Advances in bacterial identification and characterization: methods and applications

Document Type : Review Paper


1 Department of biochemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran

2 Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran, Iran

3 Department of Biochemistry, Faculty of biological sciences, Tarbiat Modares University, Tehran, Iran

4 Bioprocess Engineering Research Group; Institute of Industrial and Environmental Biotechnology (IIEB); National Institute of. Genetic Engineering and. Biotechnology


Characterization and identification of bacteria and microorganisms are crucial in several fields such as medical, agricultural, and industrial microbiology. Conventional phenotype-based identification methods use low-precision scoring systems and therefore are affected by species phenotypic variations. These methods have low levels of reproducibility, which results in a decrease in the accuracy coefficient. Furthermore, conventional phenotype-based identification techniques include several methods, such as observation of growth and colony morphology, biochemical characterization, and conventional available biochemical methods, that are less accurate. Molecular-based methods have better strategies to identify and characterize microorganisms and bacteria. The development of molecular-based techniques has improved our ability to identify bacterial species in culture-dependent and culture-independent samples. Most of these techniques are only capable of identifying single bacterial strains or small groups of organisms at a time. However, some methods can be used to identify and characterize the bacterial communities in a range of hundreds to thousands of single strains. We also know that each of these methods has weaknesses and shortcomings that limit their application and usability. However, some of these methods have the strengths and potentials to improve conventional methods and to compensate for their shortcomings. In the present review, we highlighted recent progress in the field of bacterial characterization and identification using molecular-based techniques and discussed their abilities and limitations.