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

359
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...
359

You might also read

Related Articles

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

Sort by
Same author

Safety and Immunogenicity of a PD-1-Enhanced HIV-1 Therapeutic DNA Vaccine: A Randomized, Double-Blind, Placebo-Controlled, Dose-Escalating Phase I Clinical Trial in People With HIV-1 on Antiretroviral Therapy.

The Journal of infectious diseases·2026
Same author

Non-contact Heart Sound Measurement by Defocused Speckle Imaging.

IEEE journal of biomedical and health informatics·2026
Same author

Rapid and quantitative phage susceptibility test by ramanome.

mLife·2026
Same author

Discovery and Structural Characterization of a Highly Protective Neutralizing Antibody Targeting the Mpox Virus A35R Protein.

MedComm·2026
Same author

Are we ready to replace animal models? A perspective on regulatory challenges of human-relevant drug testing systems.

Drug discoveries & therapeutics·2026
Same author

Metabolomic and transcriptomic features of the cardiometabolic disease spectrum in people living with HIV.

Infectious diseases & immunity·2026

Related Experiment Video

Updated: Nov 16, 2025

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing
08:05

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing

Published on: March 19, 2018

20.2K

A streamlined clinical metagenomic sequencing protocol for rapid pathogen identification.

Xiaofang Jia1, Lvyin Hu1, Min Wu1

  • 1Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.

Scientific Reports
|February 24, 2021
PubMed
Summary

We developed a streamlined metagenomic next-generation sequencing (mNGS) protocol for rapid, unbiased pathogen identification from diverse clinical samples. This method enhances diagnostic accuracy and supports precision medicine applications.

More Related Videos

Generating Whole Bacterial Genomes from Clinical Samples using a Target Enrichment Workflow
10:44

Generating Whole Bacterial Genomes from Clinical Samples using a Target Enrichment Workflow

Published on: August 15, 2025

853
Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
06:34

Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS

Published on: July 11, 2016

19.5K

Related Experiment Videos

Last Updated: Nov 16, 2025

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing
08:05

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing

Published on: March 19, 2018

20.2K
Generating Whole Bacterial Genomes from Clinical Samples using a Target Enrichment Workflow
10:44

Generating Whole Bacterial Genomes from Clinical Samples using a Target Enrichment Workflow

Published on: August 15, 2025

853
Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
06:34

Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS

Published on: July 11, 2016

19.5K

Area of Science:

  • Molecular Biology
  • Genomics
  • Infectious Disease Diagnostics

Background:

  • Metagenomic next-generation sequencing (mNGS) offers unbiased pathogen identification but requires simplified, reproducible assays for clinical utility.
  • Current mNGS protocols can be complex and time-consuming, limiting their application in rapid diagnostics.

Purpose of the Study:

  • To develop and validate a streamlined DNA/RNA library preparation protocol for Illumina and Oxford Nanopore sequencing.
  • To create a rapid data analysis pipeline for efficient pathogen identification.
  • To assess the clinical utility of the developed mNGS method for diverse sample types.

Main Methods:

  • Developed a simplified library preparation protocol for both Illumina and Oxford Nanopore platforms.
  • Evaluated Illumina mNGS sensitivity using known influenza A (H1N1) viral loads.
  • Tested Nanopore sequencing for rapid detection of influenza A and adenoviruses.
  • Analyzed clinical samples (respiratory swabs, sputum, CSF) using the developed mNGS protocol.
  • Compared mNGS results with quantitative PCR (qPCR) for pathogen detection.

Main Results:

  • Illumina mNGS demonstrated high sensitivity for RNA viruses (<6.4 × 10² EID50/mL for influenza A, H1N1) with good correlation between viral load and mapped reads.
  • Nanopore sequencing provided rapid turnaround times for viral detection.
  • An 81.8% concordance was observed between Illumina mNGS and qPCR for pathogen identification in respiratory samples.
  • The method successfully identified HIV-1 RNA and Toxoplasma gondii in CSF samples from patients with meningitis/encephalitis.

Conclusions:

  • A simplified, efficient mNGS protocol has been developed for comprehensive pathogen identification.
  • The protocol supports both Illumina and Oxford Nanopore sequencing, offering flexibility and speed.
  • The developed method enables clinically relevant pathogen detection from various sample types within a meaningful timeframe.