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

Phylogenetic Trees03:21

Phylogenetic Trees

49.2K
Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
49.2K
A Practical Guide to Phylogenetics for Nonexperts12:00

A Practical Guide to Phylogenetics for Nonexperts

36.0K
Here we describe a step-by-step pipeline for generating reliable phylogenies from nucleotide or amino acid sequence datasets. This guide aims to serve researchers or students new to phylogenetic...
36.0K
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

16.4K
A method of constructing a phylogenetic tree based on sequence homology of SWEETs from eukaryotes and SemiSWEETs from prokaryotes is described. Phylogenetic analysis is a useful tool for explaining the evolutionary relatedness between homologous proteins or genes from different organism...
16.4K
Quantification of the Potential Impact of Glyphosate-Based Products on Microbiomes07:42

Quantification of the Potential Impact of Glyphosate-Based Products on Microbiomes

4.7K
Glyphosate-based products (GBP) are the most common broad-spectrum herbicides worldwide. In this article, we introduce general guidelines to quantify the effect of GBP on microbiomes, from field experiments to bioinformatics...
4.7K
The Tree of Life - Bacteria, Archaea, Eukaryotes02:40

The Tree of Life - Bacteria, Archaea, Eukaryotes

37.8K
The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the common ancestor to all life on Earth. All other species radiate from this point, much like the branches of a tree. The numerous tips of these branches on the tree of life represent every living, or extant, species. Extinct species, which are species that no longer exist, can be found towards the center of the tree. Currently, these organisms, both...
37.8K
Application of Flow Vermimetry for Quantification and Analysis of the Caenorhabditis elegans Gut Microbiome08:38

Application of Flow Vermimetry for Quantification and Analysis of the Caenorhabditis elegans Gut Microbiome

1.1K
Caenorhabditis elegans is a powerful model to examine the molecular determinants driving host-microbiome interactions. We present a high throughput pipeline profiling the single animal levels of gut microbiome colonization together with key aspects of the C. elegans...
1.1K

You might also read

Related Articles

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

Sort by
Same author

The medical impact of emergent banning of N-nitrosodimethylamine: contaminated antihypertensive drug.

The Korean journal of internal medicine·2026
Same author

Longer Asthma Duration Is Associated With Elevated Non-T2 Sputum Biomarkers and Reduced T2 Inflammation in Severe Asthma.

Allergy·2026
Same author

Development of a First-tier Risk Assessment Tool for Occupational Hazards Among Public Officials.

Safety and health at work·2026
Same author

Refined obesity, smoking exposure, and lipid metrics in mortality risk assessment: a nationwide cohort analysis.

PloS one·2026
Same author

Association of Sodium-Glucose Cotransporter-2 Inhibitors With Incident Gout Risk: A Population-Based Comparative Cohort Study With Genetic Evidence From Mendelian Randomisation.

Diabetes, obesity & metabolism·2026
Same author

A Bayesian approach to estimate ambient dose equivalent for liquid radioactive waste measurements.

Applied radiation and isotopes : including data, instrumentation and methods for use in agriculture, industry and medicine·2026

Related Experiment Video

Updated: Jan 19, 2026

Evolutionary Relationships and Phylogenetic Trees
03:21

Evolutionary Relationships and Phylogenetic Trees

Published on: October 23, 2025

49.2K

Phylogenetic tree-based microbiome association test.

Kang Jin Kim1, Jaehyun Park2, Sang-Chul Park3

  • 1Department of Public Health Sciences, Graduate School of Public Health, South Korea.

Bioinformatics (Oxford, England)
|September 11, 2019
PubMed
Summary

A new phylogenetic tree-based microbiome association test (TMAT) improves the detection of disease-associated microbial communities. TMAT offers higher statistical power and deeper insights into bacterial pathology compared to existing methods.

More Related Videos

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

36.0K
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.4K

Related Experiment Videos

Last Updated: Jan 19, 2026

Evolutionary Relationships and Phylogenetic Trees
03:21

Evolutionary Relationships and Phylogenetic Trees

Published on: October 23, 2025

49.2K
A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

36.0K
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.4K

Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Human microbiome studies face challenges due to high inter-subject variation in operational taxonomic units (OTUs).
  • Existing non-parametric methods like Mann-Whitney U-test and Wilcoxon rank-sum test for identifying disease-associated OTUs suffer from information loss and high false-negative rates.
  • These methods rely solely on abundance ranks, neglecting valuable phylogenetic information.

Purpose of the Study:

  • To introduce a novel phylogenetic tree-based microbiome association test (TMAT) for analyzing associations between microbiome OTU abundances and disease phenotypes.
  • To leverage phylogenetic relationships among OTUs to enhance the accuracy and power of microbiome association studies.
  • To provide a more sensitive method for identifying microbial signatures linked to host diseases.

Main Methods:

  • Developed the phylogenetic tree-based microbiome association test (TMAT).
  • TMAT utilizes phylogenetic tree information to analyze microbiome OTU abundances.
  • Test statistics are generated for each node in the phylogenetic tree and combined to identify disease-associated mutations.

Main Results:

  • Extensive simulations based on real absolute abundances demonstrated TMAT's superior performance.
  • TMAT effectively preserves the nominal type-1 error rate.
  • Statistical power estimates for TMAT generally outperformed existing methods across various scenarios.
  • TMAT successfully detected phylogenetic mutations associated with host diseases, offering deeper insights into bacterial pathology.

Conclusions:

  • TMAT is a powerful and efficient tool for microbiome association studies.
  • The method enhances the detection of disease-associated microbial patterns by incorporating phylogenetic information.
  • TMAT provides a more in-depth understanding of bacterial pathology in relation to host diseases.