Single-cell Stereo-seq reveals the effects of microorganisms on immunity and metabolism in mouse liver

The sterile environment may lead to liver phenotype or function alterations, but there is a lack of systematic studies on this aspect. Therefore, this study utilized a new spatial enhanced resolution omics-sequencing (Stereo-seq) to construct spatial transcriptome (ST) profiles of germ-free (GF) and specific pathogen-free (SPF) mice liver. Combined spatial transcriptomic, single-cell transcriptomic, and metabolomic analyses identified defects in the immune system and altered fatty acid and steroid metabolic processes in the livers of GF mice at a subcellular resolution. Contribute to the understanding of the interactions between host and microbiota.