Recently [1,2], we argued that a particular model of string-inspired quantum space-time foam (D-foam) may induce oscillations and mixing among flavoured particles. As a result, rather than the mass-eigenstate vacuum, the correct ground state to describe the underlying dynamics is the flavour vacuum, proposed some time ago by Blasone and Vitiello as a description of quantum field theories with mixing. At the microscopic level, the breaking of target-space supersymmetry is induced in our space-time foam model by the relative transverse motion of brane defects. Motivated by these results, we show that the flavour vacuum, introduced through an inequivalent representation of the canonical (anti-) commutation relations, provides a vehicle for the breaking of supersymmetry (SUSY) at a low-energy effective field theory level; on considering the flavour-vacuum expectation value of the energy-momentum tensor and comparing with the form of a perfect relativistic fluid, it is found that the bosonic sector contributes as dark energy while the fermion contribution is like dust. This indicates a strong and novel breaking of SUSY, of a non-perturbative nature, which may characterize the low energy field theory of certain quantum gravity models.