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  1. Article: Unique Insights into How Plants and Soil Microbiomes Interact Are at Our Fingertips.

    Armengaud, Jean

    mSystems

    2022  Volume 7, Issue 5, Page(s) e0058922

    Abstract: Global warming endangers our world, with probably a drastic drop in food production as one of the first vital consequences for humanity. To maintain or improve quality and sustainable yields, the burning imperative for agriculture is to rapidly integrate ...

    Abstract Global warming endangers our world, with probably a drastic drop in food production as one of the first vital consequences for humanity. To maintain or improve quality and sustainable yields, the burning imperative for agriculture is to rapidly integrate the essential component for plant development and soil regeneration, namely, the soil microbiome. Although enormous progress has been made in identifying the components of this microbiome, the way in which they interact with each other and with plants remains poorly understood. Lidbury I, Raguideau S, Borsetto C, Murphy A, et al. (mSystems 7:e00025-22, 2022, https://doi.org/10.1128/mSystems.00025-22) illustrate how metaproteomics helps define key interactions between plants and microorganisms at the rhizospheric interface. The many extracellular proteins identified and quantified by this methodology uniquely explain the observed phenotype. This study shows that the adoption of metaproteomics is no longer an option that microbiologists should consider but a must!
    Language English
    Publishing date 2022-08-17
    Publishing country United States
    Document type Journal Article
    ISSN 2379-5077
    ISSN 2379-5077
    DOI 10.1128/msystems.00589-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Metaproteomics to understand how microbiota function: The crystal ball predicts a promising future.

    Armengaud, Jean

    Environmental microbiology

    2022  Volume 25, Issue 1, Page(s) 115–125

    Abstract: In the medical, environmental, and biotechnological fields, microbial communities have attracted much attention due to their roles and numerous possible applications. The study of these communities is challenging due to their diversity and complexity. ... ...

    Abstract In the medical, environmental, and biotechnological fields, microbial communities have attracted much attention due to their roles and numerous possible applications. The study of these communities is challenging due to their diversity and complexity. Innovative methods are needed to identify the taxonomic components of individual microbiota, their changes over time, and to determine how microoorganisms interact and function. Metaproteomics is based on the identification and quantification of proteins, and can potentially provide this full picture. Due to the wide molecular panorama and functional insights it provides, metaproteomics is gaining momentum in microbiome and holobiont research. Its full potential should be unleashed in the coming years with progress in speed and cost of analyses. In this exploratory crystal ball exercise, I discuss the technical and conceptual advances in metaproteomics that I expect to drive innovative research over the next few years in microbiology. I also debate the concepts of 'microbial dark matter' and 'Metaproteomics-Assembled Proteomes (MAPs)' and present some long-term prospects for metaproteomics in clinical diagnostics and personalized medicine, environmental monitoring, agriculture, and biotechnology.
    MeSH term(s) Proteomics/methods ; Microbiota ; Biotechnology ; Proteome
    Chemical Substances Proteome
    Language English
    Publishing date 2022-10-18
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2020213-1
    ISSN 1462-2920 ; 1462-2912
    ISSN (online) 1462-2920
    ISSN 1462-2912
    DOI 10.1111/1462-2920.16238
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Protecting our environment, a motivating outdoor game for proteomics!

    Armengaud, Jean

    Proteomics

    2022  Volume 22, Issue 10, Page(s) e2200055

    Abstract: The global Earth ecosystem faces many intertwined threats, primarily anthropogenic pollution, drastic reduction of wild spaces, faster spread of pathogens, and global climate warming. Ecotoxicology, the integration of toxicology and ecology, aims to ... ...

    Abstract The global Earth ecosystem faces many intertwined threats, primarily anthropogenic pollution, drastic reduction of wild spaces, faster spread of pathogens, and global climate warming. Ecotoxicology, the integration of toxicology and ecology, aims to describe the effects of toxicants on organisms, whether at the level of the population, the community, the ecosystem, or the biosphere. Sentinel species are employed to assess threats to life, giving advance warning of danger. In this issue of Proteomics, Wilde and collaborators (Proteomics 2022, 22, https://doi.org/10.1002/pmic.202100289) present a comprehensive coverage of the proteome of the crustacean Daphnia magna, a species used to evaluate aquatic pollution. This study illustrates how current shotgun proteomics technology allows straightforward quantitation of any protein for whole animals or dissected organs, making global molecular phenotyping a reality for animals. Tandem mass spectrometry operated in data-independent acquisition can be used to compare the response of sentinels to various environmental conditions. The current low number of well-annotated animal or plant genomes, the high diversity of genetic backgrounds of each species, and the paucity of knowledge about protein functions for most of the relevant sentinels pose huge challenges for data interpretation. As a result, ecology and ecotoxicology today constitute an exceptional field for proteomics.
    MeSH term(s) Animals ; Daphnia/metabolism ; Ecosystem ; Ecotoxicology/methods ; Proteome/metabolism ; Proteomics/methods
    Chemical Substances Proteome
    Language English
    Publishing date 2022-04-22
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2032093-0
    ISSN 1615-9861 ; 1615-9853
    ISSN (online) 1615-9861
    ISSN 1615-9853
    DOI 10.1002/pmic.202200055
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Metaproteomics to understand how microbiota function: The crystal ball predicts a promising future

    Armengaud, Jean

    Environmental Microbiology. 2023 Jan., v. 25, no. 1 p.115-125

    2023  

    Abstract: In the medical, environmental, and biotechnological fields, microbial communities have attracted much attention due to their roles and numerous possible applications. The study of these communities is challenging due to their diversity and complexity. ... ...

    Abstract In the medical, environmental, and biotechnological fields, microbial communities have attracted much attention due to their roles and numerous possible applications. The study of these communities is challenging due to their diversity and complexity. Innovative methods are needed to identify the taxonomic components of individual microbiota, their changes over time, and to determine how microoorganisms interact and function. Metaproteomics is based on the identification and quantification of proteins, and can potentially provide this full picture. Due to the wide molecular panorama and functional insights it provides, metaproteomics is gaining momentum in microbiome and holobiont research. Its full potential should be unleashed in the coming years with progress in speed and cost of analyses. In this exploratory crystal ball exercise, I discuss the technical and conceptual advances in metaproteomics that I expect to drive innovative research over the next few years in microbiology. I also debate the concepts of ‘microbial dark matter’ and ‘Metaproteomics‐Assembled Proteomes (MAPs)’ and present some long‐term prospects for metaproteomics in clinical diagnostics and personalized medicine, environmental monitoring, agriculture, and biotechnology.
    Keywords biotechnology ; diagnostic techniques ; exercise ; microbiome ; microorganisms ; precision medicine ; proteome
    Language English
    Dates of publication 2023-01
    Size p. 115-125.
    Publishing place John Wiley & Sons, Inc.
    Document type Article ; Online
    Note JOURNAL ARTICLE
    ZDB-ID 2020213-1
    ISSN 1462-2920 ; 1462-2912
    ISSN (online) 1462-2920
    ISSN 1462-2912
    DOI 10.1111/1462-2920.16238
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Unleashing immuno-mass spectrometry superpowers to detect SARS-CoV-2.

    Armengaud, Jean

    EBioMedicine

    2021  Volume 69, Page(s) 103480

    Abstract: In this article of EBioMedicine, Santosh Renuse and ... ...

    Abstract In this article of EBioMedicine, Santosh Renuse and colleagues
    MeSH term(s) COVID-19 ; Humans ; Mass Spectrometry ; Pandemics ; SARS-CoV-2 ; Spectrum Analysis
    Language English
    Publishing date 2021-07-10
    Publishing country Netherlands
    Document type Journal Article ; Comment
    ZDB-ID 2851331-9
    ISSN 2352-3964
    ISSN (online) 2352-3964
    DOI 10.1016/j.ebiom.2021.103480
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: The proteomics contribution to the counter-bioterrorism toolbox in the post-COVID-19 era.

    Armengaud, Jean

    Expert review of proteomics

    2020  Volume 17, Issue 7-8, Page(s) 507–511

    MeSH term(s) Animals ; Bioterrorism/prevention & control ; COVID-19 ; Coronavirus Infections/epidemiology ; Coronavirus Infections/prevention & control ; Disease Reservoirs ; Expert Testimony ; Humans ; Infections/diagnosis ; Infections/therapy ; Pandemics/prevention & control ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/prevention & control ; Proteomics/methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Tandem Mass Spectrometry
    Keywords covid19
    Language English
    Publishing date 2020-09-29
    Publishing country England
    Document type Editorial ; Research Support, Non-U.S. Gov't
    ZDB-ID 2299100-1
    ISSN 1744-8387 ; 1478-9450
    ISSN (online) 1744-8387
    ISSN 1478-9450
    DOI 10.1080/14789450.2020.1822745
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Did Saint Leonard suffer from Madura foot at the time of death? Infectious disease diagnosis by paleo-proteotyping.

    Charlier, Philippe / Armengaud, Jean

    The Journal of infection

    2023  Volume 88, Issue 1, Page(s) 61–62

    MeSH term(s) Humans ; Mycetoma/diagnosis ; Communicable Diseases
    Language English
    Publishing date 2023-10-30
    Publishing country England
    Document type Letter
    ZDB-ID 424417-5
    ISSN 1532-2742 ; 0163-4453
    ISSN (online) 1532-2742
    ISSN 0163-4453
    DOI 10.1016/j.jinf.2023.10.021
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Impact de l’environnement sur la santé. Partie 1. Enfant : le concept des 1 000 premiers jours.

    Simeoni, Umberto / Armengaud, Jean-Baptiste

    La Revue du praticien

    2023  Volume 73, Issue 6, Page(s) 679–685

    Title translation Impact of the environment on health. Part 1. Child: the concept of the first 1 000 days.
    MeSH term(s) Child ; Humans ; Infant ; Child Development
    Language French
    Publishing date 2023-07-17
    Publishing country France
    Document type Journal Article
    ZDB-ID 205365-2
    ISSN 2101-017X ; 0035-2640
    ISSN (online) 2101-017X
    ISSN 0035-2640
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Unleashing immuno-mass spectrometry superpowers to detect SARS-CoV-2

    Jean Armengaud

    EBioMedicine, Vol 69, Iss , Pp 103480- (2021)

    2021  

    Abstract: In this article of EBioMedicine, Santosh Renuse and colleagues1 show the relevance of combining immunoaffinity capture with targeted mass spectrometry measurement to detect SARS-CoV-2 nucleocapsid proteins in nasopharyngeal swab samples. The COVID-19 ... ...

    Abstract In this article of EBioMedicine, Santosh Renuse and colleagues1 show the relevance of combining immunoaffinity capture with targeted mass spectrometry measurement to detect SARS-CoV-2 nucleocapsid proteins in nasopharyngeal swab samples. The COVID-19 pandemic has confirmed the need to improve the toolbox available to diagnose respiratory infections. Rapid, reliable, and highly specific detection is essential if we are to mount immediate preventive and therapeutic responses. This report stands out from previous studies as it implements immunocapture along with robust validation for a large cohort of subjects. The results presented show that mass spectrometry is definitively at a crossroads for large-scale clinical applications.
    Keywords Mass spec ; Immuno-capture ; SARS-CoV-2 ; Medicine ; R ; Medicine (General) ; R5-920
    Language English
    Publishing date 2021-07-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Microbiology and infectious diseases - A wealth of novelty for the clinical laboratory.

    Armengaud, Jean

    Clinical mass spectrometry (Del Mar, Calif.)

    2019  Volume 14 Pt A, Page(s) 1–2

    Language English
    Publishing date 2019-05-02
    Publishing country Netherlands
    Document type Editorial
    ISSN 2376-9998
    ISSN (online) 2376-9998
    DOI 10.1016/j.clinms.2019.04.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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