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Spatial metaTranscriptomics resolves host-bacteria-fungi interactomes

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Ashkenazy,  H       
Department Molecular Biology, Max Planck Institute for Biology Tübingen, Max Planck Society;

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Carlos,  V
Department Molecular Biology, Max Planck Institute for Biology Tübingen, Max Planck Society;

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Weigel,  D       
Department Molecular Biology, Max Planck Institute for Biology Tübingen, Max Planck Society;

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Citation

Saarenpää, S., Shalev, O., Ashkenazy, H., Carlos, V., Lundberg, D., Weigel, D., et al. (2023). Spatial metaTranscriptomics resolves host-bacteria-fungi interactomes. Poster presented at Science Summit 2023: Genomics of Biodiversity and Evolution, Stockholm, Sweden.


Cite as: https://hdl.handle.net/21.11116/0000-000F-6E90-3
Abstract
Microbial diversity forms complex interaction networks with the host. Despite the recent advances in infection biology to study the host response and quantify microbes, we lack a comprehensive understanding of the microbial diversity at the spatial scale and the impact of these microbial taxa on host gene expression. To fill this gap, we present Spatial metaTranscriptomics (SmT), a sequencing-based technology that leverages 16S-18S/ ITS-poly-d(T) multimodal arrays for simultaneous host transcriptome- and microbiome- wide characterization of tissues at 55-μm resolution. We showcase SmT on Arabidopsis thaliana leaves to study the spatial microbial distributions and the associated host response identifying 1,376 and 1,159 unique bacterial and fungal taxa, respectively. We unveiled leaf-scale spatial microbial hotspots and uncovered that the spatial distribution of microbes consistently drives their interactions. SmT demonstrates the feasibility of studying spatially resolved host-pathogen interactions and microbial diversity elucidating complex infection processes where the spatial context is key for understanding infection processes.