Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Modern Molecular Taxonomy

Modern Molecular Taxonomy

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...

You might also read

Related Articles

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

Sort by

Same author

Linkage-aware inference of fitness from short-read time-series genomic data.

Virus evolution·2026

Same author

MMRN1-EGFR drives sialylglycan-Siglec immune evasion in AML leukemia stem cells.

Cell stem cell·2026

Same author

PhaBOX2: an enhanced web server for discovering and analyzing viral contigs in metagenomic data.

Nucleic acids research·2026

Same author

A metatranscriptome based approach to predict multidrug resistance phenotypes in Klebsiella pneumoniae without culturing.

Journal of global antimicrobial resistance·2026

Same author

Fast and accurate identification of emerging viral reassortment from genome sequences.

Nucleic acids research·2026

Same author

PhaGCN_Cluster: A Scalable and Robust Framework for Automated Classification and Discovery of Viral Dark Matter from Metagenomes.

Interdisciplinary sciences, computational life sciences·2026

Same journal

Museomics reveals uncultured symbionts with biosynthetic potential in nudibranchs.

Microbiome·2026

Same journal

Population-based characterisation of child and adolescent oral bacterial microbiomes.

Microbiome·2026

Same journal

Uncovering transcriptional processes in microbial communities adapted to differing saline conditions in salt-weathered historic buildings.

Microbiome·2026

Same journal

IL-17A deficiency in HLA-DR3 transgenic mice enriches beneficial Prevotella species in gut to promote Tregs and reduce CNS autoimmunity.

Microbiome·2026

Same journal

Whole metagenome sequencing: not deep enough for complete microbial function recovery.

Microbiome·2026

Same journal

Differential rumen and hindgut microbiome and metabolome in Holstein female calves with divergent feed efficiency.

Microbiome·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jul 19, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

High-resolution strain-level microbiome composition analysis from short reads.

Herui Liao¹, Yongxin Ji¹, Yanni Sun²

¹Department of Electrical Engineering, City University of Hong Kong, Kowloon, China.

|August 16, 2023

Summary

This summary is machine-generated.

StrainScan offers high-resolution bacterial strain analysis for short reads, improving accuracy in identifying multiple strains within samples. This tool enhances microbial community composition analysis for researchers.

Keywords:

Metagenomic data Strain composition analysis k-mers indexing structure

More Related Videos

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

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

Published on: May 2, 2018

Analysis of Fecal Microbiota Dynamics in Lupus-Prone Mice Using a Simple, Cost-Effective DNA Isolation Method

Analysis of Fecal Microbiota Dynamics in Lupus-Prone Mice Using a Simple, Cost-Effective DNA Isolation Method

Published on: May 2, 2022

Related Experiment Videos

Last Updated: Jul 19, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

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

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

Published on: May 2, 2018

Analysis of Fecal Microbiota Dynamics in Lupus-Prone Mice Using a Simple, Cost-Effective DNA Isolation Method

Analysis of Fecal Microbiota Dynamics in Lupus-Prone Mice Using a Simple, Cost-Effective DNA Isolation Method

Published on: May 2, 2022

Area of Science:

Microbiology
Bioinformatics
Genomics

Background:

Bacterial strain variation necessitates precise composition analysis for understanding microbial community dynamics.
Metagenomic sequencing is crucial for microbial analysis, but existing tools struggle with highly similar genomes and multiple strains per species.
Accurate strain-level analysis is vital for fields ranging from clinical diagnostics to environmental microbiology.

Discussion:

StrainScan utilizes a novel tree-based k-mers indexing structure to enhance strain identification accuracy and manage computational complexity.
The tool was rigorously tested on simulated and real sequencing data, outperforming established methods like Krakenuniq and StrainSeeker.
StrainScan demonstrates superior performance in distinguishing between closely related bacterial strains.

Key Insights:

StrainScan achieves higher accuracy and resolution in strain-level composition analysis compared to current state-of-the-art tools.
The tool improves the F1 score by 20% in identifying multiple strains at the strain level.
Its novel indexing structure provides more informative analyses for single or multiple samples.

Outlook:

StrainScan's high-resolution capability enables more detailed insights into microbial populations.
The freely available source code facilitates broader adoption and further development in the research community.
Future applications may include improved diagnostics and ecological studies requiring precise strain-level data.