Accessible spatial host-microbe profiling in tumour tissues

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.