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Related Concept Videos

Methods to Assess Microbial Populations01:30

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 visible...
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Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...
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Updated: Jun 7, 2026

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
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Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Published on: August 25, 2018

Quantifying microbial communities with 454 pyrosequencing: does read abundance count?

Anthony S Amend1, Keith A Seifert, Thomas D Bruns

  • 1Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA. a.amend@berkeley.edu

Molecular Ecology
|November 6, 2010
PubMed
Summary
This summary is machine-generated.

Pyrosequencing read abundance is generally quantitative within species but can be biased between species due to sequence structure. Careful processing is crucial for accurate fungal community analysis.

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Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization
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Last Updated: Jun 7, 2026

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
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Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization
12:37

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

Published on: April 14, 2016

Area of Science:

  • Microbial ecology
  • Bioinformatics
  • Molecular sequencing

Background:

  • Pyrosequencing is widely used for microbial community analysis, interpreting read abundance as taxon abundance.
  • Potential biases in sample processing, amplification, and sequencing can affect quantitative accuracy.

Purpose of the Study:

  • To investigate the relationship between read abundance and biological abundance in pyrosequencing data.
  • To assess biases in quantitative metrics for microbial community comparisons.

Main Methods:

  • Analyzing 454 pyrosequencing data from a house dust sample spiked with known fungal quantities.
  • Examining the impact of read-quality processing stringency on abundance metrics.
  • Comparing pyrosequencing results with cloning and Sanger sequencing.

Main Results:

  • Significant differences (one order of magnitude) in read abundance were observed among fungal species.
  • Quantification precision within species varied (R(2) 0.96-0.54).
  • Read-quality stringency and read orientation biased abundance for species with long homopolymers.

Conclusions:

  • Read abundance is approximately quantitative within species but can be biased between species due to inherent sequence properties.
  • A trade-off exists between sequence quality stringency and quantification accuracy.
  • Careful consideration of processing and analysis methods is essential for hypothesis testing with pyrosequencing data.