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

Development of Human Microbiota01:30

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...

You might also read

Related Articles

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

Sort by
Same author

Evaluation of a novel experimental NanoQuil vaccine against <i>Staphylococcus aureus-</i>induced mastitis.

The Journal of dairy research·2026
Same author

Metabolic and hormonal effects of whole grains of rye, oats and wheat in dog food.

Journal of animal science·2025
Same author

Broadly Sourced Alternative Proteins Alter Muscle Metabolome While Maintaining Sensory Quality in Rainbow Trout (<i>Oncorhynchus mykiss</i>).

Journal of agricultural and food chemistry·2025
Same author

Metabolite Biomarkers Linking a High-Fiber Rye Intervention with Cardiometabolic Risk Factors: The RyeWeight Study.

Journal of agricultural and food chemistry·2025
Same author

Evaluation of an automatic image classifier for analysis of bacterial growth on a multiple-agar plate developed for bovine mastitis.

PloS one·2025
Same author

Methodological aspects of investigating the resistome in pig farm environments.

Journal of microbiological methods·2025

Related Experiment Video

Updated: Jul 10, 2026

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

9.9K

Similarity in milk microbiota in replicates.

Josef Dahlberg1, Erik Pelve2, Johan Dicksved3

  • 1Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.

Microbiologyopen
|October 25, 2023
PubMed
Summary

Reproducible science requires consistent results. Repeated DNA extraction and sequencing significantly impact low microbial biomass studies, affecting species richness and overall variation, challenging reproducibility in microbiome research.

Keywords:
microbiotamilkmock communityrepeatabilityreproducibility

More Related Videos

An Efficient Single&mdash;Person Technique for Milk Sampling from Laboratory Mice
04:56

An Efficient Single—Person Technique for Milk Sampling from Laboratory Mice

Published on: March 28, 2025

664
Individualized Reconstitution of Human Milk Microbiota: A Feasible Approach in Real-World Settings
04:16

Individualized Reconstitution of Human Milk Microbiota: A Feasible Approach in Real-World Settings

Published on: February 7, 2025

484

Related Experiment Videos

Last Updated: Jul 10, 2026

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

9.9K
An Efficient Single&mdash;Person Technique for Milk Sampling from Laboratory Mice
04:56

An Efficient Single—Person Technique for Milk Sampling from Laboratory Mice

Published on: March 28, 2025

664
Individualized Reconstitution of Human Milk Microbiota: A Feasible Approach in Real-World Settings
04:16

Individualized Reconstitution of Human Milk Microbiota: A Feasible Approach in Real-World Settings

Published on: February 7, 2025

484

Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Scientific reproducibility is crucial, yet challenges persist, particularly in microbiome studies.
  • Low microbial biomass environments present unique difficulties for consistent analysis.
  • Previous studies have highlighted a reproducibility crisis in science, impacting various fields.

Purpose of the Study:

  • To assess the impact of repeated DNA extraction and sequencing on bovine milk microbiota analysis.
  • To quantify the variability introduced by different sequencing runs in microbiome studies.
  • To investigate the reproducibility of results in low microbial biomass samples.

Main Methods:

  • DNA extraction was performed twice on 44 bovine milk samples.
  • The V3-V4 region of the 16S rRNA gene was sequenced in two separate runs.
  • Bioinformatic analysis of FASTQ files used identical pipelines and settings for comparison.

Main Results:

  • Significant differences in species richness were observed between sequencing runs.
  • Sequencing run was identified as a significant driver of variation in multivariate analyses.
  • Average similarity between samples and sequencing runs ranged from 42%-45%, indicating substantial run-dependent variability.

Conclusions:

  • Repeated DNA extraction and sequencing can significantly alter results in low microbial biomass studies.
  • Variability introduced by technical procedures like DNA extraction and sequencing impacts microbiome reproducibility.
  • Findings underscore the need for careful consideration of technical protocols in microbiome research to ensure reliable results.