Nature aggregates granular materials such as sand, silt and clay into form beach rocks, anthills and other forms of microbialites. A common bio-geo-chemical cementation occurs due to the mineralization of calcium through bacterial enzymatic action, often called Microbial Induced Calcium Carbonate Precipitation (MICP). Unlike engineered cement, which consumes very high amounts of energy and emits large quantities of CO2, this natural cementation occurs in ambient conditions, with negligible energy consumption. Hence, it is a sustainable construction method. Natural cementation is a gradual process, where grains are initially bonded to form clumps. The clumps grow in size to form aggregates, finally creating free standing columns. Numerical models of the mechanical behaviors of cemented grains at the various stages of aggregation offer a way to explore and understand this process. In this paper, we propose a discrete element method (DEM) of aggregated granular materials formed due to MICP. The model is applied to study different levels of aggregation of sand, from sand heaps involving unbonded and bonded grains to free standing columns. The results are compared against experiments and the most important parameters are discussed.