GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE289nnn/GSE289589/primaryOK200TranscriptomicsMus musculusExpression profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE289589GEOGSEfalseIndigenous gut microbes modulate neural cell state and neurodegenerative disease susceptibility [snRNA-seq]The native microbiome influences a plethora of host processes, including neurological function. However, its impacts on diverse brain cell types remains poorly understood. Here, we performed single nucleus RNA sequencing on hippocampi from wildtype, germ-free mice and reveal the microbiome-dependent transcriptional landscape across all major neural cell types. We found conserved impacts on key adaptive immune and neurodegenerative transcriptional pathways, underscoring the microbiome’s contributions to disease-relevant processes. In addition, mono-colonization with Escherichia coli was found to induce a distinct adaptive immune and neurogenerative disease-associated cell state, suggesting increased disease susceptibility.2026/02/03GSE289589GSM8794711GSM8794712GSM8794713GSM8794714GSM8794715GSM8794716GSM8794717GSM879471834290289589Mus musculus