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Biological microorganisms and artificial micro-swimmers often locomote in heterogeneous viscous environments consisting of networks of obstacles embedded into viscous fluid media. In this work, we use the squirmer model and present a numerical investigation of the effects of shape on swimming in a heterogeneous medium. Specifically, we analyse the microorganism's propulsion speed as well as its energetic cost and swimming efficiency. The analysis allows us to probe the general characteristics of swimming in a heterogeneous viscous environment in comparison with the case of a purely viscous fluid. We found that a spheroidal microorganism always propels faster, expends less energy and is more efficient than a spherical microorganism in either a homogeneous fluid or a heterogeneous medium. Moreover, we determined that above a critical eccentricity, a spheroidal microorganism in a heterogeneous medium can swim faster than a spherical microorganism in a homogeneous fluid. Based on an analysis of the forces acting on the squirmer, we offer an explanation for the decrease in the squirmer's speed observed in heterogeneous media compared with homogeneous fluids.