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DNA Isolation

DNA Isolation

DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...

DNA Isolation

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Updated: Jun 5, 2026

Collection and Extraction of Saliva DNA for Next Generation Sequencing

Collection and Extraction of Saliva DNA for Next Generation Sequencing

Published on: August 27, 2014

Effect of saliva processing on bacterial DNA extraction.

Kamila Polgárová¹, Michal Behuliak, Peter Celec

¹Institute of Pathophysiology, Faculty of Medicine, Comenius University, Bratislava, Slovak Republic. kamila.polgarova@gmail.com

The New Microbiologica

|January 11, 2011

Summary

Optimizing bacterial DNA extraction from saliva is crucial for understanding oral microbiome and disease. Fresh saliva and specific methods like benzyl chloride or Chelex-100 yield the best results for molecular analysis.

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Last Updated: Jun 5, 2026

Collection and Extraction of Saliva DNA for Next Generation Sequencing

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Published on: August 27, 2014

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Area of Science:

Microbiology
Molecular Biology
Genomics

Background:

The human oral cavity harbors over 700 bacterial species, forming a complex microbial community.
Alterations in this oral microbiome are linked to various oral diseases, necessitating detailed study.
Molecular techniques, particularly PCR-based methods, are preferred for analyzing unculturable oral bacteria.

Purpose of the Study:

To investigate the impact of saliva sample processing on bacterial DNA extraction efficiency.
To compare the effectiveness of different non-commercial DNA isolation procedures for salivary microbial DNA.

Main Methods:

Bacterial chromosomal DNA was extracted from three saliva matrices: fresh, diluted, and pelleted.
Four distinct DNA extraction methods were employed: phenol-chloroform, benzyl-chloride, Chelex-100, and Triton X.
The effectiveness of DNA extraction was evaluated across different sample types and methods.

Main Results:

Saliva processing and DNA extraction methods significantly influenced DNA yield and quality.
Fresh saliva samples provided the most suitable matrix for bacterial DNA extraction.
The benzyl-chloride protocol and Chelex-100 extraction demonstrated the highest efficacy in isolating salivary DNA.

Conclusions:

The choice of saliva sample preparation and DNA extraction method is critical for accurate oral microbiome analysis.
Fresh saliva is the optimal sample type for molecular studies of the oral microbiome.
Benzyl-chloride and Chelex-100 protocols are recommended for efficient salivary DNA extraction in oral microbiome research.