Reference

The phage glossary

54 terms across phage biology, therapy, resistance, regulation, and the microbiome — defined in plain English.

Biology Therapy Resistance Regulatory Microbiome

Biology

Adsorption: The first step of infection, in which a phage attaches to a receptor on the bacterial surface before injecting its genome. Adsorption rate strongly influences how effectively a phage kills its host.
Bacteriophage (phage): A virus that infects and replicates only inside bacteria, and is harmless to human and animal cells. They are the most abundant biological entities on Earth and are the basis of phage therapy.
Burst size: The average number of new phage particles released when an infected bacterium lyses. A larger burst size means faster amplification of the phage population.
Capsid: The protein shell (head) of a phage that encloses and protects its genetic material. Its structure helps define the phage's identity and stability.
CRISPR-Cas (in phage context): A bacterial immune system that uses guided enzymes to recognize and cut phage DNA; phages in turn carry anti-CRISPR countermeasures. CRISPR-Cas can also be engineered into phages to make programmable antibacterials.
Lysogeny: The dormant state in which a temperate phage's genome is integrated into or carried within a bacterium and replicated along with it, without producing new virions until induced.
Lytic phage: A phage that hijacks a bacterial cell to make new phage particles and then bursts (lyses) the cell to release them, killing the host. Lytic (virulent) phages are preferred for therapy because they reliably destroy bacteria.
Multiplicity of infection (MOI): The ratio of phage particles to bacterial cells in a given exposure. MOI is used to standardize experiments and to describe dosing in phage treatment.
Plaque: A clear zone in a lawn of bacteria on an agar plate where phages have killed the cells. Counting plaques is the standard way to measure how many infectious phages are present.
Prophage: The phage genome in its dormant, integrated form inside a bacterial host during lysogeny. A prophage can later be triggered to enter the lytic cycle.
Receptor: The specific molecule on a bacterium's surface (such as a sugar, protein, or pilus) that a phage binds to in order to initiate infection. Loss or alteration of the receptor is a common route to phage resistance.
Tail fibers: The leg-like protein appendages a phage uses to recognize and attach to specific molecules on the surface of a target bacterium. They are a key determinant of which bacteria a phage can infect.
Temperate (lysogenic) phage: A phage that can insert its genome into the host bacterium and lie dormant as a prophage instead of immediately killing it. These are generally avoided in therapy because they can transfer genes and do not consistently lyse the host.
Titre / PFU (plaque-forming units): A measure of phage concentration, expressed as plaque-forming units per milliliter (PFU/mL). The titre indicates how many infectious phage particles a preparation contains.
Transduction: The transfer of bacterial DNA from one bacterium to another by a phage. Transduction can spread genes, including antibiotic-resistance and virulence genes, which is one reason temperate phages are avoided therapeutically.

Therapy

Bacteremia: The presence of bacteria in the bloodstream, which can progress to sepsis if the body responds with widespread inflammation. Bloodstream infections by resistant bacteria are serious targets for phage therapy.
Cystic fibrosis (CF): A genetic disease causing thick mucus in the lungs that fosters chronic, hard-to-treat bacterial infections, especially with Pseudomonas aeruginosa. CF patients are a key population in phage therapy clinical trials.
Decolonization: The deliberate removal or reduction of a specific colonizing organism, such as a drug-resistant bacterium carried in the gut or nose, to prevent later infection or spread. Phages are being explored as targeted decolonization tools.
Depolymerase: A phage enzyme that degrades the protective capsule or biofilm polysaccharides surrounding bacteria, exposing them to phages, antibiotics, or the immune system. Depolymerases are valued for stripping bacterial defenses.
Endolysin (enzybiotic): A phage-encoded enzyme that breaks down the bacterial cell wall to release new phages, and which can be purified and used as an antibacterial drug on its own. Such enzyme-based antibacterials are called enzybiotics.
Engineered phage: A phage whose genome has been deliberately modified to improve host range, remove undesirable genes, add payloads, or make it strictly lytic. Genetic engineering is used to tailor phages for safer, more effective therapy.
Host range: The set of bacterial strains or species a given phage is able to infect. Phages typically have a narrow host range, which makes them precise but requires matching the phage to the patient's pathogen.
Necrotizing enterocolitis (NEC): A severe intestinal disease primarily affecting premature infants, in which gut tissue becomes inflamed and can die, often associated with harmful bacteria and microbiome imbalance. NEC is an active area of interest for phage-based prevention and treatment.
Phage cocktail: A defined mixture of multiple phages combined into one preparation to broaden coverage and reduce the chance bacteria evolve resistance. Cocktails are a common format for therapeutic phage products.
Phage steering: A strategy that uses phages to drive bacteria toward an evolutionary trade-off, forcing them to either resist the phage or stay sensitive to antibiotics. Steering exploits resistance costs to make infections easier to treat.
Phage susceptibility testing (phagogram): A laboratory test that determines which phages can kill a specific patient's bacterial isolate, analogous to an antibiotic susceptibility test. The resulting phagogram guides selection of phages for personalized treatment.
Phage-antibiotic synergy (PAS): The phenomenon in which phages and antibiotics together kill bacteria more effectively than either alone, sometimes even resensitizing resistant strains. PAS is a leading rationale for combining the two therapies.

Resistance

Antimicrobial resistance (AMR): The ability of microbes to survive drugs designed to kill them, making infections harder to treat. AMR is a global health crisis driving interest in alternatives like phage therapy.
Biofilm: A structured community of bacteria embedded in a self-produced slime matrix that sticks to surfaces and shields cells from antibiotics and the immune system. Phages and their enzymes can penetrate and disrupt biofilms.
ESKAPE pathogens: A group of six bacteria (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) that frequently cause hospital infections and 'escape' antibiotics. They are top priority targets for phage therapy.
MDR (multidrug-resistant): A bacterium that is non-susceptible to at least one agent in three or more classes of antibiotics. MDR organisms limit treatment options and are common candidates for phage therapy.
MIC (minimum inhibitory concentration): The lowest concentration of an antibiotic that prevents visible bacterial growth, used to gauge how susceptible a strain is. MIC values guide antibiotic selection and dosing.
PDR (pandrug-resistant): A bacterium resistant to every antibiotic in all available classes, leaving no standard treatment options. PDR infections represent the most extreme form of resistance.
Persister cell: A small subpopulation of dormant, slow-growing bacteria that survive antibiotic exposure without being genetically resistant, often causing relapsing infections. Persisters tolerate drugs by being metabolically inactive rather than mutating.
Phage resistance: The ability of bacteria to evade phage infection, commonly by altering or losing the surface receptor the phage targets. Resistance often comes with fitness costs that therapy can exploit, and is countered using cocktails or phage-antibiotic combinations.
XDR (extensively drug-resistant): A bacterium resistant to all but one or two remaining antibiotic classes. XDR infections leave very few effective drugs and are a major reason patients seek experimental phage treatment.

Regulatory

Antimicrobial stewardship: Coordinated efforts to use antibiotics appropriately, choosing the right drug, dose, and duration to preserve their effectiveness and slow resistance. Stewardship programs increasingly consider non-antibiotic options such as phages.
BLA (Biologics License Application): The US FDA application required to market a biological product, which is the regulatory category phage therapeutics fall under. Approval of a BLA would allow a phage product to be sold commercially.
Compassionate use: The provision of an experimental treatment to a seriously ill patient who has exhausted approved options, typically on a case-by-case basis. Much early modern phage therapy in the West has occurred under compassionate-use arrangements.
eIND (emergency IND) / expanded access: An FDA pathway allowing a patient with a serious or life-threatening condition to receive an unapproved therapy outside a clinical trial when no alternatives exist. Many US phage cases have been treated under emergency or expanded-access INDs.
GMP (Good Manufacturing Practice): The regulated quality standards governing how medicines are produced, tested, and documented for safety, purity, and consistency. Clinical-grade phage preparations must be manufactured under GMP.
IND (Investigational New Drug): A US FDA application that permits an unapproved drug, such as a phage product, to be used in human clinical trials. Obtaining an IND is the gateway to formal phage clinical research in the United States.
Magistral preparation: A medicine compounded by a pharmacist for an individual patient according to a prescription, used in some countries (notably Belgium) as a legal route to provide tailored phage preparations. It enables personalized phage therapy outside standard mass-market approval.
Master / working phage bank: A characterized, quality-controlled stock of a phage from which therapeutic batches are produced; the master bank is the original reference stock and working banks are derived from it for routine manufacturing. This two-tier banking system ensures consistency and traceability.
Phage characterization: The full genetic and biological profiling of a phage, including sequencing to confirm it is strictly lytic and free of toxin or resistance genes. Thorough characterization is required before a phage can be used therapeutically.

Microbiome

Colonization vs infection: Colonization means bacteria are present on or in the body without causing harm, whereas infection means they are invading tissue and causing disease. Distinguishing the two is essential to deciding when treatment is needed.
crAss-phage: A highly abundant family of phages first discovered computationally in human gut data, infecting common Bacteroides bacteria. crAss-phages are among the most prevalent viruses in the human gut and serve as markers of human fecal contamination.
Dysbiosis: An imbalance or disruption of the normal microbiome, often marked by loss of beneficial microbes or overgrowth of harmful ones. Dysbiosis is linked to infections and many chronic diseases.
Fecal microbiota transplantation (FMT): A procedure that transfers stool from a healthy donor into a patient to restore a balanced gut microbiome, most established for recurrent Clostridioides difficile infection. FMT is a microbiome-restoration therapy distinct from but conceptually related to phage approaches.
Keystone species: A microbe that exerts an outsized influence on the structure and function of a microbial community relative to its abundance. Loss of a keystone species can destabilize the whole microbiome.
Microbiome: The community of microorganisms (bacteria, viruses, fungi, and others) and their genes living in a particular environment such as the human gut. A healthy microbiome supports digestion, immunity, and resistance to pathogens.
Pathobiont: A normally harmless member of the microbiome that can cause disease under certain conditions, such as dysbiosis or a weakened immune system. Pathobionts blur the line between commensal and pathogen.
Phageome: The complete collection of phages within a particular environment or body site, such as the gut. The phageome is a major component of the microbiome's viral fraction.
Virome: The total community of viruses, including phages, present in a sample or body site. The gut virome is dominated by bacteriophages and shapes the bacterial community.