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 Experiment Video

Updated: Feb 24, 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

10.3K

Microbial Metagenomics Mock Scenario-based Sample Simulation (M3S3).

Y Motro1, J Moran-Gilad2

  • 1Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.

Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases
|August 17, 2017
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

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

Sort by
Same author

A real-time PCR for specific detection of the Legionella pneumophila serogroup 1 ST1 complex.

Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases·2019
Same author

Operational models and criteria for incorporating microbial whole genome sequencing in hospital microbiology - A systematic literature review.

Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases·2019
Same author

Diagnostic stewardship: are we using the right term?

Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases·2018
Same author

Bacterial next generation sequencing (NGS) made easy.

Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases·2018
Same author

A primer on microbial bioinformatics for nonbioinformaticians.

Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases·2018
Same author

Practical issues in implementing whole-genome-sequencing in routine diagnostic microbiology.

Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases·2017
Same journal

How stable are antimicrobial susceptibility profiles in serial clinical isolates? A retrospective study informing repeat-testing strategies.

Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases·2026
Same journal

Impact of low-dose chest CT and multiplex PCR on antibiotic usage for community-acquired pneumonia: multicentre prospective controlled before-after study with cluster randomisation (CAP-NEXT study).

Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases·2026
Same journal

Clinical Microbiology and Infection: how did we do in 2025?

Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases·2026
Same journal

Automate the work, not the decision: aligning expectations for AI in clinical microbiology.

Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases·2026
Same journal

Doxycycline prophylaxis and gonococcal resistance: reassurance, residual signals, and the case for surveillance.

Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases·2026
Same journal

Oral metronidazole versus clindamycin to treat bacterial vaginosis in pregnancies at risk for preterm labor.

Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases·2026
See all related articles

A new tool, Microbial Metagenomics Mock Scenario-based Sample Simulation (M3S3), generates virtual metagenomics samples for clinical microbiology. This aids in standardizing and validating culture-independent diagnostic methods by simulating diverse infectious disease scenarios.

Area of Science:

  • Clinical Microbiology
  • Bioinformatics
  • Metagenomics

Background:

  • Shotgun sequencing is increasingly used for unbiased, culture-independent diagnosis in clinical microbiology.
  • Standardization and validation of metagenomics methods are crucial for clinical integration.
  • Virtual metagenomics samples can serve as a substitute for real samples in validation processes.

Purpose of the Study:

  • To develop a novel solution for simulating metagenomics samples based on user-defined clinical scenarios.
  • To create a tool that aids in the validation of metagenomics applications for clinical use.

Main Methods:

  • The Microbial Metagenomics Mock Scenario-based Sample Simulation (M3S3) workflow was designed to generate virtual samples from raw reads or assemblies.
  • M3S3 outputs mock samples in FASTQ or FASTA format.
Keywords:
BioinformaticsDiagnosticsMetagenomicsQuality assuranceSimulation

More Related Videos

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
11:23

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

37.7K
Metagenomic Analysis of Silage
08:43

Metagenomic Analysis of Silage

Published on: January 13, 2017

19.2K

Related Experiment Videos

Last Updated: Feb 24, 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

10.3K
Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
11:23

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

37.7K
Metagenomic Analysis of Silage
08:43

Metagenomic Analysis of Silage

Published on: January 13, 2017

19.2K
  • The workflow was tested using 10 infectious disease scenarios with in silico spiked pathogens, generating 80 replicate samples analyzed by Taxonomer and Kraken db.

    • Main Results:

    • All 10 challenge scenarios were successfully simulated, producing virtual samples that accurately reflected user-defined sequence compositions.
    • Spiked pathogen sequences were identified in most replicates with acceptable abundance, showing minor variations between analysis software.
    • The virtual samples demonstrated the predicted composition and pathogen presence according to the input parameters.

    Conclusions:

    • The M3S3 tool successfully generates virtual samples on-demand, simulating various clinical diagnostic scenarios of differing complexity.
    • M3S3 provides a proof-of-concept for supporting the development and validation of standardized metagenomics applications in routine microbiology.
    • Despite the tool's capability, the integration of clinical metagenomics into routine practice remains a significant challenge.