Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Modern Molecular Taxonomy

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Prospects of multipurpose biomonitoring for fisheries assessment based on environmental nucleic acids.

Journal of fish biology·2026

Same author

Vertebrate biodiversity via eDNA at the air-water interface.

iScience·2026

Same author

Mapping the marine distribution of eulachon (Thaleichthys pacificus) in the Northeast Pacific using environmental DNA.

Communications biology·2026

Same author

Estimating Organism Abundance Using Within-Sample Haplotype Frequencies of eDNA Data.

Molecular ecology resources·2026

Same author

Understanding practical barriers to the global adoption of environmental DNA (eDNA) methods, tools, and standards.

BMC research notes·2026

Same author

Fast, Flexible, Feasible: A Transparent Framework for Evaluating eDNA Workflow Trade-Offs in Resource-Limited Settings.

Molecular ecology resources·2026

Same journal

Consequences of phenological shifts are determined by the number of generations per season.

Ecology·2026

Same journal

Mechanistic and scale-specific analyses advance the preference-performance hypothesis.

Ecology·2026

Same journal

Ground-to-canopy monitoring reveals hidden ecological patterns in Congo Basin mammals.

Ecology·2026

Same journal

Combining individual and close-kin mark-recapture to design an effective wildlife population survey.

Ecology·2026

Same journal

Cross-stressor resilience of soil microbial growth and carbon metabolism under climate change.

Ecology·2026

Same journal

Oh deer! Videography reveals a range of defensive behaviors against a cervid by a ground-nesting bird.

Ecology·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Aug 23, 2025

Metagenomic Analysis of Silage

Metagenomic Analysis of Silage

Published on: January 13, 2017

Toward quantitative metabarcoding.

Andrew Olaf Shelton¹, Zachary J Gold^1,2, Alexander J Jensen^2,3

¹Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA.

|November 2, 2022

Summary

This summary is machine-generated.

This study presents a new quantitative method for amplicon sequencing data, also known as metabarcoding. This approach models the DNA amplification process to accurately estimate original DNA proportions for ecological and health applications.

Keywords:

amplicon sequencing bias adjustment community structure compositional analysis diet analysis environmental DNA

More Related Videos

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

Published on: May 23, 2018

Competitive Genomic Screens of Barcoded Yeast Libraries

Competitive Genomic Screens of Barcoded Yeast Libraries

Published on: August 11, 2011

Related Experiment Videos

Last Updated: Aug 23, 2025

Metagenomic Analysis of Silage

Metagenomic Analysis of Silage

Published on: January 13, 2017

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

Published on: May 23, 2018

Competitive Genomic Screens of Barcoded Yeast Libraries

Competitive Genomic Screens of Barcoded Yeast Libraries

Published on: August 11, 2011

Area of Science:

Ecology
Genomics
Bioinformatics

Background:

Amplicon sequencing (metabarcoding) is crucial for ecology, conservation, and health.
Current metabarcoding methods often lack quantitative accuracy, limiting biological interpretation.
There is a growing need for robust quantitative analyses in ecological studies.

Purpose of the Study:

To develop a quantitative framework for amplicon sequencing data.
To link genetic observations to underlying biological realities more accurately.
To improve the reliability of metabarcoding in diverse scientific fields.

Main Methods:

Modeling the polymerase chain reaction (PCR) mechanism underlying amplicon data generation.
Estimating initial DNA proportions from mixed samples by modeling the data's origin.
Calibrating the model using mock communities and validating with simulated and empirical data.

Main Results:

Demonstrated a generalizable model explaining amplicon data patterns.
Successfully estimated starting DNA proportions from complex mixtures.
Validated the quantitative approach across various datasets.

Conclusions:

The developed modeling approach enhances the quantitative power of metabarcoding.
This method improves the accuracy of ecological and health-related conclusions drawn from genetic data.
Facilitates more reliable applications of eDNA and microbiome research.