From microbes to molecules: unveiling host-microbe interactions with spatial metabolomics

Spatial metabolomics is transforming our understanding of microbial systems by uncovering the localized molecular dynamics within complex microbial communities. By using advanced mass spectrometry imaging techniques, researchers can now visualize metabolites at the micron scale and show how microbes interact, form biofilms, and influence their environments at unprecedented levels of detail. These approaches not only provide molecular insights they also highlight the need of integrating activity measurements and temporal analyses to capture the dynamic nature of microbial assemblages. Incorporating these dimensions in future will enable a deeper understanding of microbial interactions over time, bridging the gap between static snapshots and the evolving processes that drive microbial ecosystems. This commentary explores important aspects in microbial spatial metabolomics, underscores the need for activity and time-resolved studies, and advocates for a deeper exploration of microbial systems to advance chemical ecological concepts, host–microbe interactions, and metabolic mechanisms in microbial communities.