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bioRxiv · 10.64898/2026.07.02.735997

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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Abstract

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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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.. 2026-07-03. Accessible spatial host-microbe profiling in tumour tissues. https://doi.org/10.64898/2026.07.02.735997

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