Related Experiment Video
Updated: Jul 18, 2026
09:40
Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
Published on: June 11, 2015
First complete genome sequence of two Staphylococcus epidermidis bacteriophages
Anu Daniel1, Penelope E Bonnen, Vincent A Fischetti
1Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, NY 10021, USA. adaniel@rockefeller.edu
Journal of Bacteriology
|December 19, 2006
Summary
This study presents the first complete genome sequences for two Staphylococcus epidermidis phages, phiPH15 and phiCNPH82. These findings offer new insights into phage-host interactions and the evolution of S. epidermidis phages.
Area of Science:
- Microbiology
- Virology
- Genomics
Background:
- Staphylococcus epidermidis is a significant opportunistic pathogen causing hospital-acquired infections, particularly in patients with medical implants.
- Bacteriophages are crucial mediators of horizontal gene transfer, influencing the evolution of bacterial virulence factors.
- Understanding phage genomes is essential for elucidating phage-host biology and evolutionary dynamics.
Purpose of the Study:
- To present the complete genome sequences and molecular characterization of two novel S. epidermidis phages, phiPH15 and phiCNPH82.
- To investigate the genomic similarities and functional differences between these two phages.
- To establish a phylogenetic framework for S. epidermidis phages within the broader Siphoviridae family.
Main Methods:
- Whole-genome sequencing and assembly of phiPH15 and phiCNPH82.
- Bioinformatic analysis of genome sequences, including homology and gene content comparison.
- Phylogenetic analysis of Siphoviridae using phage proteomic tree data.
- In vivo splicing assays for phage-derived introns.
Main Results:
- The complete genomes of phiPH15 and phiCNPH82, both belonging to the Siphoviridae family, were elucidated.
- Both phages formed stable lysogens, with high sequence homology but distinct functional differences in their lysogeny modules.
- The phiPH15 genome contained two introns demonstrating in vivo splicing, with predicted secondary structures similar to those of Streptococcus thermophilus phage introns.
- Phylogenetic analyses revealed that phiPH15 and phiCNPH82 form a novel clade within the Staphylococcus aureus phage group, enhancing siphophage resolution.
Conclusions:
- This study provides the first comprehensive genomic and molecular description of S. epidermidis phages.
- The findings highlight the role of bacteriophages in S. epidermidis evolution and provide a foundation for future research into phage-host interactions.
- The identified novel phage clade offers improved resolution within the Siphoviridae family phylogenetic tree.
Related Concept Videos
01:26DNA Bacteriophages
Bacteriophages, or phages, are viruses that specifically infect bacteria, utilizing their genetic material to hijack host cellular machinery for replication. DNA bacteriophages employ single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) genomes. These phages exhibit diverse replication strategies and host interactions, influencing their ecological roles and applications in biotechnology and medicine.ssDNA BacteriophagesssDNA phages, with their small genomes, utilize unique strategies to...
01:23Bacteriophages of the Human Virome
Bacteriophages are found throughout the human body. They may even outnumber eukaryotic viruses, forming an important and dynamic component of the human virome. Indeed, phages represent the most abundant viral entities, with densities in the gut reaching up to 10⁹ particles per gram of fecal matter, and many belonging to orders such as Caudovirales and Microviridae, while a substantial proportion remains unclassified as viral “dark matter.”Lysogeny and Genetic ExchangeIn the gut, bacteriophages...
01:30Lytic Cycle of Bacteriophages
Bacteriophages, also known as phages, are specialized viruses that infect bacteria. A key characteristic of phages is their distinctive “head-tail” morphology. A phage begins the infection process (i.e., lytic cycle) by attaching to the outside of a bacterial cell. Attachment is accomplished via proteins in the phage tail that bind to specific receptor proteins on the outer surface of the bacterium. The tail injects the phage’s DNA genome into the bacterial cytoplasm. In the lytic replication...
00:43Lysogenic Cycle of Bacteriophages
In contrast to the lytic cycle, phages infecting bacteria via the lysogenic cycle do not immediately kill their host cell. Instead, they combine their genome with the host genome, allowing the bacteria to replicate the phage DNA along with the bacterial genome. The incorporated copy of the phage genome is called the prophage. Some prophages can re-activate and enter the lytic cycle. This often occurs in response to a perturbation, such as DNA damage, but can also transpire in the absence of...
01:20Viral Replication: Lytic Cycle
Bacteriophages, or phages, are viruses that specifically infect bacteria. Among them, T-even bacteriophages, such as T4, exhibit a well-characterized lytic replication cycle in Escherichia coli (E. coli). This process ensures the rapid proliferation of the virus while ultimately leading to the destruction of the bacterial host.Attachment and DNA InjectionThe infection process begins with the recognition and binding of the T4 phage to the E. coli cell surface. Tail fibers of the phage...
01:29Viruses of Archaea
Archaeal viruses play a crucial role in the ecosystems of extremophilic archaea, particularly those belonging to the phyla Euryarchaeota and Crenarchaeota. By shaping host evolution and facilitating gene transfer, these viruses influence microbial communities and contribute to genetic diversity in extreme environments. The archaea they infect thrive in acidic hot springs and hydrothermal vents characterized by high temperatures and low pH. Archaeal viruses exhibit remarkable structural...