Accessible spatial host-microbe profiling in tumour tissues
Wan, Y. K.; Ng, A.; Tham, J. Y.; Li, B.; Lim, M. G. K.; Tan, I. B. H.; Prabhakar, S.; Nagarajan, N.; Yeo, G. H. T.; Chia, M.
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The ability of current spatial transcriptomics platforms to sensitively and specifically detect tissue-resident microbes alongside the whole host transcriptome remains limited. Here we present HOst MicrobE Spatial-seq (HOMES-seq), a Visium-based workflow for joint spatial profiling of microbial species and the host transcriptome in formalin-fixed paraffin-embedded (FFPE) colorectal tumours. HOMES-seq incorporates an analytical framework to distinguish contaminant-derived signals from bona fide tissue-resident microbes while improving detection sensitivity and reducing sequencing costs relative to existing approaches.
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