Evidence map›Paper›PMID 39628703›Full record

ReviewEngineering microbiology2022

Methods of DNA introduction for the engineering of commensal microbes.

Dake Liu, Nicole E Siguenza, Amir Zarrinpar, Yousong Ding

Erratum issuedAbstract readReview
In one paragraph

Review in Engineering microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. 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.

  1. Review
  2. Review
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  4. Review
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

4 authors.

Dake LiuDepartment of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville 32610, Florida, United States.
Nicole E SiguenzaDivision of Gastroenterology, Center for Microbiome Innovation, University of California, La Jolla, San Diego 92093, California , United States.
Amir ZarrinparDivision of Gastroenterology, Center for Microbiome Innovation, University of California, La Jolla, San Diego 92093, California , United States.
Yousong DingDepartment of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville 32610, Florida, United States.

Funding

UC San Diego Clinical and Translational Research InstituteUL1TR001442 · NCATS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI FIRESTEIN, GARY S, HOGARTH, MICHAEL · 2015 to 2024
$88.3M
Viral Vector Core (VVC)P30CA014195 · NCI · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI Reuben Shaw · 1985 to 2026
$82.8M
The Southernearch Center for ALPD and CirrhosisP50AA011999 · NIAAA · UNIVERSITY OF SOUTHERN CALIFORNIA · PI ANNA S. GUKOVSKAYA · 1999 to 2026
$45.8M
Transgenic & Knock-out MouseP30DK063491 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Andrea L Hevener · 2003 to 2026
$40.4M
San Diego Digestive Diseases Research CenterP30DK120515 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Bernd G. Schnabl · 2019 to 2026
$10.8M
Engineering Native E. coli to Detect, Report, and Treat Colorectal CancerU01CA265719 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ZARRINPAR, AMIR · 2021 to 2025
$3.1M
Design and characterization of bacterial population dynamics in solid tumor modelsR01EB030134 · NIBIB · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI HASTY, JEFF M, TSIMRING, LEV S · 2021 to 2024
$2.5M
NCATS NIH HHS UL1 TR001442NCI NIH HHS P30 CA014195NCI NIH HHS U01 CA265719NIAAA NIH HHS P50 AA011999NIBIB NIH HHS R01 EB030134NIDDK NIH HHS P30 DK063491NIDDK NIH HHS P30 DK120515
6 · The paper itself

Abstract

The microbiome is an essential component of ecological systems and is comprised of a diverse array of microbes. Over the past decades, the accumulated observational evidence reveals a close correlation between the microbiome and human health and disease. Many groups are now manipulating individual microbial strains, species and the community as a whole to gain a mechanistic understanding of the functions of the microbiome. Here, we discuss three major approaches for introducing DNA to engineer model bacteria and isolated undomesticated bacteria, including transformation, transduction, and conjugation. We provide an overview of these approaches and describe the advantages and limitations of each method. In addition, we highlight examples of human microbiome engineering using these approaches. Finally, we provide perspectives for the future of microbiome engineering.

Indexed as

ConjugationGenetic engineeringMicrobiomeTherapeutic applicationsTransductionTransformationUndomesticated microbes

Identifiers

PMID39628703
PMCPMC11610962

What OpenQuestion holds

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LicenceCC BY-NC-ND
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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.