Metaproteomics

We pioneered the concept of “phylopeptidomics”, revolutionizing the identification of the taxonomical units present in a metaproteomic sample and enabling accurate estimation of  relative biomasses of all the taxa. Our groundbreaking work encompasses the development of innovative sample preparation and mass spectrometry methods, as well as advanced bioinformatics pipelines, to unravel the intricacies of microbiota functionality.

Applying this methodology, we have successfully characterized a wide range of samples, including medical samples such as the gut microbiome, respiratory tract microbiome, and oral microbiome. Furthermore, our investigations have extended to diverse environmental samples such as soil, marine sediments, and sea water. We have also ventured into biotechnological applications by studying microbiota from industrial processes. In addition, our methodologies have been applied to the analysis of historical relics, including those of notable figures such as Napoléon, Louis XIV King of France, Henri IV King of France, and artifacts from the Dahomey King palace, to name a few examples.

Armengaud, 2022 - Clinical and environmental diagnostics by metaproteomics

By pushing the boundaries of phylopeptidomics, we continue to unlock new possibilities for understanding microbial ecosystems in various contexts, shaping the forefront of metaproteomic research.

    • Armengaud J (2022) Metaproteomics to understand how microbiota function: the crystal ball predicts a promising future. Env Microbiol, in press. doi: 10.1111/1462-2920.16238.
    • Hardouin P, Pible O, Marchandin H, Culotta K, Armengaud J, Chiron R, Grenga L (2022) Quick and wide-range taxonomical repertoire establishment of the cystic fibrosis lung microbiota by tandem mass spectrometry on sputum samples. Frontiers in Microbiology, 13:975883. doi:10.3389/fmicb.2022.975883.
    • Grenga L, Pible O, Miotello G, Culotta K, Ruat S, Roncato MA, Gas F, Bellanger L, Claret PG, Dunyach-Remy C, Laureillard D, Sotto A, Lavigne JP, Armengaud J (2022) Taxonomical and functional changes in COVID-19 faecal microbiome could be related to SARS-CoV-2 faecal load. Env Microbiol. 24(9):4299-4316. doi: 10.1111/1462-2920.16028.
    • Hirtz  C, Mannaa  A, Moulis E, Pible O, O’Flynn R, Armengaud J, Jouffret V, Lemaistre C, Dominici G, Martinez AY, Dunyach-Rémy C, Tiers L, Lavigne J-P, Tramini P, Goldsmith M-C, Lehmann S, Deville de Périère D, Vialaret J (2022) Deciphering Black Extrinsic Tooth Stains composition in Children using metaproteomics. ACS Omega 7(10):8258-8267. doi: 10.1021/acsomega.1c04770.
    • Armengaud J (2022) Unique insights into how plants and soil microbiomes interact are at our fingertips. mSystems, in press. :e0058922. doi: 10.1128/msystems.00589-22.
    • Van Den Bossche T, Arntzen MØ, Becher D, Benndorf D, Eijsink VGH, Henry C, Jagtap PD, Jehmlich N, Juste C, Kunath BJ, Mesuere B, Muth T, Pope PB, Seifert J, Tanca A, Uzzau S, Wilmes P, Hettich R, Armengaud J (2021) The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes. Microbiome 9(1):243.
    • Van Den Bossche T, Kunath BJ, Schallert K, Schäpe SS, Abraham PE, Armengaud J, et al. (2021) Critical Assessment of Metaproteome Investigation (CAMPI): a Multi-Lab Comparison of Established Workflows. Nature Communication 12(1):7305. doi: 10.1038/s41467-021-27542-8.
    • Van Eesbeeck V, Props R, Mysara M, Petit P, Rivasseau C, Armengaud J, Monsieurs P, Mahillon J, Leys N (2021) Cyclical patterns affect microbial dynamics in the water basin of a nuclear research reactor. Frontiers in Microbiology. 12:744115. doi: 10.3389/fmicb.2021.744115.
    • Jouffret V, Miotello G, Culotta K, Ayrault S, Pible O, Armengaud J (2021) Increasing the power of interpretation for soil metaproteomics data. Microbiome, 9:195. doi: 10.3389/fmicb.2021.744115.
    • Gouveia D, Grenga L, Pible O, Armengaud J (2020) Quick microbial molecular phenotyping by differential shotgun proteomics. Environ Microbiol. 22(8):2996-3004. doi: 10.1111/1462-2920.14975.
    • Hardouin P, Chiron R, Marchandin H, Armengaud J, Grenga L (2021) Metaproteomics to Decipher CF Host-Microbiota Interactions: Overview, Challenges and Future Perspectives. Genes 12(6) 892. doi: 10.3390/genes12060892.
    • Petit PCM, Pible O, Van Eesbeeck V, Alban C, Steinmetz G, Mysara M, Monsieurs P, Armengaud J, Rivasseau C (2020) Direct meta-analyses reveal unexpected microbial life in the highly radioactive water of an operating nuclear reactor core. Microorganisms 8(12):1857.
    • Gouveia D, Pible O, Culotta K, Jouffret V, Geffard O, Chaumot A, Degli-Esposti D, Armengaud J (2020) Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host. NPJ Biofilms Microbiomes 5;6(1):23. doi: 10.1038/s41522-020-0133-2.

    • Pible O, Allain F, Jouffret V, Culotta K, Miotello G, Armengaud J (2020) Estimating relative biomasses of organisms in microbiota using “phylopeptidomics”. Microbiome 8:30. doi: 10.1186/s40168-020-00797-x.