Bacteriophage

A bacteriophage, often abbreviated to phage, is a virus that infects and replicates within bacteria. The name derives from Greek, meaning “bacteria-eater”, reflecting its ability to destroy bacterial cells. Bacteriophages are found wherever bacteria exist and are now recognised as some of the most abundant and diverse biological entities on Earth. Beyond their ecological importance, they are central tools in molecular biology and are increasingly explored as alternatives or complements to antibiotics in the treatment of bacterial infections.

Definition and General Characteristics

Bacteriophages are viruses whose specific hosts are bacteria. Like all viruses, they are obligate intracellular parasites, lacking their own metabolic machinery and relying on the host cell to replicate.
Structurally, most bacteriophages consist of:

• A protein capsid enclosing their nucleic acid genome.
• A genome composed of either DNA or RNA, which may be single- or double-stranded.
• In many cases, additional elaborate tail structures used for host recognition and genome injection.

Their genomes vary enormously in size and complexity, from phages encoding as few as four genes (for example, some RNA phages such as bacteriophage MS2) to phages with hundreds of genes. Replication begins when the phage recognises specific receptors on the bacterial surface, attaches, and injects its genome into the bacterial cytoplasm. The viral genetic material then subverts the host, directing the production of new phage particles.

Diversity, Abundance and Ecological Roles

Bacteriophages are ubiquitous. They are present in soil, freshwater, marine environments, sewage, animal intestines, and any habitat where bacteria can grow. It is estimated that there are more than 10³¹ bacteriophages on Earth, a number exceeding all other organisms combined. Viruses in general, with bacteriophages making up a major fraction, are the most abundant biological entities in the oceans, where astonishing densities—up to hundreds of millions of viral particles per millilitre—have been recorded in microbial mats at the surface.
In marine and other microbial ecosystems, up to a large proportion of bacteria may be infected by phages at any given time. This constant infection and lysis of bacteria contributes to:

• Nutrient recycling via release of cellular contents.
• Regulation of bacterial population sizes.
• Maintenance of microbial diversity through “kill-the-winner” dynamics, where dominant bacterial strains are preferentially targeted.

Classification and Taxonomy

Bacterial viruses do not share a single common ancestor and therefore are distributed across several unrelated taxonomic groups. Modern viral taxonomy places bacteriophages in multiple realms and lineages, reflecting the independent evolution of different nucleic acid types and virion architectures.
Key higher-level taxa that include bacterial viruses encompass:

• Realm Duplodnaviria – including tailed double-stranded DNA phages in the class Caudoviricetes. These “head–tail” phages are often grouped by tail morphology into
  • Podoviruses (short tails),
  • Myoviruses (long contractile tails),
  • Siphoviruses (long non-contractile tails).
• Realm Monodnaviria – including bacterial viruses in the kingdoms Loebvirae and Sangervirae, primarily small single-stranded DNA viruses.
• Realm Riboviria – including several RNA virus lineages that infect bacteria, such as those placed in the phyla Artimaviricota and Lenarviricota, and classes such as Leviviricetes.
• Realm Singelaviria – with bacterial viruses in families such as Matsushitaviridae.
• Realm Varidnaviria – incorporating certain double-stranded DNA bacteriophages in classes such as Ainoaviricetes and orders such as Vinavirales, and members of the subphylum Prepoliviricotina.

In addition, families such as Obscuriviridae and Plasmaviridae remain unassigned to higher taxa but consist of bacterial viruses. This broad taxonomic spread underlines the evolutionary diversity of bacteriophages.

Historical Discovery and Early Phage Therapy

The antibacterial activity of filterable agents was noted before phages were formally recognised. In 1896, Ernest Hanbury Hankin reported that waters from the Ganges and Yamuna rivers in India contained an agent capable of killing Vibrio cholerae, even after filtration through porcelain filters that removed bacteria.
In 1915, British bacteriologist Frederick Twort described a mysterious agent that caused bacterial cultures to become glassy and clear. Unsure of its nature, he proposed that it might be a stage in the bacterial life cycle, an enzyme, or a virus.
Independent of Twort, French–Canadian microbiologist Félix d’Hérelle at the Pasteur Institute announced in 1917 that he had discovered an “invisible microbe” parasitic on bacteria. He coined the term bacteriophage, meaning “bacteria-devourer”, and soon applied his discovery clinically, reporting dramatic recovery in patients with bacterial dysentery. By 1919, d’Hérelle had carried out the first documented therapeutic use of bacteriophages in Paris, and by 1922 phage treatment was being trialled in the United States.

Structure and Replication Strategies

While phage morphology is diverse, many well-studied bacteriophages share a broadly similar architecture:

• An icosahedral head (capsid) containing the genome.
• A tail structure used for host recognition and genome delivery.
• Tail fibres and baseplates for specific binding to bacterial cell surface receptors.

Once attached, the phage injects its nucleic acid into the host. Classical phages exhibit two main types of life cycle:

• Lytic cycle – the phage commandeers host machinery to produce progeny virions, culminating in lysis of the bacterium and release of new phage particles.
• Temperate or lysogenic cycle – the phage integrates its genome into the bacterial chromosome (as a prophage) or persists as a plasmid-like element, replicating along with the host and potentially later entering the lytic cycle.

These strategies underpin both their ecological role and their utility in genetics and biotechnology.

Nobel Prize-Winning Phage Research

Bacteriophages have been central to foundational discoveries in molecular biology. In 1969, Max Delbrück, Alfred Hershey, and Salvador Luria received the Nobel Prize in Physiology or Medicine for their work using bacteriophages to elucidate principles of viral replication and genetic structure.
Key contributions include:

• The Hershey–Chase experiment (1952), which demonstrated that DNA, not protein, is the hereditary material, by tracking radioactively labelled phage components during infection.
• The Luria–Delbrück fluctuation test, which showed that bacterial mutations occur spontaneously and randomly, supporting Darwinian natural selection rather than Lamarckian inheritance.

These experiments established phages as powerful model systems for studying fundamental genetic processes.

Phage Therapy and Clinical Trials

Phage therapy—the use of bacteriophages to treat bacterial infections—was widely pursued during the early and mid-20th century, particularly in the former Soviet Union, Georgia, and parts of Central and Eastern Europe. Institutions such as the Eliava Institute in Tbilisi became major centres for phage research and clinical application. Phage preparations were used to treat a variety of infections, including wound and intestinal diseases, and were administered to soldiers in the Red Army.
In Western countries, enthusiasm waned after the discovery and mass production of antibiotics, which were easier to manufacture, standardise, and store. Limited understanding of phage biology and inconsistent trial designs further undermined confidence, and the Cold War climate discouraged adoption of Soviet-developed technologies.
Interest has revived in the context of rising antibiotic resistance. Modern clinical work includes:

• A regulated randomised double-blind Phase I trial published in 2009 that assessed a phage cocktail for infected venous leg ulcers. The study demonstrated safety but did not show clear efficacy, possibly because components of standard wound care such as silver and lactoferrin may have inactivated the phages.
• A controlled trial in Western Europe evaluating phage treatment for chronic ear infections caused by Pseudomonas aeruginosa, which reported safety and evidence of clinical benefit.

Numerous animal studies and experimental human applications have explored phage therapy for infected burns, chronic wounds, and respiratory infections such as those associated with cystic fibrosis.

Phage–Host and Immune Interactions

Bacteriophages interact with host systems in complex ways. Indirectly, they alter bacterial behaviour by encoding proteins that affect bacterial virulence, surface structures, and immune evasion. Directly, phages can influence the innate immune response and the clearance of bacteria from the body.
While many phages are explored as therapeutics, some, including members of the family Inoviridae, can complicate infections. These filamentous phages may contribute to the formation and stability of bacterial biofilms, reinforcing protective matrices and shielding bacteria from antibiotics, thereby promoting chronic infection.

Modern Applications and Engineered Phages

Contemporary research focuses on harnessing phages as precision tools against multidrug-resistant bacteria. Strategies include:

• Engineering phages able to overcome bacterial resistance mechanisms.
• Modifying phage genomes to express enzymes that degrade biofilms, enhancing antibiotic penetration.
• Using phage-derived enzymes such as endolysins as standalone antibacterial agents.
• Designing phage cocktails tailored to specific pathogens based on genomic analysis