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

Bacterial Transformation01:33

Bacterial Transformation

60.1K
In 1928, bacteriologist Frederick Griffith worked on a vaccine for pneumonia, which is caused by Streptococcus pneumoniae bacteria. Griffith studied two pneumonia strains in mice: one pathogenic and one non-pathogenic. Only the pathogenic strain killed host mice.
Griffith made an unexpected discovery when he killed the pathogenic strain and mixed its remains with the live, non-pathogenic strain. Not only did the mixture kill host mice, but it also contained living pathogenic bacteria that...
60.1K
Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

32.8K
Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
32.8K
Thermal Strain01:19

Thermal Strain

2.9K
Thermal strain is a concept that arises when we consider how temperature changes affect structures. Unlike the conventional assumption that structures remain constant under load, real-world scenarios often involve temperature fluctuations that can significantly impact these structures. Consider a homogeneous rod with a uniform cross-section resting freely on a flat horizontal surface. If the rod's temperature increases, the rod elongates. This elongation is proportional to the temperature...
2.9K
Shearing Strain01:20

Shearing Strain

1.4K
The shearing strain represents a cubic element's angular change when subjected to shearing stress. This type of stress can transform a cube into an oblique parallelepiped without influencing normal strains. The cubic element experiences a significant transformation when exposed solely to shearing stress. Its shape alters from a perfect cube into a rhomboid, clearly demonstrating the effect of shearing strain. The degree of this strain is considered positive if it reduces the angle between the...
1.4K
Measurements of Strain01:27

Measurements of Strain

2.6K
Strain quantifies the deformation of a material under force, typically measured as normal strain, which represents the change in length when compared with the original length. Electrical strain gauges are used for enhanced accuracy. These devices consist of a conductive wire mounted on a paper backing that adheres to the material's surface. These gauges operate on the piezoresistive effect, where the wire's electrical resistance changes in response to mechanical deformation. The strain...
2.6K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

11.9K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
11.9K

You might also read

Related Articles

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

Sort by
Same author

A more complete picture: capturing single nucleotide variant diversity in extended-spectrum beta-lactamase producing <i>Escherichia coli</i> using post-enrichment metagenomics.

Microbial genomics·2026
Same author

Pre-clinical efficacy of a candidate outer membrane vesicle gonococcal vaccine in comparison with 4CMenB.

NPJ vaccines·2026
Same author

CRISPR-based environmental detection of Burkholderia pseudomallei identifies sanitation gaps and melioidosis risk in northeast Thailand.

Nature communications·2026
Same author

Bayesian network tool for analyzing the cost-effectiveness of bulk forensic trace DNA profiling.

Journal of forensic sciences·2026
Same author

Strain-level transmission inference across multi-kingdom metagenomic data using TRACS.

Nature microbiology·2026
Same author

Antibiotic and healthcare exposure impact on dynamics of third-generation cephalosporin-resistant Enterobacterales colonisation in Cambodian children: a six-month cohort study.

Antimicrobial resistance and infection control·2026
Same journal

Isolation of Mesenchymal Stem Cell-Derived Extracellular Vesicles.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Modeling Melanoma Immune Surveillance by CAR-T Cells in Human Skin Organoids.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Stepwise Optimization of a Matrigel-Based In Vitro Angiogenesis Assay for Reproducible and Quantifiable 2D-Tube Formation Using HUVECs.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Quantifying Mechanical Properties of Fresh Ovarian Tissue with Optical Brillouin Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

3D Chromatin Architecture During Early Development: New Methods and New Findings.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Metabolic Plasticity in Embryogenesis Throughout the Lens of NAD<sup></sup>.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Feb 7, 2026

Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing
09:44

Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing

Published on: December 23, 2022

2.9K

Identifying Bacterial Strains from Sequencing Data.

Tommi Mäklin1, Jukka Corander1,2, Antti Honkela3,4

  • 1Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.

Methods in Molecular Biology (Clifton, N.J.)
|July 22, 2018
PubMed
Summary
This summary is machine-generated.

Accurately identifying organisms in mixed bacterial samples is challenging. The new BIB method uses clustering to estimate relative abundances of bacterial species and strains from sequencing data.

Keywords:
Abundance estimationBacteriaMetagenomicsProbabilistic modellingStrain identification

More Related Videos

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project
10:19

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Published on: April 8, 2017

18.1K
High Throughput Yeast Strain Phenotyping with Droplet-Based RNA Sequencing
07:55

High Throughput Yeast Strain Phenotyping with Droplet-Based RNA Sequencing

Published on: May 21, 2020

7.5K

Related Experiment Videos

Last Updated: Feb 7, 2026

Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing
09:44

Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing

Published on: December 23, 2022

2.9K
Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project
10:19

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Published on: April 8, 2017

18.1K
High Throughput Yeast Strain Phenotyping with Droplet-Based RNA Sequencing
07:55

High Throughput Yeast Strain Phenotyping with Droplet-Based RNA Sequencing

Published on: May 21, 2020

7.5K

Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Mixed bacterial communities are prevalent in environmental and clinical settings.
  • Accurate identification and quantification of individual bacterial species and strains within these complex mixtures remain a significant challenge.
  • High-throughput sequencing generates vast amounts of data, necessitating robust analytical methods.

Purpose of the Study:

  • To introduce BIB, a novel probabilistic method for analyzing mixed bacterial samples.
  • To enable accurate estimation of relative abundances of bacterial species and strains in complex microbial communities.
  • To leverage short-read high-throughput sequencing data for microbial community profiling.

Main Methods:

  • Development of BIB, a probabilistic computational pipeline.
  • Grouping of closely related bacterial strains into distinct clusters.
  • Application of the BIB pipeline to analyze short-read high-throughput sequencing data from mixed samples.

Main Results:

  • BIB effectively estimates the relative abundances of bacterial clusters within mixed samples.
  • The method facilitates the differentiation and quantification of closely related strains.
  • Successful application of BIB for microbial community analysis.

Conclusions:

  • BIB provides a robust solution for quantifying bacterial abundances in mixed samples.
  • The clustering approach enhances the accuracy of strain-level abundance estimation.
  • BIB is a valuable tool for microbial ecology and clinical diagnostics.