Spatial Meta-transcriptomes of human and murine intestines

Abstract

We developed an analysis pipeline that can extract microbial sequences from Spatial Transcriptomic data and assign taxonomic labels to them, generating a spatial microbial abundance matrix in addition to the default host expression one, enabling simultaneous analysis of host expression and microbial distribution. We applied it on both human and murine intestinal datasets and validated the spatial microbial abundance information with alternative assays. Finally, we present a few biological insights that can be gained from this novel data. In summary, this proof of concept work demonstrated the feasibility of Spatial Meta-transcriptomic analysis, and pave the way for future experimental optimization.