Agent based modeling uses interacting agents and a governing rule to understand a complex phenomenon. It is an important mode of inquiry in the field of life sciences. For this paper a Haploid Evolutionary Constructor (HEC) tool was used for modeling and simulation of two sample models. The model samples were analyzed under the same and varying level of specific and non-specific substrates. In the first part of each experiment, the survival rate of the models was examined based on the model’s inputs and outputs. However, since close association of microbes enhances the probability of Horizontal Gene Transfer (HGT) between organisms, HGT behavior was introduced within the populations in the second sets of experiments. This enabled them to adapt to dwindling resources in their environment and creation of new populations that are better suited for the ecosystem. Based on the obtained results, the behavior of the dominant population(s) is assessed.