Identification of unknown microbe species is important in various applications, such as disease diagnosis and infection treatment in the health industry, criminal investigation, environmental studies or inoculum preparation in the wine and brewing industry. Microbe identification can be performed with several methods, as follows:
Colony morphology identification. Each microorganism has a distinct characteristic when grown on certain media agar in Petri dish.
Bacteria shape can be identified under the microscope.
形态学identification
In morphology identification, gross and microscopic morphology are examined to determine the species of the microbe of interest. Gross morphology includes colony shape, size, color and surface features. Using a microscope, one can also determine the shape of the microorganisms. But the, morphology identification method exhibits some drawbacks, since it can be used only for organisms that can be cultivatedin vitro.
Saccharomyces cerevisiaeColony morphology on Sabouraud dextrose agar: cream colored and smooth.
Microscopic morphology: large, globose to ellipsoidal budding yeast-like cells.
LactobacillusColony morphology:Circular form and entire margin.
Microscopic morphology:Gram positive rod.
Biochemical tests
形态学identification has some limitations, making it less specific. Closely related organisms can be differentiated using a series of biochemical tests that identify various metabolic properties of different bacterial species. Biochemical tests that have been used to identify bacteria as follows:
Table 1. Biochemical tests
| Biochemical Test | Function | |
|---|---|---|
| 能动性 | Identifies the bacteria's ability to move (flagellated cell) | |
| Oxidase | Demonstrates the bacteria's ability to produce cytochrome-c oxidase, hence the capability of reducing oxygen | |
| Glucose Fermentation | Determines the ability of a bacterium to ferment the sugar glucose, and to convert pyruvic acid into gaseous by products. | |
| Nitrate | Determines the ability of a bacterium to produce the enzyme nitratase, hence its capability of converting nitrate into nitrite | |
| Fluid Thioglycollate | Shows oxygen usage | |
| Urea | Determines the ability of a bacterium to produce the enzyme urease, hence its capability of hydrolyzing urea. | |
| 胰蛋白胨肉汤/吲哚 | Determines the ability of a bacterium to produce the enzyme tryptophanase. | |
| MR-Methyl Red | Indicator of low pH. Determines the fermentation ability of bacteria. | |
| VP- Voges Proskauer | Determines the ability of a bacterium to produce acetoin. | |
| Simmons citrate slant | Demonstrates the ability of Gram-negative bacteria to use citrate as an energy source. |
Molecular Methods
The classical methods of microbe identification are relatively laborious. Identification using the molecular method has greatly improved the speed and specificity of the identification process. In this method, nucleic acid sequences (DNA and RNA) from unknown species and known species (from a database) are compared to determine their similarities. Basically, there are two types of identification using the molecular method:
Genotypic methodsThis methods involves extraction of genomic DNA from an unknown microbe species, which is further analysed with Southern blot, Polymerase chain reaction (PCR), or Restriction Fragment Length Polymorphism (RFLP).
Protein-based methodsThis method includes Western blot, Immuno-precipitation and Enzyme Linked Immuno-sorbant Assay (ELISA), which use antibodies to detect specific proteins that are unique to an organism.