The gut microbiota is complex ecosystem, which has a crucial role in maintaining the host well-being. Colonization of the gastrointestinal track is initiated at birth, with the exposure to maternal microorganisms, developing to highly diverse microbial populations in adults. Various factors influence individual’s microbiome including host physiology, environment and host genetics. The gut microflora mostly composed of the bacterial domain; however, it contains also members of the eukaryotic domain, which was left relatively unexplored. Thus, here we study the effect of the host genotype on the gut eukaryotic communities in a murine model. Total DNA was extracted from feces of BALB/c and C57BL mouse lines and their F1 reciprocal offspring, at different ages. Automated-Ribosomal-Intergenic-Spacer-Analysis (ARISA) of eukaryotic conserved rDNA sequences revealed different flora patterns between the two mouse lines. This significant variation is a result of either presence of diverse eukaryotic organisms and/or different distribution of the same organisms between the lines. Comparison within lines revealed that the age, as well as the cage has no significant effect on the eukaryotic population supporting the role of host’s genetic in determining gut microflora. Furthermore, both reciprocal F1 hybrids present similar flora patterns but different from that of the parental lines. Our findings suggest that mouse genetics has a major effect on the eukaryotic composition in the murine gut, rather than maternal inoculation. Finally, exploring and understanding the gut eukaryotic diversity can provide new insights on the role of this domain and complete the picture of the microbial communities inhabiting the gut.
