Evidence map›Paper›PMID 36993556›Full record

ArticlebioRxiv : the preprint server for biology2023

A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut.

Emily C Fogarty, Matthew S Schechter, Karen Lolans, Madeline L Sheahan, Iva Veseli, Ryan Moore, Evan Kiefl, Thomas Moody, Phoebe A Rice, Michael K Yu and 6 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. 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, 6 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

16 authors at 7 institutions in 2 countries.

Emily C FogartyCommittee on Microbiology, University of Chicago, Chicago, IL 60637, USA.
Matthew S SchechterCommittee on Microbiology, University of Chicago, Chicago, IL 60637, USA.
Karen LolansDepartment of Medicine, University of Chicago, Chicago, IL 60637, USA.
Madeline L SheahanDuchossois Family Institute, University of Chicago, Chicago, IL 60637, USA.
Iva VeseliDepartment of Medicine, University of Chicago, Chicago, IL 60637, USA.
Ryan MooreCenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA.
Evan KieflDepartment of Medicine, University of Chicago, Chicago, IL 60637, USA.
Thomas MoodyDepartment of Systems Biology, Columbia University, New York, NY, 10032 USA.
Phoebe A RiceCommittee on Microbiology, University of Chicago, Chicago, IL 60637, USA.
Michael K YuToyota Technological Institute at Chicago.
Mark MimeeCommittee on Microbiology, University of Chicago, Chicago, IL 60637, USA.
Eugene B ChangDepartment of Medicine, University of Chicago, Chicago, IL 60637, USA.
Sandra L MclellanSchool of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53204, USA.
Amy D WillisDepartment of Biostatistics, University of Washington, Seattle, WA, 98195, USA.
Laurie E ComstockDuchossois Family Institute, University of Chicago, Chicago, IL 60637, USA.
A Murat ErenMarine Biological Laboratory, Woods Hole, MA, 02543, USA.
University of Chicago · USAlfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung · DEColumbia University · USToyota Technological Institute at Chicago · USUniversity of Delaware · USUniversity of Washington · USUniversity of Wisconsin–Milwaukee · US

Funding

ULTRASTRUCTURE AND CYTOMORPHOLOGY COREP30DK042086 · NIDDK · UNIVERSITY OF CHICAGO · PI CHANG, EUGENE B · 1990 to 2025
$29.8M
Host and microbial basis of human ulcerative colitis and pouchitis: Identification, role, mechanisms, and resource development of host susceptibility and pathobiont factorsRC2DK122394 · NIDDK · UNIVERSITY OF CHICAGO · PI CHANG, EUGENE B · 2019 to 2023
$10.2M
Statistical methods to enhance reproducible microbiome discoveryR35GM133420 · NIGMS · UNIVERSITY OF WASHINGTON · PI Amy D Willis · 2019 to 2026
$2.8M
NIDDK NIH HHS P30 DK042086NIDDK NIH HHS RC2 DK122394NIGMS NIH HHS R35 GM133420
6 · The paper itself

Abstract

Plasmids are extrachromosomal genetic elements that often encode fitness enhancing features. However, many bacteria carry 'cryptic' plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes, and is 14 times as numerous as crAssphage, currently established as the most abundant genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales and although it does not appear to impact bacterial host fitness

Identifiers

PMID36993556
PMCPMC10055365
OpenAlexW4360960496

What OpenQuestion holds

Textmetadata
LicenceCC BY-ND
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 OpenQuestion graph.