Commensal Microbiota Regulate Renal Gene Expression

The gut microbiome impacts host gene expression not only in the colon, but also at distal sites including liver, white adipose tissue, and spleen. The gut microbiome also influences the kidney and is associated with renal diseases and pathologies; however, a role for the gut microbiome to modulate renal gene expression has not been examined. To determine if microbes modulate renal gene expression, we used whole-organ RNA sequencing (RNA-Seq) to compare gene expression in C57Bl/6 mice that are germ-free (lacking gut microbiota) versus conventionalized (with gut microbiota). 16S sequencing showed that males and females were similarly conventionalized, although Verrucomicrobia was higher in male mice. We find that renal gene expression is differentially regulated in the presence versus absence of microbiota, and that these changes are largely sex-specific. Although microbes also influence gene expression in the liver and large intestine, most differentially expressed genes (DEGs) in the kidney are not similarly regulated in the liver or large intestine. This demonstrates that the influence of the gut microbiota on gene expression is tissue specific. However, a minority of genes (n=4 in males, n=6 in females) were similarly regulated in all three tissues examined, including genes associated with circadian rhythm (Per1 in males and Per2 in females) and metal binding (Mt1 and Mt2 in both males and females). Finally, using a previously published single cell RNA-Seq (scRNA-Seq) dataset, we assigned a subset of DEGs to specific kidney cell types, revealing clustering of DEGs by cell type and/or sex. NEW & NOTEWORTHY It is unknown whether the microbiome influences host gene expression in the kidney. Here, we utilize an unbiased, bulk RNA-Seq approach to compare gene expression in the kidneys of male and female mice with or without gut microbiota, as well as in liver and large intestine. This report demonstrates that renal gene expression is modulated by the microbiome in a sex- and tissue-specific manner.