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

875
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...
875

You might also read

Related Articles

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

Sort by
Same author

Reproducible profiling of the gut microbiota using surplus clinical faecal immunochemical test samples.

Microbial genomics·2026
Same author

Environmental enteric dysfunction influences linear growth of children through insulin-like growth factor-1: findings from the Indonesian Action Against Stunting Hub birth cohort.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences·2026
Same author

Exploring the diet-microbiome-growth axis among under-2-year-old children: a case-control study in East Lombok, Indonesia.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences·2026
Same author

Big breakfast diet composition impacts on appetite control and gut health: a randomised weight loss trial in adults with overweight or obesity.

The British journal of nutrition·2026
Same author

Microbiota and kidney disease: the road ahead.

Nature reviews. Nephrology·2025
Same author

Guidelines for preventing and reporting contamination in low-biomass microbiome studies.

Nature microbiology·2025

Related Experiment Video

Updated: Apr 21, 2026

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
07:21

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Published on: August 25, 2018

13.7K

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.

Susannah J Salter1, Michael J Cox, Elena M Turek

  • 1Pathogen Genomics Group, Wellcome Trust Sanger Institute, Hinxton, UK. sb18@sanger.ac.uk.

BMC Biology
|November 13, 2014
PubMed
Summary

Contaminating DNA is common in lab kits and reagents, affecting microbial community studies. Researchers recommend sequencing negative controls to identify and mitigate this contamination in low biomass samples.

More Related Videos

A Method for Targeted 16S Sequencing of Human Milk Samples
09:09

A Method for Targeted 16S Sequencing of Human Milk Samples

Published on: March 23, 2018

10.4K
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

31.6K

Related Experiment Videos

Last Updated: Apr 21, 2026

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
07:21

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Published on: August 25, 2018

13.7K
A Method for Targeted 16S Sequencing of Human Milk Samples
09:09

A Method for Targeted 16S Sequencing of Human Milk Samples

Published on: March 23, 2018

10.4K
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

31.6K

Area of Science:

  • Microbiology
  • Genomics
  • Molecular Biology

Background:

  • Culture-independent techniques like 16S rRNA gene sequencing and metagenomics have transformed microbial community studies.
  • A significant challenge in these methods is DNA contamination from laboratory reagents and kits.
  • This contamination can confound results, especially in samples with limited microbial biomass.

Purpose of the Study:

  • To investigate the prevalence and impact of DNA contamination in common laboratory reagents.
  • To assess how this contamination affects microbial community analysis using sequencing-based methods.
  • To provide guidance on mitigating contamination in low biomass studies.

Main Methods:

  • Analysis of DNA contamination in various commercially available DNA extraction kits and reagents.
  • Assessment of the impact of contamination on both 16S rRNA gene sequencing and shotgun metagenomics.
  • Identification of common contaminating microbial genera.

Main Results:

  • Ubiquitous DNA contamination was detected across commonly used DNA extraction kits and reagents.
  • The composition of contaminating DNA varied significantly between different kits and batches.
  • Contamination critically impacted sequencing results, particularly for samples with low microbial biomass.
  • Both PCR-based 16S rRNA gene surveys and shotgun metagenomics were affected.

Conclusions:

  • Caution is advised when using sequence-based techniques for low biomass microbial environments.
  • Concurrent sequencing of negative control samples is strongly recommended to identify and account for contamination.
  • Implementing mitigation strategies is crucial for accurate microbial community analysis.