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Related Concept Videos

Modern Molecular Taxonomy01:29

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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...
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wiSDOM: a visual and statistical analytics for interrogating microbiome.

Shih-Chi Su1,2,3, James E Galvin4, Shun-Fa Yang5,6

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|January 30, 2021
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Summary
This summary is machine-generated.

The web-based inclusionary analysis Suite for Disease-Oriented Metagenomics (wiSDOM) R Shiny application offers comprehensive metagenomic data mining. It enables microbial biomarker discovery and functional prediction for researchers without programming backgrounds.

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Area of Science:

  • Metagenomics
  • Bioinformatics
  • Microbial Ecology

Background:

  • The wiSDOM (web-based inclusionary analysis Suite for Disease-Oriented Metagenomics) application is presented.
  • It integrates six modules for comprehensive metagenomic data analysis.

Purpose of the Study:

  • To provide a user-friendly, browser-based R Shiny application for disease-oriented metagenomics.
  • To enable researchers, including those without programming expertise, to perform complex data mining and visualization.

Main Methods:

  • The application includes modules for data visualization, alpha and beta diversity analysis, microbial biomarker discovery using statistical and machine learning approaches, clinical validity assessment via ROC curves, and functional prediction (PICRUSt/Tax4Fun).
  • It utilizes various statistical and machine learning methods for biomarker discovery and ANOSIM for beta diversity analysis.

Main Results:

  • wiSDOM has been successfully evaluated in prior studies for microbial biomarker exploration, clinical validity assessment, and analysis of bacterial diversity and functionality.
  • The application offers customizable visualizations and an intuitive interface for data mining.

Conclusions:

  • wiSDOM facilitates comprehensive metagenomic data analysis and illustration through an accessible, web-based platform.
  • It empowers researchers to explore microbial communities, identify biomarkers, and predict functions effectively.