We show that spin-orbit coupling (SOC) significantly enhances the depletion of a homogeneous Bose-Einstein condensate in three dimensions. With decreasing anisotropy of the SOC, both the quantum and thermal depletion increase. In particular, different types of SOC give rise to qualitatively different dependences of the condensate depletion on microscopic variables including the scattering length, the strength of the SOC, and the temperature, which can be directly observed once these types of SOC are realized in experiments. Moreover, we point out that thermal depletion in three dimensions becomes logarithmically divergent at any given finite temperature when both the SOC and the interaction approach the isotropic limit.

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