Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Mechanistic Models: Compartment Models in Individual and Population Analysis01:23

Mechanistic Models: Compartment Models in Individual and Population Analysis

241
Mechanistic models are utilized in individual analysis using single-source data, but imperfections arise due to data collection errors, preventing perfect prediction of observed data. The mathematical equation involves known values (Xi), observed concentrations (Ci), measurement errors (εi), model parameters (ϕj), and the related function (ƒi) for i number of values. Different least-squares metrics quantify differences between predicted and observed values. The ordinary least...
241
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

503
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
503

You might also read

Related Articles

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

Sort by
Same author

Brain health and the gut microbiome (bMicrobiome Study): a proof-of-concept, feasibility study integrating shotgun metagenomics, metrology, and multidimensional phenotyping across the cognitive aging spectrum.

Gut microbes reports·2026
Same author

Evaluating the analytical performance of direct-to-consumer gut microbiome testing services.

Communications biology·2026
Same author

The microbiota-gut-brain axis in mild cognitive impairment and Alzheimer's disease: a scoping review of human studies.

Alzheimer's & dementia : the journal of the Alzheimer's Association·2026
Same author

A peanut trilogy: polyploid origin, domestication, and genomic instability.

The Plant journal : for cell and molecular biology·2025
Same author

STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies.

Nature microbiology·2025
Same author

Validation and Comparison of Live Microorganism Plating Analytical Procedures Following United States Pharmacopeia (USP) <1220> and <1210>.

Journal of dietary supplements·2025
Same journal

A set of constitutive promoters with graded strengths for gene expression in diverse cyanobacterial strains.

Applied and environmental microbiology·2026
Same journal

Sources and traits of bacteria and fungi found in the near-surface atmosphere.

Applied and environmental microbiology·2026
Same journal

Advancing One Health in Africa through continental early warning environmental surveillance.

Applied and environmental microbiology·2026
Same journal

Specificity and longevity of a bacterial interspecies mutual cooperation benefiting organic micropollutant biodegradation.

Applied and environmental microbiology·2026
Same journal

Coordinated regulation of trimethylamine catabolism in abundant marine bacteria.

Applied and environmental microbiology·2026
Same journal

Synergistic and individual effects of RNase E, II, and R in the regulation of <i>Escherichia coli</i> growth and metabolism.

Applied and environmental microbiology·2026
See all related articles

Related Experiment Video

Updated: Jan 13, 2026

Compost Microcosms as Microbially Diverse, Natural-like Environments for Microbiome Research in Caenorhabditis elegans
07:19

Compost Microcosms as Microbially Diverse, Natural-like Environments for Microbiome Research in Caenorhabditis elegans

Published on: September 13, 2022

2.7K

A mathematical framework to correct for compositionality in microbiome data sets.

Samuel P Forry1, Stephanie L Servetas1, Jason G Kralj1

  • 1Biosystems and Biomaterials Division, NIST, Gaithersburg, Maryland, USA.

Applied and Environmental Microbiology
|January 6, 2026
PubMed
Summary
This summary is machine-generated.

Metagenomic sequencing data can be distorted by compositionality. This study introduces internal standards to calculate "Scaled Abundances," improving the accuracy and precision of microbiome analysis for better health and environmental insights.

Keywords:
compositionalityexperimental designinternal standardmetagenomic sequencingscaled abundance

More Related Videos

Individualized Reconstitution of Human Milk Microbiota: A Feasible Approach in Real-World Settings
04:16

Individualized Reconstitution of Human Milk Microbiota: A Feasible Approach in Real-World Settings

Published on: February 7, 2025

835
Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
11:22

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

Published on: October 15, 2019

31.0K

Related Experiment Videos

Last Updated: Jan 13, 2026

Compost Microcosms as Microbially Diverse, Natural-like Environments for Microbiome Research in Caenorhabditis elegans
07:19

Compost Microcosms as Microbially Diverse, Natural-like Environments for Microbiome Research in Caenorhabditis elegans

Published on: September 13, 2022

2.7K
Individualized Reconstitution of Human Milk Microbiota: A Feasible Approach in Real-World Settings
04:16

Individualized Reconstitution of Human Milk Microbiota: A Feasible Approach in Real-World Settings

Published on: February 7, 2025

835
Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
11:22

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

Published on: October 15, 2019

31.0K

Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Metagenomic sequencing (MGS) is crucial for microbiome analysis but suffers from data compositionality.
  • Compositionality means taxon relative abundance depends on all other taxa, complicating accurate quantification.
  • This distortion hinders precise interpretation of microbial community roles in health and environment.

Purpose of the Study:

  • To develop and validate a method for correcting compositional distortions in metagenomic sequencing data.
  • To introduce exogenous internal standards and a mathematical framework for accurate microbiome quantification.
  • To enable reliable, quantitative comparisons of individual microbiome taxa across diverse samples.

Main Methods:

  • Incorporation of exogenous internal standards into routine metagenomic sequencing workflows.
  • Development of a mathematical framework to calculate "Scaled Abundances" from internal standard data.
  • Validation using mock microbial communities and human gut microbiome (fecal) samples.

Main Results:

  • "Scaled Abundances" were independent of sample composition and proportional to actual biological abundances.
  • The new method demonstrated superior precision and accuracy compared to traditional relative abundance measurements.
  • Reliable quantitative comparisons of individual taxa were achieved across varied compositions and abundances.

Conclusions:

  • The proposed approach using internal standards effectively corrects for compositional distortions in MGS data.
  • "Scaled Abundances" provide a pathway to accurate taxon quantification, advancing microbiome research.
  • This method has significant potential for clinical and environmental health applications requiring precise microbial profiling.