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

99
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...
99
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

64
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...
64
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.1K
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...
6.1K
Microbial Classification System01:24

Microbial Classification System

146
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...
146
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

14.0K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
14.0K
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

12.7K
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
12.7K

You might also read

Related Articles

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

Sort by
Same author

Resolving the evolutionary duality of marine symbionts: redefining the genus <i>Endozoicomonas</i> and proposing <i>Neoendozoicomonas</i> gen. nov.

ISME communications·2026
Same author

Metagenomics enables parallel detection of 176 clinically relevant targets from faecal samples.

Frontiers in cellular and infection microbiology·2026
Same author

Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments.

Genome biology and evolution·2026
Same author

A molecular inventory of the faecal microbiomes of 23 marsupial species.

Microbial genomics·2026
Same author

Metagenomic analysis of fecal microbiomes reveals genetic potential for diverse hydrogen management strategies in marsupials.

mSystems·2025
Same author

GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes.

Nucleic acids research·2025
Same journal

Cross-Domain Transfer Learning from Peptides to Metabolites Using a Multi-Property Fine-Tuned LLM.

Bioinformatics (Oxford, England)·2026
Same journal

Biomedical Concept Recognition with Error-aware Negative-enhanced Ranking Framework.

Bioinformatics (Oxford, England)·2026
Same journal

TEDLH: Domain HMMs for sensitive detection of remote homologues.

Bioinformatics (Oxford, England)·2026
Same journal

PLNFGL: Joint Estimation of Multi-Condition Gene Networks from Single-cell RNA-seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Aug 26, 2025

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens
13:03

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Published on: March 8, 2018

10.7K

GTDB-Tk v2: memory friendly classification with the genome taxonomy database.

Pierre-Alain Chaumeil1,2, Aaron J Mussig1, Philip Hugenholtz1

  • 1Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia.

Bioinformatics (Oxford, England)
|October 11, 2022
PubMed
Summary
This summary is machine-generated.

The Genome Taxonomy Database toolkit (GTDB-Tk) now requires less memory for bacterial genome classification. A new divide-and-conquer method improves accessibility for the microbiology community.

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

12.9K
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

2.3K

Related Experiment Videos

Last Updated: Aug 26, 2025

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens
13:03

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Published on: March 8, 2018

10.7K
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

12.9K
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

2.3K

Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • The Genome Taxonomy Database (GTDB) and its toolkit (GTDB-Tk) are essential for microbial taxonomy.
  • The increasing size of the GTDB bacterial reference tree has led to high memory demands (∼320 GB) for GTDB-Tk, hindering its usability.
  • Limited accessibility due to high memory requirements restricts the widespread adoption of GTDB-Tk in the microbiology community.

Purpose of the Study:

  • To present an optimized version of GTDB-Tk with reduced memory requirements.
  • To maintain high accuracy in taxonomic classification despite memory optimizations.
  • To enhance the accessibility and ease of use of GTDB-Tk for researchers.

Main Methods:

  • Implemented a divide-and-conquer strategy for taxonomic placement.
  • Initially placed user genomes into a bacterial reference tree with family-level representatives.
  • Subsequently, placed genomes into appropriate class-level subtrees containing species representatives.

Main Results:

  • Substantially reduced the memory footprint of GTDB-Tk.
  • Achieved minimal impact on the accuracy of taxonomic classification.
  • Improved the efficiency of the GTDB-Tk classification process.

Conclusions:

  • The updated GTDB-Tk effectively lowers memory requirements through a novel approach.
  • The optimized GTDB-Tk maintains classification accuracy, making it more accessible.
  • This advancement facilitates broader adoption and application of GTDB-Tk in microbial genomics research.