Evidence map›Paper›PMID 39119896›Full record

ArticleNucleic acids research2024

Discovery of antiphage systems in the lactococcal plasmidome.

Andriana Grafakou, Cas Mosterd, Matthias H Beck, Philip Kelleher, Brian McDonnell, Paul P de Waal, Irma M H van Rijswijck, Noël N M E van Peij, Christian Cambillau, Jennifer Mahony and 1 more

Abstract read
In one paragraph

Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

12 citing papers in PubMed.

  1. Revisiting the life cycle of temperate phages.Nature reviews. Microbiology · 2026
    Review
  2. A host-encoded prophage targets a Candidate Phyla Radiation bacterium and shapes episymbiotic interactions.Proceedings of the National Academy of Sciences of the United States of America · 2026
    Article
  3. Article
  4. Article
  5. Article
  6. Review
  7. Article
  8. Article
  9. The great phage escape: Activating and escaping lactococcal antiphage systems.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  10. A Plasmid-Encoded Surface Polysaccharide Partly BlocksInternational journal of molecular sciences · 2025
    Article
  11. Insight into crRNA Processing inInternational journal of molecular sciences · 2025
    Article
  12. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Andriana GrafakouSchool of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.ORCID 0000-0003-3803-4479
Cas MosterdSchool of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.ORCID 0000-0002-5369-8938
Matthias H BeckSchool of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.ORCID 0000-0003-1793-0629
Philip KelleherSchool of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.ORCID 0000-0003-3423-7930
Brian McDonnellSchool of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.ORCID 0000-0003-1704-8759
Paul P de Waaldsm-firmenich, Taste, Texture & Health, Center for Food Innovation, Delft 2613 AX, The Netherlands.
Irma M H van Rijswijckdsm-firmenich, Taste, Texture & Health, Center for Food Innovation, Delft 2613 AX, The Netherlands.
Noël N M E van Peijdsm-firmenich, Taste, Texture & Health, Center for Food Innovation, Delft 2613 AX, The Netherlands.ORCID 0009-0002-3946-4067
Christian CambillauSchool of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.ORCID 0000-0001-5502-4729
Jennifer MahonySchool of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.ORCID 0000-0001-5846-6303
Douwe van SinderenSchool of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.ORCID 0000-0003-1823-7957

Funding

ChimeraX -- Next Generation Visualization and Analysis Software for Multiscale ModelingR01GM129325 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FERRIN, THOMAS E · 2018 to 2025
$5.2M
firmenich 12/RC/2273-P1GENCI 2023-AD010714075National Institute of Allergy and Infectious DiseasesNIGMS NIH HHS R01 GM129325NIH HHS R01-GM129325Science Foundation Ireland
6 · The paper itself

Abstract

Until the late 2000s, lactococci substantially contributed to the discovery of various plasmid-borne phage defence systems, rendering these bacteria an excellent antiphage discovery resource. Recently, there has been a resurgence of interest in identifying novel antiphage systems in lactic acid bacteria owing to recent reports of so-called 'defence islands' in diverse bacterial genera. Here, 321 plasmid sequences from 53 lactococcal strains were scrutinized for the presence of antiphage systems. Systematic evaluation of 198 candidates facilitated the discovery of seven not previously described antiphage systems, as well as five systems, of which homologues had been described in other bacteria. All described systems confer resistance against the most prevalent lactococcal phages, and act post phage DNA injection, while all except one behave like abortive infection systems. Structure and domain predictions provided insights into their mechanism of action and allow grouping of several genetically distinct systems. Although rare within our plasmid collection, homologues of the seven novel systems appear to be widespread among bacteria. This study highlights plasmids as a rich repository of as yet undiscovered antiphage systems.

Indexed as

BacteriophagesLactococcusPlasmids

Identifiers

PMID39119896
PMCPMC11381338

What Socratic holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.