The gut microbiota affects host lipid metabolism and is considered an environmental factor that contributes to development of obesity. To investigate whether the gut microbiota affects the eye lipidome, we performed comprehensive lipidomic profiling of lens and retina from conventionally raised and germ-free mice. Conventionally raised mice had diminished phosphatidylcholines in the lens and elevated ethanolamine plasmalogens in the retina. Diminishment of lens phosphatidylcholines in the presence of gut microbiota suggests that the conventionally raised mice are exposed over time to more oxidative stress than germ-free mice. Consistent with this, their lifespan is also shorter. Our findings may open a new area of investigation how modulation of gut microbiota affects the eye health.