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Methods to Assess Microbial Populations

Methods to Assess Microbial Populations

Assessing microbial populations is crucial for understanding microbial roles in health, ecology, and industry. Various complementary techniques—both culture-based and molecular—enable detailed analysis of microbial abundance, diversity, and function.Viable Plate CountThe viable plate count is a traditional culture-based method used to estimate the number of living microbes in a sample. After serial dilution, the sample is spread onto nutrient agar plates. Each viable cell forms a...

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Related Experiment Video

Updated: Mar 19, 2026

An In Vitro Batch-culture Model to Estimate the Effects of Interventional Regimens on Human Fecal Microbiota

An In Vitro Batch-culture Model to Estimate the Effects of Interventional Regimens on Human Fecal Microbiota

Published on: July 31, 2019

Adjusting microbiome profiles for differences in microbial load by spike-in bacteria.

Frank Stämmler^1,2, Joachim Gläsner³, Andreas Hiergeist³

¹Chair of Statistical Bioinformatics, University of Regensburg, Am BioPark 9, 93053, Regensburg, Germany. Frank.Staemmler@klinik.uni-regensburg.de.

|June 23, 2016

Summary

Spiking the gut microbiome with external bacteria allows accurate measurement of absolute microbial abundances. This method provides new insights into gut microbiome dynamics, especially in clinical settings.

Keywords:

16S rRNA gene sequencing Bacterial communities Community analysis Microbial load Microbiome profiling Spike-in bacteria Standardization

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Last Updated: Mar 19, 2026

An In Vitro Batch-culture Model to Estimate the Effects of Interventional Regimens on Human Fecal Microbiota

An In Vitro Batch-culture Model to Estimate the Effects of Interventional Regimens on Human Fecal Microbiota

Published on: July 31, 2019

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

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Published on: October 15, 2019

Assessing the Viability of a Synthetic Bacterial Consortium on the In Vitro Gut Host-microbe Interface

Assessing the Viability of a Synthetic Bacterial Consortium on the In Vitro Gut Host-microbe Interface

Published on: July 4, 2018

Area of Science:

Microbiology
Genomics
Bioinformatics

Background:

Next-generation 16S ribosomal RNA gene sequencing is standard for analyzing mammalian gut microbiome composition.
Current methods often fail to quantify absolute microbial abundances due to variations in total microbial loads.
This limitation hinders the accurate assessment of specific operational taxonomic units (OTUs).

Purpose of the Study:

To introduce a novel method for quantifying absolute bacterial abundances in gut microbiome samples.
To enable accurate estimation of microbial load variations using exogenous spike-in bacteria.
To provide deeper insights into the dynamics of intestinal microbiomes.

Main Methods:

Spiking crude specimens with known quantities of exogenous bacteria (e.g., Salinibacter ruber, Rhizobium radiobacter, Alicyclobacillus acidiphilus).
Utilizing 16S rDNA read counts of spike-in bacteria to calibrate read counts of endogenous bacteria.
Applying spike-in based calibration to assess changes in microbial abundances in mouse and human stool samples.

Main Results:

Demonstrated accurate estimation of ratios of absolute endogenous bacterial abundances using spike-in calibration.
Successfully quantified changes in both relative and absolute abundances of gut microbial phyla.
Observed significant alterations in the genus Enterococcus in patients undergoing stem cell transplantation post-treatment.

Conclusions:

Exogenous spike-in bacteria are effective for estimating absolute OTU abundances in gut microbiome studies.
This approach enhances the understanding of microbial community structure and dynamics.
Provides novel insights into the impact of treatments on intestinal microbiomes.