Indigenous gut microbes modulate neural cell state and neurodegenerative disease susceptibility [mono-colonized_RNA-seq]

The native microbiome influences a plethora of host processes, including neuroimmune function. However, the consequences of individual gut microbes on neuroinflammatory tone remain largely unexplored. In the present dataset, we investigated the consequences of four bacterial type strains representing prevalent genera within the mammalian gut microbiome (Bacteroides thetaiotaomicron (B. theta), Clostridium celatum, Lactobacillus johnsonii, and Escherichia coli) on the transcriptional profile of CD11b+ brain myeloid cells. After 2 weeks of mono-colonization with the bacteria species of interest, it was found that each bacterial type had distinct effects on brain myeloid cell gene expression, highlighting the bacterial dependent consequences of the microbiome for neuroinflammatory outcomes. Overall design: Germ-free DBA/2NTac were either maintained as germ-free or mono-colonized with Bacteroides thetaiotaomicron, Clostridium celatum, Lactobacillus johnsonii, or Escherichia coli for 2 weeks. Brains were then perfused with PBS and CD11b+ cells were isolated by magnetic activated cell sorting for bulk RNA-seq.