Evidence map›Paper›PMID 40948444›Full record

ArticleGut microbes2025

Use of proximity ligation shotgun metagenomics to investigate the dynamics of plasmids and bacteriophages in the gut microbiome following fecal microbiota transplantation.

Samuel Bryson, Zachary Sisson, Bradley Nelson, Jonas Grove, Emily Reister, Ivan Liachko, Benjamin Auch, Carolyn Graiziger, Alexander Khoruts

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Gut microbes, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing 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

7 citing papers in PubMed.

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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

9 authors.

Samuel BrysonPhase Genomics, Seattle, WA, USA.
Zachary SissonPhase Genomics, Seattle, WA, USA.
Bradley NelsonPhase Genomics, Seattle, WA, USA.
Jonas GrovePhase Genomics, Seattle, WA, USA.
Emily ReisterPhase Genomics, Seattle, WA, USA.
Ivan LiachkoPhase Genomics, Seattle, WA, USA.
Benjamin AuchPhase Genomics, Seattle, WA, USA.
Carolyn GraizigerDepartment of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, University of Minnesota, Minneapolis, MN, USA.
Alexander KhorutsDepartment of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, University of Minnesota, Minneapolis, MN, USA.ORCID 0000-0002-3205-3188

Funding

Therapeutic phage host-range prediction using proximity-guided metagenomics and artificial intelligenceR44AI172703 · NIAID · PHASE GENOMICS, INC. · PI LIACHKO, IVAN · 2022 to 2023
$2.0M
NIAID NIH HHS R44 AI172703
6 · The paper itself

Abstract

Proximity ligation shotgun metagenomics facilitate the analysis of the relationships between mobile genetic elements, such as plasmids and bacteriophages, and their specific bacterial hosts. We applied this technique to investigate the changes in the fecal microbiome of patients receiving fecal microbiota transplantation (FMT) for recurrent

Indexed as

BacteriaBacteriophagesClostridium InfectionsFecal Microbiota TransplantationGastrointestinal MicrobiomeMetagenomicsPlasmidsClostridioides difficileFecesFemaleHumansMaleMiddle Agedantimicrobial resistance genesClostridioides difficilefecal microbiota transplantationProximity ligation shotgun metagenomics

Identifiers

PMID40948444
PMCPMC12439552

What OpenQuestion holds

Textmetadata
LicenceCC BY
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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.