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

505
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...
505
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

15.2K
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...
15.2K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.8K
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...
6.8K

You might also read

Related Articles

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

Sort by
Same author

Early-life acquisition of antimicrobial resistance genes and strain-level genomic concordance across maternal-infant compartments.

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases·2026
Same author

Nutrient enrichment and connectivity jointly shape bacterioplankton taxonomic and functional diversity.

FEMS microbiology letters·2026
Same author

Species-specific prophage induction by ciprofloxacin in human gut metagenomes.

bioRxiv : the preprint server for biology·2026
Same author

Phosphorothioate DNA modification by BREX type 4 systems in the human gut microbiome.

Nature communications·2026
Same author

Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny.

The ISME journal·2025
Same author

Clinical and environmental wastewater-based bacteriophage surveillance for high-impact diarrheal diseases, including cholera, in Bangladesh.

mBio·2025

Related Experiment Video

Updated: Dec 27, 2025

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

2.7K

Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes.

Morteza M Saber1, B Jesse Shapiro1

  • 1Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada.

Microbial Genomics
|February 27, 2020
PubMed
Summary
This summary is machine-generated.

Multi-locus models, particularly elastic nets, show superior performance in bacterial genome-wide association studies (GWAS) for identifying causal variants, outperforming single-locus methods across various evolutionary scenarios. Further development is needed for highly clonal genomes.

Keywords:
GWASbacteriabenchmarkinglinkage disequilibriumpowersimulation

More Related Videos

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays
14:06

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Published on: November 12, 2012

46.9K
Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
09:40

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

12.6K

Related Experiment Videos

Last Updated: Dec 27, 2025

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

2.7K
Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays
14:06

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Published on: November 12, 2012

46.9K
Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
09:40

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

12.6K

Area of Science:

  • Microbial genomics
  • Population genetics
  • Bioinformatics

Background:

  • Genome-wide association studies (GWAS) are crucial for understanding microbial genetics, including antibiotic resistance and virulence.
  • Bacterial GWAS face challenges due to clonal reproduction, strong population structure, and genome-wide linkage, complicating the identification of causal variants.
  • Existing GWAS methods' performance in correcting for population structure requires systematic evaluation across diverse evolutionary scenarios.

Purpose of the Study:

  • To develop and utilize a bacterial GWAS simulator (BacGWASim) for evaluating GWAS method performance.
  • To comprehensively assess the performance of single-locus and multi-locus GWAS approaches under varying evolutionary parameters.
  • To identify the most effective GWAS models for detecting causal genetic variants in bacteria.

Main Methods:

  • Development of BacGWASim to generate simulated bacterial genomes with controlled mutation, recombination, and causal variant rates.
  • Evaluation of three single-locus GWAS methods (cluster-based, dimensionality-reduction, linear mixed models) and one multi-locus elastic net model.
  • Assessment of method performance (recall and precision) across simulated sample sizes, recombination rates, and causal mutation effect sizes.

Main Results:

  • All tested GWAS methods improved with larger sample sizes and stronger causal variant effect sizes.
  • Multi-locus elastic net models demonstrated consistently high performance, superior power in detecting causal variants (low and high effect sizes), and better control for linkage disequilibrium compared to single-locus models.
  • Method performance varied with population structure correction strategies, and all methods struggled with highly clonal (low-recombining) genomes.

Conclusions:

  • Multi-locus models, especially elastic nets, hold significant potential for enhancing bacterial GWAS accuracy and power.
  • BacGWASim provides a valuable resource for benchmarking and developing new bacterial GWAS methodologies.
  • Further methodological advancements are necessary to improve GWAS performance in low-recombining bacterial populations.