Evidence map›Paper›PMID 39679684›Full record

ArticlemSystems2025

Clade-specific long-read sequencing increases the accuracy and specificity of the

Robert G Nichols, Emily R Davenport

Abstract read
In one paragraph

Article in mSystems, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
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

2 authors.

Robert G NicholsDepartment of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA.ORCID 0000-0002-5415-7877
Emily R DavenportDepartment of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA.ORCID 0000-0002-6938-4933

Funding

Characterizing human-microbiome interactions via molecular and functional genomic approaches - Equipment SupplementR35GM146980 · NIGMS · PENNSYLVANIA STATE UNIVERSITY, THE · PI Emily R. Davenport · 2022 to 2026
$2.1M
NIGMS NIH HHS R35 GM146980
6 · The paper itself

Abstract

Phylogenetic marker gene sequencing is often used as a quick and cost-effective way of evaluating microbial composition within a community. While 16S rRNA gene sequencing (16S) is commonly used for bacteria and archaea, other marker genes are preferable in certain situations, such as when 16S sequences cannot distinguish between taxa within a group. Another situation is when researchers want to study cospeciation of host taxa that diverged much more recently than the slowly evolving 16S rRNA gene. For example, the bacterial gyrase subunit B ( IMPORTANCE: Previous studies have shown that the marker gene gyrase subunit B (

Indexed as

BacteriaDNA GyrasePhylogenyDNA, BacterialGenetic MarkersHigh-Throughput Nucleotide SequencingRNA, Ribosomal, 16SSequence Analysis, DNADNA, BacterialDNA GyraseGenetic MarkersRNA, Ribosomal, 16ScodiversificationcospeciationGyrBlong-read sequencing

Identifiers

PMID39679684
PMCPMC11748558

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.