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

836
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...
836
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.8K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.8K
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

705
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
705
Phylogenetic Species Concept in Microbiology01:22

Phylogenetic Species Concept in Microbiology

204
The phylogenetic species concept (PSC) is a framework used to delineate species based on evolutionary relationships, emphasizing shared ancestry and diagnosable genetic traits. Unlike morphological or biological species concepts, the PSC is particularly advantageous for microbial taxonomy, where traditional reproductive or phenotypic criteria often fall short due to the prevalence of asexual reproduction, minimal morphological differentiation, and widespread horizontal gene transfer among...
204
Microbial Phylogeny01:28

Microbial Phylogeny

88
Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
88
Methods of Classification and Identification01:28

Methods of Classification and Identification

2.3K
Bacterial identification relies on a diverse array of techniques to classify and understand microorganisms, each tailored to uncover specific characteristics. Traditional morphological approaches, while still valuable, are limited for closely related or structurally simple organisms. Modern methods integrate biochemical, serological, genetic, and advanced molecular tools to achieve greater accuracy.Morphological and Biochemical TechniquesMorphological characteristics, such as cell shape and...
2.3K

You might also read

Related Articles

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

Sort by
Same author

Identification of enteric viral pathogens in Tanzanian children under the age of five with diarrhea using nanopore-based metagenomic sequencing.

Virology·2026
Same author

Microbial composition of archaeological middens: tracing human footprints through centuries in Greenland's ancient settlements.

Frontiers in microbiology·2026
Same author

Author Correction: Geographics and bacterial networks differently shape the acquired and latent global sewage resistomes.

Nature communications·2026
Same author

Whole-genome sequencing reveals a previously unrecognized measles virus cluster in Burundi.

PloS one·2026
Same author

Capacity building for genomic surveillance of mpox and other emerging diseases in resource-limited settings within the African Great Lakes region.

Communications medicine·2026
Same author

Impact of ceftiofur administration and <i>Escherichia coli</i> inoculation on the calf fecal microbiome.

mSystems·2026

Related Experiment Video

Updated: May 2, 2026

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

720

Benchmarking of methods for genomic taxonomy.

Mette V Larsen1, Salvatore Cosentino, Oksana Lukjancenko

  • 1Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.

Journal of Clinical Microbiology
|February 28, 2014
PubMed
Summary

Whole-genome sequencing offers advanced prokaryotic species identification beyond the limitations of 16S rRNA gene sequencing. KmerFinder demonstrated the highest accuracy, correctly identifying 93-97% of isolates in comprehensive evaluations.

More Related Videos

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

12.2K
Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

2.1K

Related Experiment Videos

Last Updated: May 2, 2026

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

720
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

12.2K
Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

2.1K

Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Accurate prokaryotic species identification is crucial in microbiology.
  • Traditional 16S rRNA gene sequencing has limitations for distinguishing closely related species.
  • Whole-genome sequencing provides a more comprehensive approach to microbial taxonomy.

Purpose of the Study:

  • To benchmark five whole-genome sequencing-based methods for prokaryotic species identification.
  • To evaluate method performance on diverse datasets including short reads and draft genomes.
  • To identify the most accurate method for microbial species delineation.

Main Methods:

  • Comparison of five methods: SpeciesFinder (16S rRNA), Reads2Type (50-mers), rMLST (ribosomal genes), TaxonomyFinder (protein domains), and KmerFinder (k-mers).
  • Training and benchmarking on a dataset of complete prokaryotic genomes.
  • Performance evaluation using three datasets comprising over 11,000 isolates.

Main Results:

  • Methods relying solely on core chromosomal genes struggled with closely related species.
  • KmerFinder exhibited the highest overall accuracy, correctly identifying 93% to 97% of isolates.
  • Evaluation covered 159 genera and 243 species, demonstrating broad applicability.

Conclusions:

  • Whole-genome based methods offer superior prokaryotic species identification compared to 16S rRNA gene sequencing.
  • KmerFinder is a highly accurate and reliable tool for microbial species delineation.
  • The study provides valuable insights for selecting appropriate genomic methods in microbiology.