TraitMech

TraitMech › GENOMICS

phage defense system

traitmech:000209 · CLASS · PROPOSED

A genomics trait describing possession of one or more bacterial or archaeal immune systems that inhibit bacteriophage infection.

Trait evidence (5)

  • DOI:10.1038/s41579-019-0278-2
    Viruses and their hosts are engaged in a constant arms race leading to the evolution of antiviral defence mechanisms

    Bernheim and Sorek define the bacterial bacteriophage-defense context and review the pan-genomic diversity and cost of antiviral defense systems.

  • DOI:10.1038/s41579-019-0278-2
    individual microorganisms often encode multiple distinct defence systems

    The pan-immune-system model supports treating possession of one or more defense systems as a strain-level genomics trait rather than a single protein, locus, or pathway.

  • DOI:10.1038/s41586-019-1894-8
    Bacteria have evolved numerous immune mechanisms, both innate and adaptive

    Hampton et al. review innate and adaptive anti-phage systems and the phage counter-defense mechanisms that evade them.

  • DOI:10.1038/s41586-019-1894-8
    Here we review the spectrum of anti-phage systems and highlight their evasion by bacteriophages

    This supports the umbrella scope spanning diverse CRISPR-Cas, restriction-modification, BREX, DISARM, abortive-infection, and related anti-phage defenses.

  • DOI:10.1126/science.aar4120
    Candidate immune systems were then experimentally validated for their activities

    The Science article summary for Doron et al. supports genomic discovery and experimental validation of antiphage defense systems from microbial pangenomes.

Antiphage defense systems resist viral challenge

Evidence-backed ontology sketch linking phage pressure to the umbrella phage-defense-system trait and its reviewed CRISPR-Cas and restriction-modification children.

NONMECHANISTIC · This parent trait groups independently reviewed genome-level anti-phage defense systems without claiming that CRISPR-Cas, restriction-modification, BREX, DISARM, abortive infection, or other defense families share one universal molecular mechanism.

Antiphage defense systems resist viral challenge Interactive directed graph showing evidence-backed causal relationships for phage defense system.

Edge evidence

  • bacteriophage pressure selects for phage defense system METPO:2007401

    Virus-host arms races select for microbial antiviral defense mechanisms.

    • DOI:10.1038/s41579-019-0278-2 constant arms race leading to the evolution of antiviral defence mechanisms Bernheim and Sorek frame bacteriophages and bacterial hosts as engaged in an evolutionary arms race.
  • CRISPR-Cas system is a phage defense system rdfs:subClassOf

    CRISPR-Cas possession is an adaptive phage-defense system.

    • DOI:10.1126/science.aar4120 well-known defense arsenals such as restriction-modification and CRISPR systems The Science article summary for Doron et al. places CRISPR systems among the recognized microbial defense arsenals.
  • restriction-modification system is a phage defense system rdfs:subClassOf

    Restriction-modification possession is an innate phage-defense system.

    • DOI:10.1126/science.aar4120 well-known defense arsenals such as restriction-modification and CRISPR systems The Science article summary for Doron et al. places restriction-modification systems among the recognized microbial defense arsenals.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1038/s41579-019-0278-2

Parent traits (1)

Children (262)

Synonyms (3)

  • antiphage defense system EXACT_SYNONYM · DOI:10.1126/science.aar4120
  • anti-phage system EXACT_SYNONYM · DOI:10.1038/s41586-019-1894-8
  • pan-immune system RELATED_SYNONYM · DOI:10.1038/s41579-019-0278-2

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Canonical examples (1)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

Discussions and Knowledge Gaps (1)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Resolve exact ontology xrefs for organism-level phage defense system possession before adding TraitRecord xrefs.

CURATION TODO OPEN phage-defense-system-xref-gap · raised by codex · 2026-09-15

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

The pinned METPO snapshot retains only obsolete phage defense, and GO:0051607 defense response to virus is a biological process rather than this GENOMICS possession trait. CRISPR-Cas, restriction-modification, BREX, DISARM, abortive-infection, and other mechanism terms are narrower than the umbrella parent curated here.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted phage defense system as a DOI-backed GENOMICS TraitRecord after an ignored-and-hidden duplicate review found only obsolete METPO phage defense and future-gap mentions; the replacement placeholder is reserved in proposals/metpo_traitmech_v86.