* Several inconsistencies exist between gene, enzyme, reaction databases, and published literature sources regarding the metabolic information of an organism. A reconstruction is a systematic verification and compilation of data from various sources that takes into account all of the discrepancies.
* The combination of relevant metabolic and genomic information of an organism.
* Metabolic comparisons can be performed between various organisms of the same species as well as between different organisms.
* Analysis of synthetic lethality
* Predict adaptive evolution outcomes
* Use in metabolic engineering for high value outputs
Reconstructions and their corresponding models allow the formulation of hypotheses about the presence of certain enzymatic activities and the production of metabolites that can be experimentally tested, complementing the primarily discovery-based approach of traditional microbial biochemistry with hypothesis-driven research. The results these experiments can uncover novel pathways and metabolic activities and decipher between discrepancies in previous experimental data.  Information about the chemical reactions of metabolism and the genetic background of various metabolic properties (sequence to structure to function) can be utilized by genetic engineers to modify organisms to produce high value outputs whether those products be medically relevant like pharmaceuticals; high value chemical intermediates such as terpenoids and isoprenoids; or biotechnological outputs like biofuels, or polyhydroxybutyrates also known as bioplastics.
Metabolic network reconstructions and models are used to understand how an organism or parasite functions inside of the host cell. For example, if the parasite serves to compromise the immune system by lysing macrophages, then the goal of metabolic reconstruction/simulation would be to determine the metabolites that are essential to the organisms proliferation inside of macrophages. If the proliferation cycle is inhibited, then the parasite would not continue to evade the hosts immune system. A reconstruction model serves as a first step to deciphering the complicated mechanisms surrounding disease. These models can also look at the minimal genes necessary for a cell to maintain virulence. The next step would be to use the predictions and postulates generated from a reconstruction model and apply it to discover novel biological functions such as drug-engineering and drug delivery techniques.