Evidence map›Paper›PMID 41756930›Full record

ArticlebioRxiv : the preprint server for biology2026

A distinct class of conjugative megaplasmids includes potential vehicles for prophage dissemination.

Ling Yuan, Yiting Qin, Jacob West-Roberts, Karthik Anantharaman, Haoyu Wang, Yuanqiang Zou, Yi Duan, Antonio Pedro Camargo, Eugene V Koonin, LinXing Chen

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

10 authors.

Ling YuanState Key Laboratory of Advanced Environmental Technology, the Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China.
Yiting QinState Key Laboratory of Advanced Environmental Technology, the Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China.
Jacob West-RobertsInnovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
Karthik AnantharamanDepartment of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.ORCID 0000-0002-9584-2491
Haoyu WangState Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Shenzhen 518083, China.
Yuanqiang ZouState Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Shenzhen 518083, China.
Yi DuanState Key Laboratory of Immune Response and Immunotherapy, Department of Infectious Diseases, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China.
Antonio Pedro CamargoDepartment of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-060, Brazil.ORCID 0000-0003-3913-2484
Eugene V KooninComputational Biology Branch, Division of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.ORCID 0000-0003-3943-8299
LinXing ChenState Key Laboratory of Advanced Environmental Technology, the Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China.ORCID 0000-0003-2774-1952

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Closely related prophages are frequently found in phylogenetically distant bacteria in the human gut, despite limited evidence of productive phage infections across broad host ranges. Thus, it remains unclear how the wide distribution of prophages could emerge. Here, we identify a potential mechanism of prophage dissemination. We describe two deeply diverged groups of conjugative megaplasmids (>300 kilobases) in the human gut microbiome, which we term Hodors. Hodors encode conserved replication, partitioning, and type IV secretion systems, together with a complex surface-associated gene module. A subset of Hodors harbor complete, intact prophage genomes, and closely related prophages are detected across phylogenetically distant Bacillota lineages, including both Bacilli and Clostridia. Further analysis indicates that Hodor-associated prophages can exist as extracellular particles and demonstrate their transcriptional activity. Our findings support a model in which conjugative megaplasmids act as composite mobile platforms that disseminate prophage genomes across bacterial lineages, providing a mechanistic explanation for the widespread occurrence of closely related prophages in phylogenetically distant gut bacteria and effectively decoupling lysogenic host range from infective host range.

Indexed as

Conjugative transferHuman gutLysogenyMetagenomicsPlasmidProphage

Identifiers

PMID41756930
PMCPMC12934698

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Registered trials

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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.