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Related Experiment Video

Updated: Oct 12, 2025

Use of a High-throughput In Vitro Microfluidic System to Develop Oral Multi-species Biofilms

Use of a High-throughput In Vitro Microfluidic System to Develop Oral Multi-species Biofilms

Published on: December 1, 2014

Assessing saliva microbiome collection and processing methods.

Abigail J S Armstrong¹, Veenat Parmar¹, Martin J Blaser²

¹Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, 08854, USA.

NPJ Biofilms and Microbiomes

|November 19, 2021

Summary

This summary is machine-generated.

Collecting saliva with preservative improves oral microbiome consistency. Depleting human DNA boosts bacterial sequence yield for accurate analysis of the oral microbiome.

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Last Updated: Oct 12, 2025

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Published on: December 18, 2013

Area of Science:

Microbiology
Genomics
Oral Health

Background:

The oral microbiome is linked to lung health and SARS-CoV-2 infection progression.
Saliva-based SARS-CoV-2 tests offer potential for oral microbiome assessment.
Current saliva collection kits lack validation for microbiome accuracy.

Purpose of the Study:

To evaluate the impact of saliva collection methods and processing on oral microbiome measurements.
To assess microbiome depth and diversity using 16S rRNA gene amplicon and shotgun metagenomics.
To determine if human DNA depletion enhances bacterial read depth in shotgun sequencing.

Main Methods:

Collected 56 saliva samples from 22 subjects, with and without preservative, and across different time points.
Performed 16S rRNA gene (V4) sequencing on all samples.
Conducted shotgun metagenomics on a subset, with and without human DNA depletion.

Main Results:

Samples collected with preservative showed smaller within-subject beta diversity over time and higher alpha diversity.
Human DNA depletion significantly increased total and relative bacterial reads in shotgun metagenomics.
Within-subject variability was lower than between-subject variability.

Conclusions:

Saliva collection with preservative enhances oral microbiome measurement consistency.
Human DNA depletion is crucial for maximizing bacterial sequence yield in shotgun metagenomics.
Optimized collection and processing methods are vital for reliable oral microbiome studies.