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Related Experiment Video

Updated: Nov 17, 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

Quantifying Live Microbial Load in Human Saliva Samples over Time Reveals Stable Composition and Dynamic Load.

Clarisse Marotz¹, James T Morton², Perris Navarro¹

¹Department of Pediatrics, University of California, San Diego, La Jolla, California, USA.

|February 17, 2021

Summary

We developed a new method to accurately count live microbes in saliva using flow cytometry and propidium monoazide (PMA) alongside metagenomic sequencing, revealing daily fluctuations in microbial load.

Keywords:

16S sequencing flow cytometry longitudinal microbial load microbiome propidium monoazide (PMA)relic DNA saliva

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Last Updated: Nov 17, 2025

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

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Published on: December 1, 2014

Oral Biofilm Sampling for Microbiome Analysis in Healthy Children

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Published on: December 31, 2017

Characterizing Microbiome Dynamics – Flow Cytometry Based Workflows from Pure Cultures to Natural Communities

Characterizing Microbiome Dynamics – Flow Cytometry Based Workflows from Pure Cultures to Natural Communities

Published on: July 12, 2018

Area of Science:

Microbiology
Genomics
Biotechnology

Background:

Metagenomic sequencing offers microbial community composition but lacks total microbial load quantification.
Detected DNA may originate from dead microorganisms, complicating analysis of live microbial presence.
Understanding live microbial dynamics is crucial for host-associated microbiome research.

Purpose of the Study:

To develop and validate a novel workflow for quantifying live microbial load in parallel with metagenomic sequencing.
To assess the dynamic changes in live microbial load in human saliva.
To evaluate the impact of relic DNA removal on microbiome analysis.

Main Methods:

Combined propidium monoazide (PMA) treatment for relic DNA removal with flow cytometry for microbial quantification.
Applied the workflow to unstimulated saliva samples collected longitudinally.
Performed metagenomic sequencing in parallel with live cell quantification.

Main Results:

Live microbial load in saliva was inversely correlated with salivary flow rate.
Microbial load fluctuated significantly (by an order of magnitude) within individuals throughout the day.
Removing relic DNA enhanced resolution in longitudinal microbiome studies and revealed variable percentages of live bacteria.

Conclusions:

The developed workflow accurately quantifies live microbial load in parallel with metagenomic data.
Human oral microbiomes are highly dynamic, with significant daily fluctuations in live microbial numbers.
Relic DNA removal is beneficial for longitudinal microbiome studies, improving the detection of true microbial dynamics.