Evidence map›Paper›PMID 32397065›Full record

ArticleMicroorganisms2020

MG-MLST: Characterizing the Microbiome at the Strain Level in Metagenomic Data.

Nathanael J Bangayan, Baochen Shi, Jerry Trinh, Emma Barnard, Gabriela Kasimatis, Emily Curd, Huiying Li

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Microorganisms, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
1.1field-weighted citation impact, top 21% of its field
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

5 citing papers in PubMed, 9 citations in OpenAlex.

  1. Review
  2. Prodrug Integrated Envelope on Probiotics to Enhance Target Therapy for Ulcerative Colitis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023
    Article
  3. Review
  4. Article
  5. Article
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 at 1 institution in 1 country.

Nathanael J BangayanDepartment of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, University of California, Los Angeles, CA 90095, USA.
Baochen ShiDepartment of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, University of California, Los Angeles, CA 90095, USA.
Jerry TrinhDepartment of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, University of California, Los Angeles, CA 90095, USA.
Emma BarnardDepartment of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, University of California, Los Angeles, CA 90095, USA.
Gabriela KasimatisDepartment of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, University of California, Los Angeles, CA 90095, USA.
Emily CurdDepartment of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, University of California, Los Angeles, CA 90095, USA.
Huiying LiDepartment of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, University of California, Los Angeles, CA 90095, USA.ORCID 0000-0001-5633-5270
University of California, Los Angeles · US

Funding

Population dynamics of P. acnes and their phages in the human skin microbiomeR01GM099530 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI LI, HUIYING · 2012 to 2015
$1.4M
Metagenomic study of the human skin microbiome associated with acneUH2AR057503 · NIAMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI LI, HUIYING · 2009 to 2010
$1.2M
Undergraduate Research Experience in Neuropsychiatric GenomicsR25MH109172 · NIMH · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ESKIN, ELEAZAR, FREIMER, NELSON B. · 2016 to 2020
$429k
NIAMS NIH HHS UH2 AR057503NIGMS NIH HHS R01 GM099530NIH HHS R01GM099530NIH HHS UH2AR057503NIMH NIH HHS R25 MH109172
6 · The paper itself

Abstract

The microbiome plays an important role in human physiology. The composition of the human microbiome has been described at the phylum, class, genus, and species levels, however, it is largely unknown at the strain level. The importance of strain-level differences in microbial communities has been increasingly recognized in understanding disease associations. Current methods for identifying strain populations often require deep metagenomic sequencing and a comprehensive set of reference genomes. In this study, we developed a method, metagenomic multi-locus sequence typing (MG-MLST), to determine strain-level composition in a microbial community by combining high-throughput sequencing with multi-locus sequence typing (MLST). We used a commensal bacterium,

Indexed as

metagenomicsmethodmicrobiomeMLSTPropionibacterium acnesstrain

Identifiers

PMID32397065
PMCPMC7284976
OpenAlexW3020995595

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.