a field. We further position the Grand Metaproteome Challenges as a next step toward coordinated, community-scale biological research, aimed at advancing functional microbiome studies across clinical, industrial, and environmental application domains, and invite engagement from the wider microbiome and omics communities.

Original language	English
Article number	186
Journal	Microbiome
Volume	14
Issue number	1
DOIs	https://doi.org/10.1186/s40168-026-02463-0
State	Published - Dec 2026

Funding

T.V.D.B. acknowledges funding from the Research Foundation Flanders (FWO) [1286824N]. L.G. acknowledges the French National Agency for Research (France 2030, the French Proteomics Infrastructure INBS ProFI, grant number ANR-24-INBS-0015-05). G.A. was supported in part by the Intramural Research Program of the National Institutes of Health (NIH). The contributions of the NIH author(s) are considered Works of the United States Government. The findings and conclusions presented in this paper are those of the author(s) and do not necessarily reflect the views of the NIH or the US Department of Health and Human Services. M.Ø.A. acknowledges the European Research Council (ERC-CoG 863664). D.B., R.H., N.J. and J.S. acknowledge NFDI4Microbiota Flex Fund “MetaProt,” “MetaProtRDM,” and “MetaProt-KG.” M.B. was supported by Fonds de la Recherche Scientifique - FNRS Télévie grant (2024, 7.4564.24, 40025650), FNR INTER mobility grant (INTER/MOBILITY/2024/BM/18912571/). R.L.H. acknowledges the US Department of Energy, Office of Science, Biological and Environmental Research, Genomic Science Program as part of the Plant-Microbe Interfaces Science Focus Area at Oak Ridge National Lab. L.L acknowledges the State Key Laboratory of Medical Proteomics. P.B.P was supported by the Australian Research Council (Future Fellowship: FT230100560). P.W. acknowledges the European Research Council under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 863664). B.J.K acknowledges funding from the National Research Fund Luxembourg (FNR) [INTER/Mobility/2022/BM/16965254].

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Van Den Bossche, T., Grenga, L., Alves, G., Arntzen, M., Benndorf, D., Brauer, M., Figeys, D., Henry, C., Hettich, R. L., Heyer, R., Jagtap, P. D., Jehmlich, N., Kleiner, M., Li, L., Mesuere, B., Pabst, M., Pandhal, J., Pope, P. B., Seifert, J., ... Kunath, B. J. (2026). The Metaproteomics Initiative: five years of community-driven progress. Microbiome, 14(1), Article 186. https://doi.org/10.1186/s40168-026-02463-0

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abstract = "The Metaproteomics Initiative was officially launched in 2021 to strengthen collaboration, promote knowledge exchange, and support and lead standardization efforts within the growing metaproteomics community. Over the past 5 years, the Initiative has developed into a structured, global network of researchers. It has launched community-driven benchmark studies, helped shape emerging metadata and reporting standards, developed practical guidance and training materials, organized international symposia, and fostered connections across the microbiome research landscape (https://metaproteomics.org/). We outline the Initiative{\textquoteright}s organization, activities, achievements, and ongoing efforts, and reflect on how sustained, community-led coordination has shaped the development of metaproteomics as a field. We further position the Grand Metaproteome Challenges as a next step toward coordinated, community-scale biological research, aimed at advancing functional microbiome studies across clinical, industrial, and environmental application domains, and invite engagement from the wider microbiome and omics communities.",

author = "\{Van Den Bossche\}, Tim and Lucia Grenga and Gelio Alves and Magnus Arntzen and Dirk Benndorf and Madita Brauer and Daniel Figeys and Celine Henry and Hettich, \{Robert L.\} and Robert Heyer and Jagtap, \{Pratik D.\} and Nico Jehmlich and Manuel Kleiner and Leyuan Li and Bart Mesuere and Martin Pabst and Jagroop Pandhal and Pope, \{Phillip B.\} and Jana Seifert and Anke Trautwein-Schult and Pieter Verschaffelt and Paul Wilmes and Jean Armengaud and Kunath, \{Benoit J.\}",

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Van Den Bossche, T, Grenga, L, Alves, G, Arntzen, M, Benndorf, D, Brauer, M, Figeys, D, Henry, C, Hettich, RL, Heyer, R, Jagtap, PD, Jehmlich, N, Kleiner, M, Li, L, Mesuere, B, Pabst, M, Pandhal, J, Pope, PB, Seifert, J, Trautwein-Schult, A, Verschaffelt, P, Wilmes, P, Armengaud, J & Kunath, BJ 2026, 'The Metaproteomics Initiative: five years of community-driven progress', Microbiome, vol. 14, no. 1, 186. https://doi.org/10.1186/s40168-026-02463-0

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AU - Van Den Bossche, Tim

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AU - Pandhal, Jagroop

AU - Pope, Phillip B.

AU - Seifert, Jana

AU - Trautwein-Schult, Anke

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AB - The Metaproteomics Initiative was officially launched in 2021 to strengthen collaboration, promote knowledge exchange, and support and lead standardization efforts within the growing metaproteomics community. Over the past 5 years, the Initiative has developed into a structured, global network of researchers. It has launched community-driven benchmark studies, helped shape emerging metadata and reporting standards, developed practical guidance and training materials, organized international symposia, and fostered connections across the microbiome research landscape (https://metaproteomics.org/). We outline the Initiative’s organization, activities, achievements, and ongoing efforts, and reflect on how sustained, community-led coordination has shaped the development of metaproteomics as a field. We further position the Grand Metaproteome Challenges as a next step toward coordinated, community-scale biological research, aimed at advancing functional microbiome studies across clinical, industrial, and environmental application domains, and invite engagement from the wider microbiome and omics communities.

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DO - 10.1186/s40168-026-02463-0

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AN - SCOPUS:105045676795

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VL - 14

JO - Microbiome

JF - Microbiome

IS - 1

M1 - 186

ER -

The Metaproteomics Initiative: five years of community-driven progress

Abstract

Funding

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