Related Experiment Video
Updated: Mar 21, 2026
10:18
A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae
Published on: April 25, 2015
10.8K
PneumoWiki: a pan-genome-based database for the pathogen Streptococcus pneumoniae
Henry Mehlan1, Stephanie Hirschmann2, Larissa M Busch1
1Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.
Microbiology Spectrum
|March 20, 2026
Summary
PneumoWiki is a new database integrating genomic and functional data for 43 Streptococcus pneumoniae strains. This resource aids researchers in analyzing experimental data and understanding pneumococcal physiology across different strains.
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- Streptococcus pneumoniae is a significant human pathogen with extensive genomic variability and over 100 serotypes.
- It serves as a crucial model organism in basic and biomedical research, necessitating comprehensive data resources.
- Existing research often uses diverse strains, making comparative analysis challenging.
Purpose of the Study:
- To develop PneumoWiki, a manually curated, wiki-type database for Streptococcus pneumoniae.
- To integrate genomic data and functional annotations for 43 S. pneumoniae strains.
- To facilitate comparative genomics and analysis of pneumococcal strains for research.
Main Methods:
- Creation of a manually curated pan-genome database (PneumoWiki).
- Integration of genomic sequences, functional annotations, gene expression, protein function, and localization data.
- Development of interlinked pan-genome and strain-specific gene pages with comparative tools.
Main Results:
- PneumoWiki provides integrated genomic and functional data for 43 S. pneumoniae strains.
- The database features 'Gene pages' with comprehensive information including sequences, annotations, expression, function, and localization.
- Includes tools like ortholog tables, multi-strain genome viewer, and protein sequence alignment for comparative analysis.
Conclusions:
- PneumoWiki is a user-friendly, freely accessible resource for the research community.
- It supports the analysis and interpretation of experimental data for Streptococcus pneumoniae.
- Enables integration of knowledge across different S. pneumoniae strains, advancing pneumococcal research and understanding of its physiology.
More Related Videos
Related Concept Videos
01:08Evolution of Microbial Genome
2
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.
2
01:14Atypical Pneumonia
9
Atypical pneumonia, often caused by Mycoplasma pneumoniae, is a form of pulmonary infection that differs from the classical presentation of bacterial pneumonia in both its cause and clinical symptoms. Mycoplasma pneumoniae is a pleomorphic bacterium notable for its lack of a rigid cell wall. This structural characteristic imparts resistance to beta-lactam antibiotics and significantly influences the bacterium’s behavior within the human host.Other pathogens responsible for the disease...
9
00:46Genomic DNA in Prokaryotes
50.3K
The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...
Genomic Diversity in Bacteria
Although bacterial genomes are much...
50.3K
01:28Prokaryotic Gene Structure and Organization
2.7K
Prokaryotic genomes exhibit a streamlined organization of coding and non-coding regions essential for gene expression and protein synthesis. While coding regions contain the genetic instructions for proteins or functional RNAs, non-coding regions regulate the precise transcription and translation of these genes.Coding Regions: Proteins and RNAsThe primary coding regions, known as structural genes, include sequences transcribed into messenger RNA (mRNA) and ultimately translated into...
2.7K
03:36Genome Annotation and Assembly
21.4K
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.
21.4K
01:26Bacterial Phylum Proteobacteria
1.1K
Proteobacteria, one of the largest and most diverse bacterial phyla, encompasses a wide range of Gram-negative bacteria distinguished by their outer membrane composed of lipopolysaccharides. These microorganisms exhibit various metabolic capabilities, including phototrophy, chemolithotrophy, and heterotrophy, and thrive in diverse environments from soil to aquatic systems and host-associated niches. The phylum is divided into six classes: Alphaproteobacteria, Betaproteobacteria,...
1.1K