The pregnane X receptor (PXR) and constitutive androstane receptor (CAR) are important xenobiotic-sensing nuclear receptors, and their genetic polymorphisms are known to alter the pharmacokinetics of various xenobiotics. The gut microbiome is increasingly recognized as a critical modifier of host xenobiotic biotransformation, and microbial metabolites such as lithocholic acid and indole-3-propionic acid are known endogenous PXR activators. We have previously demonstrated that the gut microbiome is necessary for maintaining the constitutive expression of certain PXR- and CAR-target genes, and pharmacological activation of PXR and CAR produces gut dysbiosis and reduces secondary bile acids. However, little is known regarding to what extent PXR and CAR under basal conditions influence the gut microbiome. To fill this knowledge gap, we examined the gut microbiome compositions under three different settings: 1) two mouse strains that express different basal levels of PXR and CAR (C57BL/6J that expresses lower PXR and CAR vs FVB/NJ that expresses higher PXR and CAR); 2) wild type (WT), PXR-null, CAR-null, and PXR-CAR-double null mice; and 3) mice that carry either mouse (m) or human (h) PXR genes. 24h fecal samples were collected from these mice at adolescent (30-day-old) and adult (60-day-old) ages of both genders. 16S rDNA sequencing was performed by amplifying the hypervariable V4 region (n=5 per group). Compared to C57BL/6J mice, FVB/NJ mice had higher richness in gut microbiome in both ages and genders, and had higher percentages of certain pro-inflammatory bacteria. This correlated with higher pro-inflammatory cytokines in feces of FVB/NJ mice (cytokine array). The absence of PXR or CAR markedly increased the richness of gut microbiome, and the absence of both receptors had the highest richness of gut microbiome of both ages and genders. Most notably, the PXR-CAR-double null mice had higher percentages of the Lactobacillus genus, which is known to carry bile salt hydrolase (BSH) activities, and this corresponded to a decrease in most taurine conjugated bile acids (BAs) in feces (LC-MS). PXR-CAR-double null mice also had higher acetic acid in feces of adolescent males, and C10 in feces of adult males (GC-MS). Compared to WT mice that carry mPXR, hPXR-transgenic (TG) mice had higher Prevotella genus. In addition, there was an apparent increase in several unconjugated 12-OH BAs as well as ursodeoxycholic acid (UDCA), but an apparent decrease in several 6-OH BAs, in feces of hPXR-TG mice. hPXR-TG mice also had higher propionic acid in males, as well as lower 2-methylbutyric acid in both genders. In conclusion, the present study is among the first to show that the host genotypes of the major xenobiotic-sensing nuclear receptors PXR and CAR profoundly influence the composition and metabolites of the gut microbiome, and the basal levels of PXR and CAR may act through gut microbiome to modulate host diseases such as inflammation and metabolic syndrome.