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

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...

Microbial Phylogeny

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...

Introduction to the Human Microbiota

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...

Development of Human Microbiota

Development of Human Microbiota

The human microbiota begins developing at birth and undergoes continual change as we age. Infancy marks a critical period of microbial sensitivity, offering a “window of opportunity” during which beneficial microbes help mature the immune system. By age three, children typically develop a more stable and diverse microbial community. Newborns acquire microbes from their immediate environment; vaginal delivery favors maternal vaginal microbes, while cesarean births favor microbes from the skin...

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...

Applications of Molecular Taxonomy

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...

You might also read

Related Articles

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

Sort by

Same author

Simultaneous detection of multiple viral pathogens in vacuumed dust from different building types.

Building and environment·2026

Same author

Diet Supplementation with Pomegranate Fruit Alters Distal Gut Microbiota of Healthy Female College Students.

Microorganisms·2025

Same author

Mechanisms underlying the distinct K+ dependencies of periodic paralysis.

The Journal of general physiology·2025

Same author

Human gut microbiota-fermented asparagus powder protects human epithelial cells from injury and inflammation.

Food & function·2025

Same author

Reduced K<sup>+</sup> build-up in t-tubules contributes to resistance of the diaphragm to myotonia.

The Journal of physiology·2024

Same author

Gut Microbiota Fermentation of Digested Almond-Psyllium-Flax Seed-Based Artisan Bread Promotes Mediterranean Diet-Resembling Microbial Community.

Microorganisms·2024

Search research articles

Related Experiment Video

Updated: Jun 6, 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

Optimizing the analysis of human intestinal microbiota with phylogenetic microarray.

Laura Rigsbee¹, Richard Agans, Brent D Foy

¹Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA.

FEMS Microbiology Ecology

|December 16, 2010

Summary

This summary is machine-generated.

Optimizing phylogenetic microarrays for intestinal microbiota analysis improves bacterial detection and abundance accuracy. Adjusting for gene copy numbers and cross-hybridization enhances reliability, enabling assessment of microbial community structure and activity.

More Related Videos

Analysis of Interactions between Endobiotics and Human Gut Microbiota Using In Vitro Bath Fermentation Systems

Analysis of Interactions between Endobiotics and Human Gut Microbiota Using In Vitro Bath Fermentation Systems

Published on: August 23, 2019

Analysis of Fecal Microbiota Dynamics in Lupus-Prone Mice Using a Simple, Cost-Effective DNA Isolation Method

Analysis of Fecal Microbiota Dynamics in Lupus-Prone Mice Using a Simple, Cost-Effective DNA Isolation Method

Published on: May 2, 2022

Related Experiment Videos

Last Updated: Jun 6, 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

Analysis of Interactions between Endobiotics and Human Gut Microbiota Using In Vitro Bath Fermentation Systems

Analysis of Interactions between Endobiotics and Human Gut Microbiota Using In Vitro Bath Fermentation Systems

Published on: August 23, 2019

Analysis of Fecal Microbiota Dynamics in Lupus-Prone Mice Using a Simple, Cost-Effective DNA Isolation Method

Analysis of Fecal Microbiota Dynamics in Lupus-Prone Mice Using a Simple, Cost-Effective DNA Isolation Method

Published on: May 2, 2022

Area of Science:

Microbiology
Bioinformatics
Genomics

Background:

Phylogenetic microarrays offer high-throughput analysis of microbial communities.
Accurate assessment of intestinal microbiota is crucial for understanding health and disease.

Purpose of the Study:

To optimize the analysis of intestinal microbiota using the Microbiota Array.
To improve the accuracy of bacterial detection and abundance measurements.
To assess microbial community structure and metabolic activity.

Main Methods:

Investigated the impact of 16S rDNA-specific PCR amplification cycles on bacterial detection and abundance.
Developed mathematical algorithms to correct for 16S rDNA cross-hybridization and adjust for 16S rRNA gene copy number variations.
Utilized phylogenetic microarray analysis of both genomic DNA and total RNA from microbial communities.

Main Results:

Optimal bacterial detection was achieved with 25 PCR amplification cycles.
Mathematical algorithms reduced deviations in measured abundance values caused by PCR and cross-hybridization.
16S rRNA gene copy number adjustment revealed potential overestimation of Clostridia in some studies.
Analysis of total community RNA provided estimates of individual member metabolic activity.

Conclusions:

Optimized phylogenetic microarray methods enhance the reliability of intestinal microbiota profiling.
Complementary analysis of DNA and RNA allows simultaneous assessment of microbial community structure and function.
These advancements provide a more comprehensive understanding of complex microbial ecosystems.