Evidence map›Paper›PMID 40730160›Full record

ArticleCell host & microbe2025

The prototypic crAssphage is a linear phage-plasmid.

Danica T Schmidtke, Angela S Hickey, Jakob Wirbel, Jordan D Lin, Ivan Liachko, Gavin Sherlock, Ami S Bhatt

Abstract read
In one paragraph

Article in Cell host & microbe, 2025. 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. Review
  2. Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Plasmid and phage lifestyles in crAssphage.Nature reviews. Microbiology · 2025
    Article
  10. Article
  11. Article
  12. Review
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

7 authors.

Danica T SchmidtkeDepartment of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
Angela S HickeyDepartment of Genetics, Stanford University, Stanford, CA, USA.
Jakob WirbelDepartment of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA.
Jordan D LinDepartment of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA.
Ivan LiachkoPhase Genomics, Seattle, WA, USA.
Gavin SherlockDepartment of Genetics, Stanford University, Stanford, CA, USA. Electronic address: gsherloc@stanford.edu.
Ami S BhattDepartment of Genetics, Stanford University, Stanford, CA, USA; Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA. Electronic address: asbhatt@stanford.edu.

Funding

Supplement to Enhance Wellness and Resiliency in the Graduate EnvironmentT32GM007276 · NIGMS · STANFORD UNIVERSITY · PI MORRISON, ASHBY J. · 1985 to 2023
$32.9M
VAST Center: Viromes Across Space(s) and TimeU54AG089334 · NIA · STANFORD UNIVERSITY · PI Christopher Edward Mason · 2025 to 2026
$13.3M
Multisizer 4e - equipment for "Fitness Effects of Beneficial Mutations"R35GM131824 · NIGMS · STANFORD UNIVERSITY · PI Gavin J Sherlock · 2019 to 2026
$3.6M
Culture-free pathogen tracking in hospitalized patientsR01AI143757 · NIAID · STANFORD UNIVERSITY · PI BHATT, AMI SIDDHARTH · 2020 to 2023
$3.0M
Therapeutic phage host-range prediction using proximity-guided metagenomics and artificial intelligenceR44AI172703 · NIAID · PHASE GENOMICS, INC. · PI LIACHKO, IVAN · 2022 to 2023
$2.0M
Emerging novel mechanisms of antibiotic resistance in the prevalent foodborne pathogen, SalmonellaR01AI148623 · NIAID · STANFORD UNIVERSITY · PI BHATT, AMI SIDDHARTH · 2019 to 2023
$2.0M
A method for the culture-free discovery and host affiliation of novel viruses from metagenomic samplesR44AI162570 · NIAID · PHASE GENOMICS, INC. · PI LIACHKO, IVAN · 2021 to 2022
$1.6M
NIAID NIH HHS R01 AI143757NIAID NIH HHS R01 AI148623NIAID NIH HHS R44 AI162570NIAID NIH HHS R44 AI172703NIA NIH HHS U54 AG089334NIGMS NIH HHS R35 GM131824NIGMS NIH HHS T32 GM007276
6 · The paper itself

Abstract

The prototypic crAssphage (Carjivirus communis) is an abundant, prevalent, and persistent human gut bacteriophage, yet it remains uncultured and its lifestyle uncharacterized. C. communis does not readily plaque, suggesting a largely non-lytic lifestyle. Here, we find that C. communis is a linear phage-plasmid that stably persists extrachromosomally within its host. Plasmid and phage-related genes are transcribed, and multiple putative replication origins may initiate replication for multiple lifestyles and genome conformations, including both circular and linear formations. Leveraging these findings, we use a plaque-free culturing approach to measure C. communis replication on prevalent gut bacteria, notably Phocaeicola vulgatus, P. dorei, and Bacteroides stercoris, revealing a broad host range. C. communis persists without causing major cell lysis events or integrating into host chromosomes. Taken together, C. communis' ability to switch between phage and plasmid lifestyles within a wide range of hosts may contribute to its widespread presence in human gut microbiomes.

Indexed as

BacteriophagesPlasmidsBacteroidesDNA, ViralGastrointestinal MicrobiomeGenome, ViralHost SpecificityHumansDNA, ViralbacteriophageBacteroidotaCarjivirus communiscrAssphagemicrobial genomicsmicrobiomephage culturingphage-plasmidPhocaeicolaplasmid

Identifiers

PMID40730160
PMCPMC12358190

What OpenQuestion holds

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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 OpenQuestion graph.