In many cases scientists and health professionals need to identify a microbe in a given environment. Learning the members of a population of microbes present in nature can give us new insights into biochemical processes that are taking place. This leads to a better understanding of environments and the role microbes play in them. Identifying a microbe growing in a patient will identify the disease and the treatments that are effective at eliminating it. Identification tests can also be used to monitor and eliminate microbes present in the food supply, increasing food safety by eliminating pathogens and decreasing spoilage. These are just a few of the many reasons for identifying microbes.
For decades, microbial identification had dependent upon determining the biochemical capacity of the microbe by growing in various test media. These tests probe the metabolic capacity of the strain under study, determining what the microbe could use as a carbon source (fermentation broth), its relationship to oxygen (thioglycollate medium), cell wall structure (Gram stain), and many other properties. Hundreds of media and tests have been developed to help identify microbes. These tests can be fairly accurate, but because many depend upon growth of the microbe, they often require a one day incubation before they can be read. This can be a serious detriment, especially in the food and health field, rapid diagnosis is especially critical.
A search for more rapid methods lead to the development of tests based on antibodies and DNA methods. Antibody methods depend upon the reaction of a specially prepared antibody against an antigen that is unique to the target microbe. The most common DNA methods utilize the short DNA sequences called primers that hybridize to distinct sequences in the target microbe. The primers are then used as a template in PCR reactions, producing a detectible PCR fragment, that indicated the presence of the target microbe. Antibody and DNA-based methods are more rapid than classic biochemical tests, but they tend to be specialized for the presence of specific microbes.
Due to the large body of information that has been gathered on most cultured micorbes, it is now possible to design a set of tests to determine the identity of almost any microbe.