Molecular Identification Technology in the Microbial Identification

The advent of the "era of molecular biology" provides a large number of tools and technologies for a series of clinical and research purposes, which are used for bacterial detection, identification, characterization, and typing. Creative Biolabs is a diverse, knowledgeable, and agile company, with a solid leadership universally recognized in the world of live biotherapeutic product (LBP) development. Our mature technology platform and senior scientists have accumulated very deep experience in microbial identification.

Overview of Molecular Technology for Microbial Identification

Molecular techniques have provided unprecedented insights into the identification and typing of bacteria. Most molecular methods of bacterial identification are based on some variation in DNA analysis, either by amplification or sequencing. These methods range from relatively simple methods based on DNA amplification (PCR, real-time PCR, RAPD-PCR) to more complex methods based on restricted fragment analysis, target gene and whole-genome sequencing, and mass spectrometry. While the advantages and limitations of these methods vary, the choice of technique used depends on several factors, including the type of sample, the depth and accuracy of the results produced, resource and cost factors, and the expected turnaround time.

General workflow for the study of new isolates.Fig.1 General workflow for the study of new isolates. (Rivas, 2022)

Molecular Identification Technologies at Creative Biolabs

PCR-based bacterial DNA identification by amplification and sequencing of 16S rRNA genes has become a standard molecular approach, both in the laboratory and in clinical settings. The 16S rRNA gene is highly specific to each bacterial species, which makes it an ideal target for identification.

MALDI-TOF MS has become a potential tool for microbial identification and diagnosis. In the MALDI-TOF MS process, microorganisms are identified using intact cells or cell extracts, which are fast, sensitive, and economical in terms of the labor and cost involved.

PFGE is a technique used for the separation of large DNA molecules by applying to a gel matrix an electric field that periodically changes direction. It may be used for genotyping or genetic fingerprinting. For decades, it is generally considered the gold standard for epidemiological studies of pathogenic microorganisms.

RAPD is a type of PCR, but the segments of DNA that are amplified are random.

MLST is a multi-locus typing technique in molecular biology, which utilizes the DNA sequences of multiple internal fragments of housekeeping genes to characterize isolates of microbial species.

WGS is the process of determining all or nearly all of an organism's genomic DNA sequence in a single time.

Rep-PCR is a new typing method that allows amplification of DNA fragments of different sizes consisting of sequences between repeating elements by using primers complementary to dispersed repeating sequences to distinguish between microorganisms.

In contrast to phenotypic methods, molecular identification and characterization tools are more consistent, fast, reliable, and reproducible, and can even distinguish closely related groups of species that cannot be distinguished based on other phenotypes. Creative Biolabs is a leading provider of custom services with LBP development of over 10 years. Our scientists are highly qualified with extensive experience and exceptional skills in the fields of molecular identification. If you are developing an LBP product and need to identify candidate strains, you can rely entirely on our microbial identification services, please contact us for more.


  1. Rivas, G.A.; et al. Molecular tools for the analysis of the microbiota involved in malolactic fermentation: from microbial diversity to selection of lactic acid bacteria of enological interest. World Journal of Microbiology and Biotechnology. 2022, 38(2): 1-12.

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