Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Methods to Assess Microbial Communities

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...

Automated Microbial Diagnostics

Automated Microbial Diagnostics

Automated diagnostic analyzers have transformed clinical microbiology by providing rapid and reliable methods for pathogen identification and antibiotic susceptibility testing. Among these systems, the Vitek 2 is widely used because it automates the traditionally labor-intensive processes of microbial identification (ID) and antibiotic susceptibility testing (AST), delivering standardized and timely results that are essential for effective patient care.Microbial Identification with ID CardsThe...

Methods to Assess Microbial Populations

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...

Modern Molecular Taxonomy

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...

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...

Microbial Classification System

Microbial Classification System

Classification is the process of organizing organisms into hierarchically inclusive groups based on their phenotypic similarities or evolutionary relationships. A species comprises one or more strains, and closely related species are grouped into genera. Genera are further classified into families, families into orders, orders into classes, and so forth, up to the domain level, which is the broadest taxonomic rank derived from a combination of phenotypic and genotypic data.The nomenclature of...

You might also read

Related Articles

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

Sort by

Same author

Overlapping gut microbiome signatures in aging and disease are characterized by enrichment of medication-associated oral microbes in the gut.

FEBS letters·2026

Same author

Gut microbiome features associated with Bifidobacterium colonization predict personalized probiotic persistence patterns.

Nature communications·2026

Same author

Artificial intelligence in microbial metagenomics.

Progress in molecular biology and translational science·2026

Same author

Urinary Microbiome Dysbiosis in Children With Congenital Uropathies at Varying Risk for Urinary Tract Infections.

Kidney international reports·2026

Same author

Mediterranean diet in treatment of inflammatory bowel disease: A systematic review and meta-analysis.

Indian journal of gastroenterology : official journal of the Indian Society of Gastroenterology·2026

Same author

Artificial Intelligence (AI) in microbiome-directed biotherapeutics development.

Progress in molecular biology and translational science·2026

Same journal

Integrating transcriptomics and metabolomics reveals the molecular landscape of sperm maturation driven by regional differentiation in the epididymis of Guizhou-Guiqian semi-fine wool sheep.

Genomics·2026

Same journal

Impact of genotype on histopathology and clinical characters in a Chinese cohort with obstructive hypertrophic cardiomyopathy.

Genomics·2026

Same journal

A novel reusable transcriptome-wide association study workflow used to map key genes linked to important cattle traits.

Genomics·2026

Same journal

The large mitochondrial genome of Syndiclis anlungensis (Lauraceae): Genome structure, comparative analysis, and phylogenetic relationships with other Syndiclis species.

Genomics·2026

Same journal

DeepGEP: Deep learning for gene expression prediction from multi-omics in mammals.

Genomics·2026

Same journal

Molecular features of external Auditory Canal cholesteatoma by microbial metagenomic sequencing.

Genomics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 8, 2026

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

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

Published on: October 15, 2019

Community-analyzer: a platform for visualizing and comparing microbial community structure across microbiomes.

Bhusan K Kuntal¹, Tarini Shankar Ghosh, Sharmila S Mande

¹Bio-Sciences R&D Division, TCS Innovation Labs, Tata Research Development & Design Centre, Tata Consultancy Service Ltd., 54-B Hadapsar Industrial Estate, Pune 411 013, Maharashtra, India.

|August 28, 2013

Summary

This summary is machine-generated.

Community-Analyzer is a new application for comparative metagenomics analysis. It visualizes microbial community differences and interactions, aiding in identifying key microbial groups and their roles in environments.

Keywords:

Algorithms Metagenomics Microbial interactions Software

More Related Videos

Characterizing Microbiome Dynamics – Flow Cytometry Based Workflows from Pure Cultures to Natural Communities

Characterizing Microbiome Dynamics – Flow Cytometry Based Workflows from Pure Cultures to Natural Communities

Published on: July 12, 2018

Isolation and Analysis of Microbial Communities in Soil, Rhizosphere, and Roots in Perennial Grass Experiments

Isolation and Analysis of Microbial Communities in Soil, Rhizosphere, and Roots in Perennial Grass Experiments

Published on: July 24, 2018

Related Experiment Videos

Last Updated: May 8, 2026

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

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

Published on: October 15, 2019

Characterizing Microbiome Dynamics – Flow Cytometry Based Workflows from Pure Cultures to Natural Communities

Characterizing Microbiome Dynamics – Flow Cytometry Based Workflows from Pure Cultures to Natural Communities

Published on: July 12, 2018

Isolation and Analysis of Microbial Communities in Soil, Rhizosphere, and Roots in Perennial Grass Experiments

Isolation and Analysis of Microbial Communities in Soil, Rhizosphere, and Roots in Perennial Grass Experiments

Published on: July 24, 2018

Area of Science:

Microbiology
Bioinformatics
Computational Biology

Background:

Comparative metagenomics aims to link microbial communities to environmental characteristics.
These characteristics arise from complex inter-microbial interactions within ecosystems.

Purpose of the Study:

To introduce Community-Analyzer, a novel GUI-based application for comparative metagenomic analysis.
To facilitate visualization of microbial community differences and uncover inter-microbial interaction patterns.

Main Methods:

Development of a GUI-based application named Community-Analyzer.
Implementation of a correlation-based graph layout algorithm for community analysis.
Inclusion of interactive functionalities for standard microbiome comparative analyses.

Main Results:

Community-Analyzer enables rapid visualization of taxonomic composition differences between microbial communities.
The application provides insights into inherent inter-microbial interactions.
Metagenomes can be grouped based on probable inter-microbial interaction patterns, moving beyond simple abundance comparisons.

Conclusions:

Community-Analyzer offers a powerful tool for comparative metagenomic analysis, enhancing the understanding of microbial community structure and function.
The application's unique layout algorithm aids in identifying microbial groups responsible for specific environmental characteristics through interaction patterns.