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

Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

815
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...
815

You might also read

Related Articles

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

Sort by
Same author

Analytic attributes of the 16S rRNA gene sequencing methodology for human gut microbiota characterization.

Applied microbiology and biotechnology·2026
Same author

Antagonistic drug interactions protect commensal <i>Bacteroidaceae</i> from macrolides via an RND-type efflux pump.

Gut microbes·2025
Same author

Non-antibiotics disrupt colonization resistance against enteropathogens.

Nature·2025
Same author

An anti-virulence drug targeting the evolvability protein Mfd protects against infections with antimicrobial resistant ESKAPE pathogens.

Nature communications·2025
Same author

Circulating hs-CRP, IL-18, Chemerin, Leptin, and Adiponectin Levels Reflect Cardiometabolic Dysfunction in Adults with Excess Weight.

International journal of molecular sciences·2025
Same author

Balancing act: counteracting adverse drug effects on the microbiome.

Trends in microbiology·2024

Related Experiment Video

Updated: Mar 16, 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

31.4K

Considerations For Optimizing Microbiome Analysis Using a Marker Gene.

Jacobo de la Cuesta-Zuluaga1, Juan S Escobar1

  • 1Vidarium - Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa , Medellín , Colombia.

Frontiers in Nutrition
|August 24, 2016
PubMed
Summary

Next-generation sequencing advances gut microbiome research using 16S rRNA analysis. Standardizing workflows is crucial for reproducible results in human microbiome studies.

Keywords:
16S rRNAgut microbiomenext-generation sequencingpersonalized medicinepersonalized nutrition

More Related Videos

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere
09:55

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere

Published on: May 2, 2018

28.4K
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

9.4K

Related Experiment Videos

Last Updated: Mar 16, 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

31.4K
Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere
09:55

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere

Published on: May 2, 2018

28.4K
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

9.4K

Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Next-generation sequencing (NGS) has revolutionized host-microbe interaction studies, particularly human gut microbiome research.
  • 16S rRNA gene sequencing is a key method for analyzing microbial communities, enhancing understanding of health, disease, and metabolism.
  • Current 16S rRNA workflows lack standardization, impacting study transparency and reproducibility.

Purpose of the Study:

  • To discuss common challenges in the 16S rRNA sequencing workflow.
  • To recommend essential technical information for publication to ensure reproducibility.
  • To encourage the use of tools that address common microbiome analysis problems.

Main Methods:

  • Review of the archetypical 16S rRNA sequencing workflow.
  • Identification of challenges in DNA extraction, PCR amplification, and sequencing.
  • Discussion of bioinformatic steps including denoising, chimera removal, OTU clustering, and taxonomic classification.

Main Results:

  • Identified key challenges in DNA extraction, PCR, sequencing, and bioinformatic processing.
  • Highlighted the impact of these steps on the reliability of gut microbiome study outcomes.
  • Emphasized the need for standardized reporting of methods and tools.

Conclusions:

  • Standardization of the 16S rRNA workflow is essential for reproducible gut microbiome research.
  • Clear reporting of technical details and use of appropriate bioinformatics tools can mitigate common analytical challenges.
  • Further efforts are needed to establish best practices for transparent and reliable microbiome studies.