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

You might also read

Related Articles

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

Sort by
Same author

Comparative efficacy of postoperative adjuvant chemoradiotherapy versus no chemoradiotherapy in the treatment of pancreatic adenocarcinoma.

BMC cancer·2026
Same author

Application of cerium dioxide nanoparticles in the treatment of intervertebral disc degeneration induced by oxidative stress.

Journal of translational medicine·2026
Same author

Retraction: MALAT1 predicts poor survival in osteosarcoma patients and promotes cell metastasis through associating with EZH2.

Oncotarget·2026
Same author

Integrated transcriptomic identification and validation reveal key autophagy-associated biomarkers in sleep deprivation.

PeerJ·2026
Same author

Copper and cuproptosis: mechanisms, biology, and roles in disease.

Science bulletin·2026
Same author

Rapid slide-level assessment of glomerular yield using virtual staining of unstained renal biopsy sections.

Diagnostic pathology·2026

Related Experiment Video

Updated: Oct 6, 2025

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

30.0K

EasyMicroPlot: An Efficient and Convenient R Package in Microbiome Downstream Analysis and Visualization for Clinical

Bingdong Liu1,2, Liujing Huang2,3, Zhihong Liu2

  • 1The First Affiliated Hospital of Jinan University, Guangzhou, China.

Frontiers in Genetics
|January 21, 2022
PubMed
Summary
This summary is machine-generated.

A new R package, EasyMicroPlot (EMP), simplifies clinical microbiome data analysis. EMP efficiently processes large datasets, aiding researchers in understanding gut microbiota and disease connections.

Keywords:
16s rDNA sequencingclinical datamicrobiotanext-generation sequencingscript

More Related Videos

A Method to Define the Effects of Environmental Enrichment on Colon Microbiome Biodiversity in a Mouse Colon Tumor Model
08:14

A Method to Define the Effects of Environmental Enrichment on Colon Microbiome Biodiversity in a Mouse Colon Tumor Model

Published on: February 28, 2018

8.9K
Assisted Selection of Biomarkers by Linear Discriminant Analysis Effect Size LEfSe in Microbiome Data
04:57

Assisted Selection of Biomarkers by Linear Discriminant Analysis Effect Size LEfSe in Microbiome Data

Published on: May 16, 2022

16.3K

Related Experiment Videos

Last Updated: Oct 6, 2025

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

30.0K
A Method to Define the Effects of Environmental Enrichment on Colon Microbiome Biodiversity in a Mouse Colon Tumor Model
08:14

A Method to Define the Effects of Environmental Enrichment on Colon Microbiome Biodiversity in a Mouse Colon Tumor Model

Published on: February 28, 2018

8.9K
Assisted Selection of Biomarkers by Linear Discriminant Analysis Effect Size LEfSe in Microbiome Data
04:57

Assisted Selection of Biomarkers by Linear Discriminant Analysis Effect Size LEfSe in Microbiome Data

Published on: May 16, 2022

16.3K

Area of Science:

  • Microbiology
  • Bioinformatics
  • Computational Biology

Background:

  • Next-generation sequencing (NGS) has advanced microbial studies, particularly in clinical settings.
  • The human microbiota is increasingly recognized for its role in disease pathogenesis.
  • Analyzing massive microbiome data presents significant computational challenges for researchers, especially those new to the field.

Purpose of the Study:

  • To develop an efficient and user-friendly software package for clinical microbiome data analysis.
  • To provide a tool that integrates popular microbial analysis and visualization techniques for clinical research.
  • To address the challenges posed by large-scale microbiome datasets and complex metadata in clinical investigations.

Main Methods:

  • Development of the EasyMicroPlot (EMP) package, an R-based tool for metagenomic downstream analysis.
  • Application of the EMP package to analyze 694 bio-samples from the Guangdong Gut Microbiome Project (GGMP).
  • Incorporation of popular microbial analysis and visualization methods tailored for clinical microbiome studies.

Main Results:

  • The EMP package demonstrated powerful analytical capabilities and excellent convenience in handling clinical microbiome data.
  • Analysis of the GGMP cohort using EMP revealed significant influences of dietary style on gut microbiota composition.
  • The study validated the utility of EMP for addressing complex questions in clinical microbiome research.

Conclusions:

  • The EasyMicroPlot (EMP) package offers an accessible solution for clinical microbiome data analysis.
  • EMP facilitates the exploration of host-microbe interactions and the impact of lifestyle factors like diet on the gut microbiome.
  • The developed tool empowers researchers to overcome computational hurdles and advance clinical microbiome research.