SmT/SHM-seq: simultaneously capturing spatial transcriptome and microbiome information in plants

Spatial metatranscriptomics (SmT) and spatial host-microbiome sequencing (SHM-seq) techniques provide spatial distribution information of microorganisms on plant microstructures. SmT technology uses strategies 1 and 3 with a resolution of 55 μm, while SHM-seq employs strategy 2 with a resolution of 100 μm. Strategy 1 extracts microbial sequences from original spatial transcriptome data to create host expression and spatial microbial abundance matrices through bioinformatics analysis. Strategy 2 captures variable regions of host transcripts and 16S bacterial ribosomal RNA by integrating a 16S probe into the spatial capture area. Strategy 3 employs a multimodal array of probes [16S, 18S, internal transcribed spacer (ITS), and poly-d(T)] to capture host transcriptome expression data along with bacterial and fungal abundance.