Intestinal transcriptomes and microbiota of mice with loss of MHCII on intestinal epithelial cells.

The study goals were to determine how the loss of MHCII function (using H2-Ab1 conditional deletion) impacts intestinal microbiota and immune cell functions. Targeted 16S rRNA gene sequencing was used for assessing intestinal and fecal bacteria in WT mice and mice lacking H2-Ab1 on intestinal epithelial cells (IECs). Bulk tissue RNAseq, sorted intestinal epithelial cell RNAseq, and single-cell RNAseq of CD45+ small intestine lamina propria cells were used to assess host differences.