The Gut Microbiota Modulates Gene Expression in the Kidney.

Gut microbiota are a diverse array of commensal bacteria in the intestinal lumen, and shifts in the composition of gut microbes can influence host health. We have previously established a link between the gut microbiota and host kidney function by showing that gut microbial metabolites can activate G protein-coupled receptors in the kidney. Although host-microbiome interactions have been studied at the signaling level, the influence of gut microbes on gene expression at the transcriptional level is unclear. Evidence demonstrates that gut microbiota alters gene transcription in the colon (J. Allen, Genome Medicine, 2019); however, it is entirely unknown whether gut microbiota influences host gene expression at distal sites, such as the kidney. To address this question for the first time, we utilized an unbiased RNA sequencing (RNASeq) approach to compare gene expression in the kidneys of male and female mice which were either germ-free (GF; without gut microbes) or conventionalized (Conv; with gut microbes). All mice were born on a C57Bl/6 background and housed in the Johns Hopkins GF facility. At four weeks of age, a subset of mice (n=5 males, n=5 females) were conventionalized via oral gavage using a fecal slurry of mixed stool from age-matched specific-pathogen free (SPF) mice (n=3 males, n=3 females); whereas an additional cohort of mice (n=5 males, n=5 females) were maintained as GF. Eight weeks after conventionalization both GF and Conv mice were sacrificed, whole kidneys were processed for RNASeq, and fecal pellets from Conv mice were collected for 16S rRNA sequencing. For RNASeq analysis, differentially expressed genes (DEGs) were defined as having a log2fold change ≥ ± 0.5 and base mean ≥ 15 (the average of the normalized count values, dividing by size factors, taken over all samples). We identified a clear effect of the gut microbiota on renal gene expression: 578 DEGs between GF and Conv males, and 340 DEGs between GF and Conv females. Only 73 of these DEGs were common to both males and females. These data demonstrate that the gut microbiota not only impacts gene expression in the kidney, but does so in a sex-specific manner. In addition, 16S rRNA sequencing showed no differences in bacterial colonization between male and female Conv mice, establishing that the renal transcriptomic differences are not a consequence of differing gut microbes; rather, the same microbes have differential effects in males and females, presumably through differences in either signals (i.e., microbial metabolites), or differences in host responses. Furthermore, DAVID pathway analysis revealed that DEGs are involved in pathways including aldosterone synthesis and secretion, mineral absorption, proximal tubule bicarbonate reclamation, and vasopressin-regulated water reabsorption. In sum, we demonstrate that the gut microbiota influences kidney gene expression in a sex-specific manner, and that these transcriptional changes are poised to impact kidney physiology and regulation. We are now working to identify physiologically relevant signals from the microbiome and/or host that mediate these sex-specific differences, and to determine how they influence renal function.