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  1. Article ; Online: Host-microbe metabolic dialogue.

    Michellod, Dolma / Liebeke, Manuel

    Nature microbiology

    2024  Volume 9, Issue 2, Page(s) 318–319

    MeSH term(s) Symbiosis ; Microbiota
    Language English
    Publishing date 2024-02-05
    Publishing country England
    Document type Journal Article
    ISSN 2058-5276
    ISSN (online) 2058-5276
    DOI 10.1038/s41564-023-01592-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Drying Enhances Signal Intensities for Global GC⁻MS Metabolomics.

    Liebeke, Manuel / Puskás, Erik

    Metabolites

    2019  Volume 9, Issue 4

    Abstract: We report here that a straightforward change of the standard derivatization procedure for GC⁻MS metabolomics is leading to a strong increase in metabolite signal intensity. Drying samples between methoxymation and trimethylsilylation significantly ... ...

    Abstract We report here that a straightforward change of the standard derivatization procedure for GC⁻MS metabolomics is leading to a strong increase in metabolite signal intensity. Drying samples between methoxymation and trimethylsilylation significantly increased signals by two- to tenfold in extracts of yeast cells, plant and animal tissue, and human urine. This easy step reduces the cost of sample material and the need for expensive new hardware.
    Language English
    Publishing date 2019-04-05
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662251-8
    ISSN 2218-1989
    ISSN 2218-1989
    DOI 10.3390/metabo9040068
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Visualization of metabolites and microbes at high spatial resolution using MALDI mass spectrometry imaging and in situ fluorescence labeling.

    Bourceau, Patric / Geier, Benedikt / Suerdieck, Vincent / Bien, Tanja / Soltwisch, Jens / Dreisewerd, Klaus / Liebeke, Manuel

    Nature protocols

    2023  Volume 18, Issue 10, Page(s) 3050–3079

    Abstract: Label-free molecular imaging techniques such as matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) enable the direct and simultaneous mapping of hundreds of different metabolites in thin sections of biological tissues. ... ...

    Abstract Label-free molecular imaging techniques such as matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) enable the direct and simultaneous mapping of hundreds of different metabolites in thin sections of biological tissues. However, in host-microbe interactions it remains challenging to localize microbes and to assign metabolites to the host versus members of the microbiome. We therefore developed a correlative imaging approach combining MALDI-MSI with fluorescence in situ hybridization (FISH) on the same section to identify and localize microbial cells. Here, we detail metaFISH as a robust and easy method for assigning the spatial distribution of metabolites to microbiome members based on imaging of nucleic acid probes, down to single-cell resolution. We describe the steps required for tissue preparation, on-tissue hybridization, fluorescence microscopy, data integration into a correlative image dataset, matrix application and MSI data acquisition. Using metaFISH, we map hundreds of metabolites and several microbial species to the micrometer scale on a single tissue section. For example, intra- and extracellular bacteria, host cells and their associated metabolites can be localized in animal tissues, revealing their complex metabolic interactions. We explain how we identify low-abundance bacterial infection sites as regions of interest for high-resolution MSI analysis, guiding the user to a trade-off between metabolite signal intensities and fluorescence signals. MetaFISH is suitable for a broad range of users from environmental microbiologists to clinical scientists. The protocol requires ~2 work days.
    Language English
    Publishing date 2023-09-06
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2244966-8
    ISSN 1750-2799 ; 1754-2189
    ISSN (online) 1750-2799
    ISSN 1754-2189
    DOI 10.1038/s41596-023-00864-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Multiplexed neuropeptide mapping in ant brains integrating microtomography and three-dimensional mass spectrometry imaging.

    Geier, Benedikt / Gil-Mansilla, Esther / Liutkevičiūtė, Zita / Hellinger, Roland / Vanden Broeck, Jozef / Oetjen, Janina / Liebeke, Manuel / Gruber, Christian W

    PNAS nexus

    2023  Volume 2, Issue 5, Page(s) pgad144

    Abstract: Neuropeptides are important regulators of animal physiology and behavior. Hitherto the gold standard for the localization of neuropeptides have been immunohistochemical methods that require the synthesis of antibody panels, while another limiting factor ... ...

    Abstract Neuropeptides are important regulators of animal physiology and behavior. Hitherto the gold standard for the localization of neuropeptides have been immunohistochemical methods that require the synthesis of antibody panels, while another limiting factor has been the brain's opacity for subsequent in situ light or fluorescence microscopy. To address these limitations, we explored the integration of high-resolution mass spectrometry imaging (MSI) with microtomography for a multiplexed mapping of neuropeptides in two evolutionary distant ant species,
    Language English
    Publishing date 2023-04-25
    Publishing country England
    Document type Journal Article
    ISSN 2752-6542
    ISSN (online) 2752-6542
    DOI 10.1093/pnasnexus/pgad144
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Determination of Abundant Metabolite Matrix Adducts Illuminates the Dark Metabolome of MALDI-Mass Spectrometry Imaging Datasets

    Janda, Moritz / Seah, Brandon K. B. / Jakob, Dennis / Beckmann, Janine / Geier, Benedikt / Liebeke, Manuel

    Analytical chemistry. 2021 June 07, v. 93, no. 24

    2021  

    Abstract: Spatial metabolomics using mass spectrometry imaging (MSI) is a powerful tool to map hundreds to thousands of metabolites in biological systems. One major challenge in MSI is the annotation of m/z values, which is substantially complicated by background ... ...

    Abstract Spatial metabolomics using mass spectrometry imaging (MSI) is a powerful tool to map hundreds to thousands of metabolites in biological systems. One major challenge in MSI is the annotation of m/z values, which is substantially complicated by background ions introduced throughout the chemicals and equipment used during experimental procedures. Among many factors, the formation of adducts with sodium or potassium ions, or in case of matrix-assisted laser desorption ionization (MALDI)-MSI, the presence of abundant matrix clusters strongly increases total m/z peak counts. Currently, there is a limitation to identify the chemistry of the many unknown peaks to interpret their biological function. We took advantage of the co-localization of adducts with their parent ions and the accuracy of high mass resolution to estimate adduct abundance in 20 datasets from different vendors of mass spectrometers. Metabolites ranging from lipids to amines and amino acids form matrix adducts with the commonly used 2,5-dihydroxybenzoic acid (DHB) matrix like [M + (DHB-H₂O) + H]⁺ and [M + DHB + Na]⁺. Current data analyses neglect those matrix adducts and overestimate total metabolite numbers, thereby expanding the number of unidentified peaks. Our study demonstrates that MALDI-MSI data are strongly influenced by adduct formation across different sample types and vendor platforms and reveals a major influence of so far unrecognized metabolite–matrix adducts on total peak counts (up to one third). We developed a software package, mass2adduct, for the community for an automated putative assignment and quantification of metabolite–matrix adducts enabling users to ultimately focus on the biologically relevant portion of the MSI data.
    Keywords 2,5-dihydroxybenzoic acid ; analytical chemistry ; automation ; computer software ; data collection ; desorption ; ionization ; matrix-assisted laser desorption-ionization mass spectrometry ; metabolites ; metabolome ; metabolomics ; potassium ; sodium
    Language English
    Dates of publication 2021-0607
    Size p. 8399-8407.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.0c04720
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: Determination of Abundant Metabolite Matrix Adducts Illuminates the Dark Metabolome of MALDI-Mass Spectrometry Imaging Datasets.

    Janda, Moritz / Seah, Brandon K B / Jakob, Dennis / Beckmann, Janine / Geier, Benedikt / Liebeke, Manuel

    Analytical chemistry

    2021  Volume 93, Issue 24, Page(s) 8399–8407

    Abstract: Spatial metabolomics using mass spectrometry imaging (MSI) is a powerful tool to map hundreds to thousands of metabolites in biological systems. One major challenge in MSI is the annotation ... ...

    Abstract Spatial metabolomics using mass spectrometry imaging (MSI) is a powerful tool to map hundreds to thousands of metabolites in biological systems. One major challenge in MSI is the annotation of
    MeSH term(s) Diagnostic Imaging ; Lipids ; Metabolome ; Metabolomics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
    Chemical Substances Lipids
    Language English
    Publishing date 2021-06-07
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.0c04720
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Connecting structure and function from organisms to molecules in small-animal symbioses through chemo-histo-tomography.

    Geier, Benedikt / Oetjen, Janina / Ruthensteiner, Bernhard / Polikarpov, Maxim / Gruber-Vodicka, Harald R / Liebeke, Manuel

    Proceedings of the National Academy of Sciences of the United States of America

    2021  Volume 118, Issue 27

    Abstract: Our understanding of metabolic interactions between small symbiotic animals and bacteria or parasitic eukaryotes that reside within their bodies is extremely limited. This gap in knowledge originates from a methodological challenge, namely to connect ... ...

    Abstract Our understanding of metabolic interactions between small symbiotic animals and bacteria or parasitic eukaryotes that reside within their bodies is extremely limited. This gap in knowledge originates from a methodological challenge, namely to connect histological changes in host tissues induced by beneficial and parasitic (micro)organisms to the underlying metabolites. We addressed this challenge and developed chemo-histo-tomography (CHEMHIST), a culture-independent approach to connect anatomic structure and metabolic function in millimeter-sized symbiotic animals. CHEMHIST combines chemical imaging of metabolites based on mass spectrometry imaging (MSI) and microanatomy-based micro-computed X-ray tomography (micro-CT) on the same animal. Both high-resolution MSI and micro-CT allowed us to correlate the distribution of metabolites to the same animal's three-dimensional (3D) histology down to submicrometer resolutions. Our protocol is compatible with tissue-specific DNA sequencing and fluorescence in situ hybridization for the taxonomic identification and localization of the associated micro(organisms). Building CHEMHIST upon in situ imaging, we sampled an earthworm from its natural habitat and created an interactive 3D model of its physical and chemical interactions with bacteria and parasitic nematodes in its tissues. Combining MSI and micro-CT, we present a methodological groundwork for connecting metabolic and anatomic phenotypes of small symbiotic animals that often represent keystone species for ecosystem functioning.
    MeSH term(s) Animals ; Bacteria/cytology ; Histological Techniques ; Host-Parasite Interactions ; Imaging, Three-Dimensional ; Mass Spectrometry ; Oligochaeta/cytology ; Oligochaeta/physiology ; Symbiosis/physiology ; X-Ray Microtomography
    Language English
    Publishing date 2021-06-29
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2023773118
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Differential regulation of degradation and immune pathways underlies adaptation of the ectosymbiotic nematode Laxus oneistus to oxic-anoxic interfaces.

    Paredes, Gabriela F / Viehboeck, Tobias / Markert, Stephanie / Mausz, Michaela A / Sato, Yui / Liebeke, Manuel / König, Lena / Bulgheresi, Silvia

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 9725

    Abstract: Eukaryotes may experience oxygen deprivation under both physiological and pathological conditions. Because oxygen shortage leads to a reduction in cellular energy production, all eukaryotes studied so far conserve energy by suppressing their metabolism. ... ...

    Abstract Eukaryotes may experience oxygen deprivation under both physiological and pathological conditions. Because oxygen shortage leads to a reduction in cellular energy production, all eukaryotes studied so far conserve energy by suppressing their metabolism. However, the molecular physiology of animals that naturally and repeatedly experience anoxia is underexplored. One such animal is the marine nematode Laxus oneistus. It thrives, invariably coated by its sulfur-oxidizing symbiont Candidatus Thiosymbion oneisti, in anoxic sulfidic or hypoxic sand. Here, transcriptomics and proteomics showed that, whether in anoxia or not, L. oneistus mostly expressed genes involved in ubiquitination, energy generation, oxidative stress response, immune response, development, and translation. Importantly, ubiquitination genes were also highly expressed when the nematode was subjected to anoxic sulfidic conditions, together with genes involved in autophagy, detoxification and ribosome biogenesis. We hypothesize that these degradation pathways were induced to recycle damaged cellular components (mitochondria) and misfolded proteins into nutrients. Remarkably, when L. oneistus was subjected to anoxic sulfidic conditions, lectin and mucin genes were also upregulated, potentially to promote the attachment of its thiotrophic symbiont. Furthermore, the nematode appeared to survive oxygen deprivation by using an alternative electron carrier (rhodoquinone) and acceptor (fumarate), to rewire the electron transfer chain. On the other hand, under hypoxia, genes involved in costly processes (e.g., amino acid biosynthesis, development, feeding, mating) were upregulated, together with the worm's Toll-like innate immunity pathway and several immune effectors (e.g., bactericidal/permeability-increasing proteins, fungicides). In conclusion, we hypothesize that, in anoxic sulfidic sand, L. oneistus upregulates degradation processes, rewires the oxidative phosphorylation and reinforces its coat of bacterial sulfur-oxidizers. In upper sand layers, instead, it appears to produce broad-range antimicrobials and to exploit oxygen for biosynthesis and development.
    MeSH term(s) Animals ; Chromadorea ; Chromatiaceae ; Hypoxia ; Nematoda/microbiology ; Oxygen/metabolism ; Sand ; Sulfides ; Sulfur/metabolism
    Chemical Substances Sand ; Sulfides ; Sulfur (70FD1KFU70) ; Oxygen (S88TT14065)
    Language English
    Publishing date 2022-06-13
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-13235-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Marine Metabolomics: a Method for Nontargeted Measurement of Metabolites in Seawater by Gas Chromatography-Mass Spectrometry.

    Sogin, Emilia M / Puskás, Erik / Dubilier, Nicole / Liebeke, Manuel

    mSystems

    2019  Volume 4, Issue 6

    Abstract: Microbial communities exchange molecules with their environment, which plays a major role in regulating global biogeochemical cycles and climate. While extracellular metabolites are commonly measured in terrestrial and limnic ecosystems, the presence of ... ...

    Abstract Microbial communities exchange molecules with their environment, which plays a major role in regulating global biogeochemical cycles and climate. While extracellular metabolites are commonly measured in terrestrial and limnic ecosystems, the presence of salt in marine habitats limits the nontargeted analyses of the ocean exometabolome using mass spectrometry (MS). Current methods require salt removal prior to sample measurements, which can alter the molecular composition of the metabolome and limit the types of compounds detected by MS. To overcome these limitations, we developed a gas chromatography MS (GC-MS) method that avoids sample altering during salt removal and that detects metabolites down to nanomolar concentrations from less than 1 ml of seawater. We applied our method (SeaMet) to explore marine metabolomes
    Language English
    Publishing date 2019-12-10
    Publishing country United States
    Document type Journal Article
    ISSN 2379-5077
    ISSN 2379-5077
    DOI 10.1128/mSystems.00638-19
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: De novo phytosterol synthesis in animals.

    Michellod, Dolma / Bien, Tanja / Birgel, Daniel / Violette, Marlene / Kleiner, Manuel / Fearn, Sarah / Zeidler, Caroline / Gruber-Vodicka, Harald R / Dubilier, Nicole / Liebeke, Manuel

    Science (New York, N.Y.)

    2023  Volume 380, Issue 6644, Page(s) 520–526

    Abstract: Sterols are vital for nearly all eukaryotes. Their distribution differs in plants and animals, with phytosterols commonly found in plants whereas most animals are dominated by cholesterol. We show that sitosterol, a common sterol of plants, is the most ... ...

    Abstract Sterols are vital for nearly all eukaryotes. Their distribution differs in plants and animals, with phytosterols commonly found in plants whereas most animals are dominated by cholesterol. We show that sitosterol, a common sterol of plants, is the most abundant sterol in gutless marine annelids. Using multiomics, metabolite imaging, heterologous gene expression, and enzyme assays, we show that these animals synthesize sitosterol de novo using a noncanonical C-24 sterol methyltransferase (C
    MeSH term(s) Animals ; Cholesterol/metabolism ; Phylogeny ; Plants/metabolism ; Sitosterols/metabolism ; Annelida/metabolism
    Chemical Substances Cholesterol (97C5T2UQ7J) ; Sitosterols
    Language English
    Publishing date 2023-05-04
    Publishing country United States
    Document type Journal Article
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.add7830
    Database MEDical Literature Analysis and Retrieval System OnLINE

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