Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Rapid Identification of Pathogens

Rapid Identification of Pathogens

MALDI-TOF MS has transformed clinical microbiology by offering a rapid and reliable method for pathogen identification. The traditional approach to microbial identification typically involves time-consuming culture techniques and biochemical tests, which can delay the initiation of appropriate antimicrobial therapy. MALDI-TOF MS avoids these delays by using characteristic ribosomal protein mass patterns of microbial cells, enabling accurate species-level identification within minutes.Principle...

Automated Microbial Diagnostics

Automated Microbial Diagnostics

Automated diagnostic analyzers have transformed clinical microbiology by providing rapid and reliable methods for pathogen identification and antibiotic susceptibility testing. Among these systems, the Vitek 2 is widely used because it automates the traditionally labor-intensive processes of microbial identification (ID) and antibiotic susceptibility testing (AST), delivering standardized and timely results that are essential for effective patient care.Microbial Identification with ID CardsThe...

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

Microbial Classification System

Microbial Classification System

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...

Modern Molecular Taxonomy

Modern Molecular Taxonomy

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...

Phylogenetic Species Concept in Microbiology

Phylogenetic Species Concept in Microbiology

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...

You might also read

Related Articles

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

Sort by

Same author

Tryptophan degradation by intestinal Bacteroides induces anti-tumor immunity and limits melanoma growth.

Cell reports. Medicine·2026

Same author

Wastewater-based epidemiology for public health - benefits and trade-offs of different molecular methods for the generation of actionable data in a small-town context.

Frontiers in public health·2026

Same author

stackPredAMR-a stacked random forest approach improves AMR phenotype prediction for multiple species and antimicrobial agents.

Bioinformatics advances·2026

Same author

Enteropathy produced in mice by intergenerational transmission of small intestinal microbiota from undernourished children.

Nature microbiology·2026

Same author

Tryptophan degradation by intestinal Bacteroides induces anti-tumor immunity and limits melanoma growth.

bioRxiv : the preprint server for biology·2026

Same author

Comparative Cost-Utility and Clinical Efficacy of 5-HT3 Receptor Antagonists in Sufentanil-Based PCIA: A Propensity Score-Matched Analysis.

Pain and therapy·2026

Search research articles

Related Experiment Video

Updated: Jul 18, 2026

From a Natural Product to Its Biosynthetic Gene Cluster: A Demonstration Using Polyketomycin from Streptomyces diastatochromogenes Tü6028

From a Natural Product to Its Biosynthetic Gene Cluster: A Demonstration Using Polyketomycin from Streptomyces diastatochromogenes Tü6028

Published on: January 13, 2017

The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation.

Leslie Klis McNeil¹, Claudia Reich, Ramy K Aziz

¹National Center for Supercomputing Applications, Urbana, IL 61801, USA. lkmcneil@ncsa.uiuc.edu

Nucleic Acids Research

|December 6, 2006

Summary

The National Microbial Pathogen Data Resource (NMPDR) offers curated bacterial genomes and biological subsystems for comparative analysis. This bioinformatics platform aids researchers in understanding pathogen genomes and developing new antimicrobial strategies.

More Related Videos

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Published on: August 25, 2018

Related Experiment Videos

Last Updated: Jul 18, 2026

From a Natural Product to Its Biosynthetic Gene Cluster: A Demonstration Using Polyketomycin from Streptomyces diastatochromogenes Tü6028

From a Natural Product to Its Biosynthetic Gene Cluster: A Demonstration Using Polyketomycin from Streptomyces diastatochromogenes Tü6028

Published on: January 13, 2017

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Published on: August 25, 2018

Area of Science:

Microbiology
Bioinformatics
Genomics

Background:

The National Microbial Pathogen Data Resource (NMPDR) is a NIAID-funded center supporting research on Category B pathogens.
It houses complete genomes of ~50 pathogenic bacterial strains and over 400 additional genomes for comparative analysis.

Purpose of the Study:

To provide a comprehensive bioinformatics platform for microbial pathogen research.
To offer integrated genome annotations using curated biological subsystems for consistent functional assignments.
To develop tools for genome analysis, including gene clustering and drug target identification.

Main Methods:

Integration of complete public genomes with curated biological subsystems.
Development of tools for genome analysis, such as gene clustering and signature gene identification.
Curation of essentiality data and development of in silico drug screening capabilities.

Main Results:

NMPDR provides access to ~50 curated pathogenic bacterial genomes and >400 contextual genomes.
Expertly curated biological subsystems enable consistent genome annotations and metabolic network reconstructions.
Tools for gene clustering, signature gene analysis, and curated essentiality data are available.

Conclusions:

NMPDR serves as a valuable resource for microbial pathogen research, offering integrated genomic data and bioinformatics tools.
The platform facilitates comparative genomics and aids in the identification of potential drug targets.
Ongoing development aims to enhance capabilities for in silico drug discovery and compound screening.