DNA Extraction From Microbial Pure Cultures

High-quality DNA extraction is crucial for any microbial genome sequencing project. The mature industry of commercial DNA extraction kit offers a wide range of options. We utilize the most reputable and cost-effective DNA extraction kits, prioritizing both performance and affordability.

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Table of Contents

Key Specs
  • A complete workflow from cell chemical/physical disruption to enzyme or beads-based DNA purification.

  • Working on various microorganisms, including gram-positive and negative bacteria, yeast, fungi, etc, either in liquid media or on agar plates.

  • Carried out in mBioWorks’ Copenhagen Laboratory, either manually or with an automatic nucleotide acid extractor. Visits are welcome.

Microbial Pure Cultures
Sample Requirements
Agar plates: 

Colonies should be easily visible and cover > 20% of the surface area on a standard-size petri dish (⌀ 90mm); the agar should not dry out and maintain a good texture for easy collection of cells with a standard sterile loop used in microbiology laboratories.


Bacterial pellets should be placed in a 1.5 mL or 2 mL centrifuge tube. The size of the pellet shall not be less than that generated by centrifuging 2 mL of E. coli cultures grown in LB overnight at 37 °C, typically covering a round area of ⌀3-5 mm.

Liquid cultures: 

Enough cells in the liquid media shall be ensured by measuring OD600. Typically, 1 mL of cloudy cultures is good enough for multiple extractions.


There are several commonly used methods for DNA extraction from microbial or environmental samples. These methods are designed to be user-friendly and efficient, generating high-quality DNA for downstream applications. 


Phenol-chloroform extraction:

This traditional method relies on the differential solubility of DNA in aqueous and organic phases. The bacterial culture is first lysed using enzymes, heat, or detergents, releasing the DNA. Then, a mixture of phenol, chloroform, and isoamyl alcohol is added, followed by centrifugation to separate the aqueous (upper) and organic (lower) phases. DNA remains in the aqueous phase, while proteins and other cellular debris move into the organic phase. The DNA is then precipitated using ethanol or isopropanol, washed, and dissolved in an appropriate buffer.


  • Well-established method
  • Yields high-quality DNA


  • Labor-intensive
  • Involves hazardous chemicals
Silica membrane-based column extraction:

In this method, bacterial cells are lysed using a combination of enzymatic and chemical treatments. The resulting lysate is then mixed with a chaotropic salt, which helps the DNA bind to a silica membrane in a spin column. The silica membrane selectively binds DNA when the lysate is passed through the column. After washing away contaminants, the DNA is eluted using a low-salt buffer or water.

The ability of DNA to bind to silica surfaces is due to the negatively charged phosphate backbone of the DNA molecule, which forms ionic interactions with the positively charged silica surface. The presence of chaotropic salts helps facilitate this binding by disrupting the hydration shell of both DNA and silica, enhancing their interaction.


  • Simple and fast
  • Yields high-quality DNA
  • Doesn’t require hazardous chemicals


  • Can be less efficient for certain samples (e.g., high GC content)
Magnetic bead-based extraction:

This method also relies on chaotropic salts for lysing bacterial cells and liberating DNA. The DNA then binds to magnetic beads in the presence of a chaotropic salt. The bead-bound DNA is separated from contaminants using a magnetic separator. After washing, the purified DNA is eluted in a low-salt buffer or water.

The principle of DNA binding to magnetic beads is similar to that of silica membrane-based extraction. Magnetic beads are coated with functional groups that can interact with the negatively charged phosphate backbone of DNA molecules. The presence of chaotropic salts enhances the binding by disrupting the hydration shell of DNA and the coated magnetic beads.


  • Highly scalable (suitable for high-throughput applications)
  • Yields high-quality DNA
  • Doesn’t require hazardous chemicals


  • Requires specialized equipment (magnetic separator)


In summary, the phenol-chloroform method is a traditional approach for DNA extraction but involves hazardous chemicals and is labour-intensive. Silica membrane-based column extraction and magnetic bead-based extraction are more user-friendly and safer alternatives, with both methods providing high-quality DNA. The choice between these methods depends on factors like sample type, desired throughput, and available equipment. At mBioWorks, we use either silica membrane or magnetic bead-based method depending on a specific project.

Key Equipment

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