Metabolites consumed and produced by microorganisms for mass and energy conservation may cause changes in a microorganism’s environment. The microorganisms are unable to tolerate a particular environment for a long period. They may leave their old existence to find a new environment to sustain life. Essentially, organisms need to maintain their metabolic processes to survive in the new environment. Limitations of experimental studies to explore cell functions and regulations in detail result in insufficient information to explain processes of metabolic expressions under environments of organisms. Consequently, mathematical modeling and computer simulations have been conducted to combine all possible cellular metabolic fluxes into single or multiple connected networks. Metabolic modeling based on linear programming (LP) subjected to constraints with an optimization approach is often applied metabolic reconstruction. The LP objective function is maximized to obtain an optimal value of biomass flux. Optimal solutions in LP problems can be used to explain how metabolites function in metabolic reactions. As an LP problem may have many optimal solutions, this study proposes a method for enumerating all alternate optimal solutions to evaluate important reactions of metabolic pathways in microorganisms. The algorithm for generating alternate optimal solutions is implemented in MetModelGUI, a Java-based software for creating and analyzing metabolic reconstructions. The algorithm is applied to models of five microorganisms: Trypanosoma cruzi, Thermobifida fusca, Helicobacter pylori, Cryptococcus neoformans and Clostridium thermocellum. The results are analyzed using principal component analysis, and insight into the essential and non-essential pathways for each organism is derived