Related Experiment Video
Updated: May 31, 2026
09:40
Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
Published on: June 11, 2015
Phage-plasmid-like elements are found throughout diverse environments and encode niche-specific functional traits.
James I Mullet1,2, Liqing Zhang3, Amy Pruden1
1Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia, United States of America.
Plos One
|May 29, 2026
Summary
Phage-plasmids, mobile genetic elements, are widespread across diverse environments. These elements carry antibiotic resistance and defense genes, influencing microbial ecology.
Area of Science:
- Microbiology
- Genomics
- Environmental Science
Background:
- Phage-plasmids are mobile genetic elements with dual functions of plasmids and temperate phages.
- Their functional traits and environmental distribution remain largely uncharacterized.
- Previous studies noted antibiotic resistance and defense genes but lacked comprehensive analysis.
Purpose of the Study:
- To identify and characterize phage-plasmids from public genome databases.
- To investigate the environmental distribution and prevalence of phage-plasmids.
- To determine the functional traits encoded by phage-plasmids across various environments.
Main Methods:
- Genome sequence mining of public phage and plasmid databases.
- Utilized a random forest classifier to identify phage-plasmid genomes.
- Performed comparative sequence analysis on identified genomes.
Main Results:
- Identified 5,712 unique phage-plasmid-like genomes from diverse environments (human, animal, plant, soil, water, etc.).
- Host-associated phage-plasmids were enriched in defense systems (CRISPR, anti-CRISPR) and antibiotic resistance genes.
- Freshwater and saltwater phage-plasmids frequently encoded biosynthetic pathway components.
- Genes for anti-CRISPR and specific antibiotic resistance were found to be enriched in phage-plasmids compared to plasmids and phages alone.
Conclusions:
- Phage-plasmids are prevalent across a wide range of environments.
- They encode diverse functional traits that vary depending on the environmental niche.
- Phage-plasmids likely play a significant role in shaping microbial ecology and evolution.
Related Concept Videos
01:28Plasmids
Plasmids are extrachromosomal DNA molecules found in bacteria, archaea, and some eukaryotic microbes like yeast. These small, circular DNA structures typically contain fewer than 30 genes, although some may exist linearly. Plasmids vary in their number within a cell, known as copy number. Single-copy plasmids are present in one copy per cell and multi-copy plasmids are present in multiple copies, reaching over 100 copies per cell.Plasmids usually replicate independently of the chromosomal DNA...
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...
01:26DNA 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...
01:16Viral Replication: Lysogenic Cycle
The lysogenic cycle is a crucial viral replication strategy that allows bacteriophages to persist within host cells without immediately destroying them. This process is primarily observed in temperate phages, such as bacteriophage lambda (λ), which infects Escherichia coli. The cycle allows the viral genome to persist across bacterial generations while keeping host cells viable.Integration of the Viral GenomeUpon infection, bacteriophage lambda attaches to the bacterial surface and injects its...
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...
01:08Evolution of Microbial Genome
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.