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In plaque-mass spectrometry imaging of a bloom-forming alga during viral infection reveals a metabolic shift towards odd-chain fatty acid lipids


Tapping into the metabolic crosstalk between a host and its virus can reveal unique strategies employed during infection. Viral infection is a dynamic process that generates an evolving metabolic landscape. Gaining a continuous view into the infection process is highly challenging and is limited by current metabolomics approaches, which typically measure the average of the entire population at various stages of infection. Here, we took an innovative approach to study the metabolic basis of host–virus interactions between the bloom-forming alga Emiliania huxleyi and its specific virus. We combined a classical method in virology, the plaque assay, with advanced mass spectrometry imaging (MSI), an approach we termed ‘in plaque-MSI’. Taking advantage of the spatial characteristics of the plaque, we mapped the metabolic landscape induced during infection in a high spatiotemporal resolution, unfolding the infection process in a continuous manner. Further unsupervised spatially aware clustering, combined with known lipid biomarkers, revealed a systematic metabolic shift during infection towards lipids containing the odd-chain fatty acid pentadecanoic acid (C15:0). Applying ‘in plaque-MSI’ may facilitate the discovery of bioactive compounds that mediate the chemical arms race of host–virus interactions in diverse model systems.

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Fig. 1: Overview of the workflow of ‘in plaque-MSI’ analysis.
Fig. 2: Targeted MSI analysis of known lipid biomarkers reveals the metabolic landscape produced during viral infection.
Fig. 3: Unsupervised spatially aware clustering allows the identification of unknown lipids.
Fig. 4: Induction of C15:0-based lipids during viral infection.
Fig. 5: Schematic model of the metabolic shift towards C15:0-based lipids in infected E.huxleyi cells.

Data availability

Data supporting the findings of this study are available within the paper (and Supplementary Information files). Raw data generated or analysed in this study have been deposited to the EMBL-EBI MetaboLights repository75 with the identifiers MTBLS767 (including LC–MS of plaque samples, LC–MS/MS of specific lipids and GC–MS) and MTBLS769 (including MALDI-MSI and Flow-probe-MSI). The data can be accessed with the following links: and


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We thank C. Kuhlisch from the Vardi lab for her assistance with GC–MS analyses and fruitful discussions, S. Graff van Creveld from the Vardi lab for her assistance in designing the figures for this manuscript and A. Mizrachi from the Vardi lab for her assistance with image analysis and processing. We also thank A. Brandis from the Targeted Metabolomics Unit at the Life Sciences Core Facilities, Weizmann Institute of Science, for his assistance in FAME derivatization, R. Rotkopf from the Bioinformatics Unit, Department of Biological Services, Weizmann Institute of Science, for his assistance with the statistical analysis, S. S. Lee from the Scientific Center for Optical and Electron Microscopy (ScopeM), ETH Zürich, for his assistance with epifluorescence microscopy and T. Luzzatto-Knaan from the Department of Marine Biology, University of Haifa, for her useful comments on the manuscript. This research was supported by the European Research Council CoG (VIROCELLSPHERE grant no. 681715) awarded to A.V. and by EMBO Short Term Fellowship (ASTF 601–2015) awarded to G.S.

Author information




G.S. and A.V. conceptualized the project and conceived and designed the experiments. G.S. and A.V. wrote the manuscript. G.S. performed all experiments. N.S. developed the computational analysis of MS data. C.Z. conducted lipid extractions and the LC–MS experiments. R.A.M. and E.J.N.H. conducted the Flow-probe-MS experiments. Y.D. conducted the MALDI-MS experiments. I.R. conducted the GC–MS experiments. D.S. isolated the vesicles and virions for lipidomics analysis. All authors provided useful feedback on the experimental design and comments on the manuscript.

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Correspondence to Assaf Vardi.

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Supplementary Information

Supplementary Figures 1–17 and Supplementary Tables 1–13.

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Supplementary Data

Supplementary Data 1–3: flow-probe-MS and MS/MS analysis of mass features found in four Flowprobe MSI clusters, LC–MS and MS/MS analysis of mass features found in four Flowprobe MSI clusters, LC–MS and MS/MS analysis of additional odd lipids.

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Schleyer, G., Shahaf, N., Ziv, C. et al. In plaque-mass spectrometry imaging of a bloom-forming alga during viral infection reveals a metabolic shift towards odd-chain fatty acid lipids. Nat Microbiol 4, 527–538 (2019).

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