Decoding Microbes: How to Identify an Unknown Bacterium

Microbes are tiny forms of life that can be found almost everywhere on the planet. These small organisms are a part of our daily lives and can affect our health in many different ways. While many of these microbes are harmless, some can cause serious illnesses, making it vital to understand and identify them accurately. In this article, we will discuss how to identify an unknown bacterium and what steps you can take to determine its strain.

What is a bacterium?

A bacterium is a single-celled microbe that can be found almost everywhere. These microorganisms can come in many different shapes and sizes, with some being responsible for causing diseases while others are important for maintaining the ecosystem.

Why Identify an Unknown Bacterium?

The identification of an unknown bacterium is essential in various fields, including food production, environmental studies, and medicine. A bacterium that causes a disease can only be treated with the correct antibiotic when identified accurately. Similarly, in food production, the presence of a particular bacterium can spoil the entire batch. Identification can help manufacturers prevent such situations from occurring.

Step-By-Step Guide to Identifying an Unknown Bacterium

Step 1: Collecting Samples

The first step in identifying an unknown bacterium is collecting a sample. This sample can be obtained from many different sources, including soil, water, food products, and the human body. It is essential to collect enough material so that there is enough for the testing process. The sample should be collected in a sterile container to prevent contamination from other microorganisms.

Step 2: Growing the Microbe

The next step is to grow the microbe in a laboratory. The sample is inoculated onto a growth medium that contains nutrients, and then incubated under the appropriate temperature and conditions. The colony is then observed and characterized by macroscopic characteristics, including color, size, shape, and elevation.

Step 3: Microscopic Evaluation

The colony is analyzed under the microscope to determine the bacteria’s morphological characteristics. These features include the shape, arrangement, and Gram stain of the cells. Based on these observations, it can be determined whether the bacterium is gram-positive or gram-negative. This information is essential in determining the appropriate antibiotics for treatment.

Step 4: Biochemical Tests

Biochemical tests are conducted to identify different enzymes and metabolic pathways that are characteristic of a particular bacterium. These tests include sugar fermentation, protein hydrolysis, coagulase tests, and many others. The results of these tests can help narrow down the number of potential bacterial strains that have similar morphological and microscopic characteristics.

Step 5: Molecular and Genetic Testing

Molecular and genetic testing are advanced laboratory techniques used to identify bacteria by analyzing their DNA. These tests are more accurate and specific than traditional tests, making them useful in identifying unknown bacteria. These tests can help identify the bacterium down to its species level and determine any antibiotic-resistant genes that it may carry.

Tools Used in Identifying Bacteria


The microscope is a critical tool for identifying bacteria’s morphological characteristics, such as size, shape, and cell arrangement.


The incubator is used to facilitate the growth of bacteria to be studied in controlled conditions. It provides an optimal environment for bacterial growth, including the right temperature, humidity, and atmospheric conditions.

Biochemical Kits

Biochemical assays help identify bacteria by testing their activity levels on different types of chemicals, such as sugars, amino acids, and proteins. Various kits are available in the market for different bacteria strains.

Polymerase Chain Reaction (PCR)

PCR is an essential technique used to amplify and analyze DNA molecules. It is used to identify different genes present in a bacterium by comparing them to known databases.

Factors that Affect Bacterial Identification


Contamination occurs when an unwanted microbe infiltrates the sample and grows alongside the target bacterium. This can result in inaccurate identification, and steps need to be taken to avoid contamination.

Culture Conditions

Culture condition parameters such as temperature, humidity, pH, and atmosphere type affect bacterial growth and can have a direct impact on the target bacterium’s identification process.

Genetic Variations

Genetic variations in bacterial strains arise due to mutations and horizontal gene transfer. These modifications can cause changes in the bacteria’s biochemical characteristics, making them difficult to identify with traditional methods.


Identifying an unknown bacterium is a crucial process in medicine, food production, and environmental studies. The process involves collecting samples, growing the colony, observing and characterizing macroscopic and microscopic characteristics, conducting biochemical tests, and performing molecular and genetic testing.

FAQs About Identifying Unknown Bacteria

  • Q1. What is the most common method for identifying an unknown bacterium?
    • A: The most common method is by using traditional laboratory techniques such as microscopy, staining, and culture identification.
  • Q2. How long does it take to identify an unknown bacterium?
    • A: The process can take anywhere from a few hours to several weeks, depending on the bacteria type and the testing techniques being used.
  • Q3. Can bacterial identification be automated?
    • A: Yes, automation of identification processes has been introduced over the years, and several techniques such as mass spectrometry, biosensors, and DNA sequencing have been automated for fast and accurate results.
  • Q4. Can bacteria change their genetic makeup?
    • A: Yes, bacteria can undergo genetic changes through mutation, horizontal gene transfer, and natural selection, making identification more challenging in some cases.


1. Finn, S., & Condell, O. (2013). Identification of Foodborne Bacterial Pathogens. In New analytical approaches for verifying the origin of food (pp. 53-72). Woodhead Publishing.

2. Janda, J. M. (2016). Recent advances in the identification and management of Vibrio infections. F1000Research, 5, F1000 Faculty Rev-522.

3. Weinberg, Z., & Greenfield, S. (2018). Automated secondary data extraction for bacterial identification using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Scientific reports, 8(1), 1-8.

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