TRIDENT Case Card: Spatial Transcriptomics of the Gut Host–Microbiome Interface (Ntekas et al., 2026)

This technical note records a structured TRIDENT case-card analysis of the spatial microbiome study by Ntekas et al. (Nature Microbiology, 2026). The paper introduces an in situ polyadenylation workflow that enables joint host–microbiome spatial transcriptomics on commercial platforms, achieving large increases in microbial RNA recovery and micrometre-scale spatial resolution. The note documents the signal layer reported in the paper (spatial colony structure, species–area scaling with exponent z ≈ 0.47, and tumour–microbiome boundary displacement) and separates it from derived inference layers developed during TRIDENT analysis. These include a dispersion-based colony spacing model, a predicted species–area scale break, and a candidate ecological overlap proxy (f = 1 − 2z) that links the observed scaling exponent to inter-colony genus sharing. All derived elements are explicitly marked as conditional hypotheses and accompanied by dataset-internal falsifiers that can be tested using the published Stereo-seq spatial transcriptomics data. The case card is integrated into the SHRF / TRIDENT corpus under the ECO branch (microscale ecological structure) with a secondary MED cross-reference (tumour–microbiome boundary interactions). Keywords: TRIDENT SHRF spatial transcriptomics microbiome ecology species-area scaling gut microbiome host–microbe interface spatial microbiome ecological scaling Stereo-seq