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
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
Microbial Classification System01:24

Microbial Classification System

1.8K
Classification is the process of organizing organisms into hierarchically inclusive groups based on their phenotypic similarities or evolutionary relationships. A species comprises one or more strains, and closely related species are grouped into genera. Genera are further classified into families, families into orders, orders into classes, and so forth, up to the domain level, which is the broadest taxonomic rank derived from a combination of phenotypic and genotypic data.The nomenclature of...
1.8K
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
Evolution of Microbial Genome01:08

Evolution of Microbial Genome

110
Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.
110
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

You might also read

Related Articles

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

Sort by
Same author

Proteomic and Metabolomic Interplay in the Regulation of Energy Metabolism During Obesity and Metabolic Syndrome.

Diabetes/metabolism research and reviews·2025
Same author

Understanding the role of microbes in health and disease of farmed aquatic organisms.

Marine life science & technology·2024
Same author

Pseudoalteromonas simplex sp. nov. Isolated from the Skin of Bandtail Puffer Fish (Sphoeroides spengleri).

Current microbiology·2024
Same author

Prospecting Specific Protein Patterns for High Body Mass Index (BMI), Metabolic Syndrome and Type 2 Diabetes in Saliva and Blood Plasma From a Brazilian Population.

Proteomics. Clinical applications·2024
Same author

The dispersant Corexit 9500 and (dispersed) oil are lethal to coral endosymbionts.

Marine pollution bulletin·2024
Same author

Role of ABC Proteins in Secondary Metabolism and Immune (=Defensive) Response in Seaweeds.

Cells·2023
Same journal

Genome-wide analysis across Indian camel populations reveals genetic distinctiveness of the Kharai camel breed.

BMC genomics·2026
Same journal

Different genomic footprint of small insertion-deletion and structural variants determines the genetic divergence of indica and japonica rice.

BMC genomics·2026
Same journal

From nurse bee to queen egg: RNA-seq analysis of Apis mellifera eggs shows dietary protein-dependent gene regulation.

BMC genomics·2026
Same journal

A genome-wide association study to identify the genetic loci underlying carbapenem resistance in Acinetobacter baumannii.

BMC genomics·2026
Same journal

Comparative transcriptome analysis to reveal key drought stress-responsive genes in sorghum (Sorghum bicolor (L.) Moench).

BMC genomics·2026
Same journal

Tissue identity is the dominant determinant of cross-species transferability of a porcine developmental programme.

BMC genomics·2026
See all related articles

Related Experiment Video

Updated: May 4, 2026

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

Microbial genomic taxonomy.

Cristiane C Thompson1, Luciane Chimetto, Robert A Edwards

  • 1Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil. thompsoncristiane@gmail.com.

BMC Genomics
|December 25, 2013
PubMed
Summary
This summary is machine-generated.

Genomic data offers a unified microbial species definition. Strains sharing high Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI) are classified as the same species.

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
Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health
08:36

Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health

Published on: October 9, 2017

9.4K

Related Experiment Videos

Last Updated: May 4, 2026

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
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
Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health
08:36

Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health

Published on: October 9, 2017

9.4K

Area of Science:

  • Microbiology
  • Genomics
  • Taxonomy

Background:

  • Emerging need for a standardized genomic species definition across microbial studies.
  • Review of recent genomic taxonomy research for diverse microbial groups.

Discussion:

  • Proposes a unified species definition based on genomic metrics: >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity across multiple alignment genes, <10 in Karlin genomic signature, and >70% in silico Genome-to-Genome Hybridization (GGDH) similarity.
  • Discusses phylogenetic congruence using 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA), and supertree analysis for species within the same genus.

Key Insights:

  • Genomic data enables simultaneous definition of coherent phenotypic and genomic groups.
  • Recommends including draft genome sequences for type strains in new taxa descriptions for a comprehensive genomic overview.

Outlook:

  • Facilitates a more precise and universally applicable microbial classification system.
  • Aims to streamline the process of microbial species identification and description using genomic information.