Microbial Identification Methods

Live biotherapeutic products (LBP) may contain commensal microorganisms isolated from a human host and/or recombinant microorganisms. Phenotypic and genotypic characterizations are critical components used to arrive at an informed assessment of LBP safety. Creative Biolabs offers well-established and innovative One-Stop-Shop LBP solutions. We can apply our considerable experience with microbial identification to develop the necessary analytics for your product.

The Necessity of Microbial Identification for LBPs

According to FDA regulations, all LBP applications must include a "description of the drug substance", including the biological name and strain designations; the source of cells from which the drug substance was derived; the culture/passage history of the strains; a description of the clinical health of the donor; a summary of the phenotype and genotype of the product strains; and documentation and summary of modifications. Complete "characterization" of an LBP must also be provided. This comprehensive list includes methods for detection and identification, antibiotic resistance, methods used and a justification for any genetic manipulation, and any support for a mechanism of action.

Traditional Microbial Identification

There are several methods for routine microbial identification in clinical and research microbiology laboratories, but microbiologists have continuously pursued efficient systems for microorganism identification. These methods are mainly determined according to the morphological and biochemical characteristics of the colonies. For example, bacterial colony morphology can be evaluated under defined growth conditions to show hemolytic capacity, by Gram staining, and by examining growth performance on selective media that allow only specific bacteria to multiply, the potential to ferment sugars, specific biochemical reactions, metabolic characteristics, antigenic and pathogenic capacity, and antibiotic susceptibility. Microscopy is frequently used to characterize microorganisms, and there are two main microscopic techniques: light microscopy and electron microscopy.

The traditional bacterial identification.Fig.1 The traditional bacterial identification. (Braga, 2013)

The Common Microbial Identification Methods

The isolation, purification, and identification of bacteria is the first step in bacteriology. Isolation is to obtain pure bacterial cultures. Obtaining pure culture is the first step in bacterial identification. Bacterial isolates can be conventionally identified based on their morphological, biochemical, and physiological characteristics. If identification is required at the species level, further biochemical characterization must be performed. The results of these tests are compared with established taxon or identification schemes.

Methods to identify microorganisms.Fig.2 Methods to identify microorganisms. (Franco, 2019)

Gram staining is a fast and easy-to-learn laboratory technique. It is one of the most important staining techniques in microbiology. The advantages of this method, especially the addition of wet mounts, suggest that the use of Gram staining may be of great use in the clinical field.

Biochemical methods for the identification of microorganisms species are now widely used and, in some cases, essential for species diagnosis. Phenotypic identification methods usually incorporate reactions to different chemicals. Phenotypic identification methods usually include reactions to different chemicals. One of the most commonly used traditional methods is simply to visually measure the growth of the organisms under test in the presence of a substrate that increases turbidity.

The advent of the "Era of Molecular Biology” has provided a wide range of tools and techniques for the detection, identification, characterization, and typing of bacteria for a range of clinical and research purposes. Molecular techniques have provided unprecedented insights into the identification and typing of bacteria.

The combined use of phenotypic, biochemical, and genotypic methods for microbial identification is referred to as a "polyphasic approach". The polyphasic approach is a recent trend in microbial taxonomy, which provides a natural and authentic system of classification of microbes.

Accurate identification of microorganisms is crucial for scientists in many fields of applied research and industry, from clinical microbiology to food production. At Creative Biolabs, we team up with you to understand your needs and develop customized services to your satisfaction. If you are interested in our microbial identification services, please contact us for more information.


  1. Braga, P.A.C.; et al. Bacterial identification: from the agar plate to the mass spectrometer. RSC advances. 2013, 3(4): 994-1008.
  2. Franco, D.R.; et al. Advances in chemical and biological methods to identify microorganisms-from past to present. Microorganisms. 2019, 7(5): 130.

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