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

Methods to Assess Microbial Communities01:19

Methods to Assess Microbial Communities

Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

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...
Modern Molecular Taxonomy01:29

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...
Methods to Assess Microbial Populations01:30

Methods to Assess Microbial Populations

Assessing microbial populations is crucial for understanding microbial roles in health, ecology, and industry. Various complementary techniques—both culture-based and molecular—enable detailed analysis of microbial abundance, diversity, and function.Viable Plate CountThe viable plate count is a traditional culture-based method used to estimate the number of living microbes in a sample. After serial dilution, the sample is spread onto nutrient agar plates. Each viable cell forms a visible...
Introduction to the Human Microbiota01:22

Introduction to the Human Microbiota

Microorganisms colonize various regions of the human body, including the mouth, nasal passages, throat, stomach, intestines, urogenital tract, and skin. The total number of microbial cells is estimated to range from 10¹³ to 10¹⁴—comparable to, or exceeding, the number of human somatic cells. This host–microbiome relationship has led to the conceptualization of humans as supraorganisms, wherein microbial communities perform vital roles in development, immunity, and disease...
Methods of Classification and Identification01:28

Methods of Classification and Identification

Bacterial identification relies on a diverse array of techniques to classify and understand microorganisms, each tailored to uncover specific characteristics. Traditional morphological approaches, while still valuable, are limited for closely related or structurally simple organisms. Modern methods integrate biochemical, serological, genetic, and advanced molecular tools to achieve greater accuracy.Morphological and Biochemical TechniquesMorphological characteristics, such as cell shape and...

You might also read

Related Articles

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

Sort by
Same author

Quality, reliability, and engagement of COPD-related videos on Chinese short-form video platforms: a cross-sectional content analysis.

Scientific reports·2026
Same author

Learning to Super-Resolve Face Images via Dual-Domain Multi-scale Feature Interaction.

IEEE transactions on image processing : a publication of the IEEE Signal Processing Society·2026
Same author

Evaluating the accuracy of sex estimation from human tooth volume: leveraging automated AI segmentation and comparative analysis of machine learning algorithms.

Head & face medicine·2026
Same author

Fatigue Failure Mechanism and Crack Growth Behavior of Ti-6Al-4V ELI Titanium Alloy Welded Joints.

Materials (Basel, Switzerland)·2026
Same author

A Fully Bio-Based Elastomer with Ultrahigh Lignin Content and Performance Rivaling Nitrile Rubber.

Advanced materials (Deerfield Beach, Fla.)·2026
Same author

Nerve Growth Factor: A Multifaceted Regulator of Pain, Inflammation, and Tissue Remodeling in Bone and Joint Disorders.

Cell biochemistry and function·2026
Same journal

Isolation of Mesenchymal Stem Cell-Derived Extracellular Vesicles.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Modeling Melanoma Immune Surveillance by CAR-T Cells in Human Skin Organoids.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Stepwise Optimization of a Matrigel-Based In Vitro Angiogenesis Assay for Reproducible and Quantifiable 2D-Tube Formation Using HUVECs.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Quantifying Mechanical Properties of Fresh Ovarian Tissue with Optical Brillouin Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

3D Chromatin Architecture During Early Development: New Methods and New Findings.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Metabolic Plasticity in Embryogenesis Throughout the Lens of NAD<sup></sup>.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: May 12, 2026

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

Network Analysis in Microbiome Research: Methods, Tools, and Applications.

Jiajun Liu1,2, Yixue Li3,4,5,6,7, Tao Huang8,9

  • 1Department of Artificial Intelligence and Digital Health, CAS Engineering Laboratory for Nutrition, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.

Methods in Molecular Biology (Clifton, N.J.)
|May 10, 2026
PubMed
Summary
This summary is machine-generated.

This study explores network analysis methods for understanding the human microbiome, from basic correlations to advanced AI. It reviews various network types and computational tools, highlighting future challenges and opportunities in microbiome research.

Keywords:
Community detectionGraph neural networksMicrobiome network analysisMulti-omics integrationNetwork topologyViral evolution networks

More Related Videos

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks
09:49

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks

Published on: September 25, 2021

Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging
09:31

Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging

Published on: July 9, 2021

Related Experiment Videos

Last Updated: May 12, 2026

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

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks
09:49

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks

Published on: September 25, 2021

Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging
09:31

Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging

Published on: July 9, 2021

Area of Science:

  • Microbiome research
  • Systems biology
  • Bioinformatics

Background:

  • The human microbiome is a complex ecosystem where microbial interactions influence host health and disease.
  • Traditional taxonomic studies are insufficient for understanding these intricate dynamics.
  • Network analysis offers a systems-level approach to decipher microbial community interactions.

Purpose of the Study:

  • To review network methodologies applicable to microbiome research.
  • To compare traditional and advanced computational approaches for analyzing microbial networks.
  • To discuss the integration of artificial intelligence techniques in microbiome network analysis.

Main Methods:

  • Systematic review of network methodologies including co-occurrence, protein-protein interaction, metabolic, multi-omics, and evolutionary transmission networks.
  • Comparison of computational tools, topology metrics, and community detection algorithms.
  • Highlighting the application of graph neural networks and protein language models.

Main Results:

  • Network analysis provides a powerful framework for studying the human microbiome beyond simple taxonomic profiling.
  • A range of computational tools and network types are available for microbiome research.
  • Advanced AI techniques like graph neural networks show promise for deeper insights.

Conclusions:

  • Network-based approaches are crucial for understanding microbiome stability, host health, and disease.
  • Integrating multi-omics data and advanced AI can reveal complex microbial interactions.
  • Addressing challenges in data standardization and model interpretability is key for future microbiome research.