Comparing saliva collection and DNA extraction methods for saliva-based microbiome profiling

Area of Science:

• Microbiome Research
• Human Microbiome
• Salivary Microbiome

Background:

• The human microbiome plays a vital role in health and disease.
• Saliva is an attractive medium for microbiome studies due to easy collection.
• Methodological challenges exist in saliva storage and DNA extraction impacting results.

Purpose of the Study:

• To systematically compare saliva collection and DNA extraction methods for 16S rRNA microbiome profiling.
• To identify reliable and reproducible protocols for salivary microbiome characterization.
• To address variability introduced by different nucleic acid extraction kits.

Main Methods:

• Compared four commercial at-home saliva collection kits for 1-week room temperature storage.
• Evaluated three commercial DNA extraction kits for salivary microbiome analysis.
• Incorporated quality control measures like water controls and differential abundance testing.

Main Results:

• DNA extraction kits significantly impacted salivary microbiome composition.
• One week of storage in preservative solution altered bacterial composition.
• Contaminants increased during incubation, posing a challenge for microbiome analysis.

Conclusions:

• Saliva microbiome studies require standardized collection and extraction protocols.
• Different extraction kits introduce systematic biases, necessitating careful consideration when comparing studies.
• Consistent use of the same nucleic acid collection and extraction kits is essential for reproducibility.