Evidence map›Paper›PMID 38688963›Full record

ArticleScientific reports2024

Harnessing the intragenomic variability of rRNA operons to improve differentiation of Vibrio species.

Amaia Leunda-Esnaola, Evgeni Bunin, Pablo Arrufat, Peter B Pearman, Vladimir R Kaberdin

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

Article in Scientific reports, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.9field-weighted citation impact, top 27% 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

2 citing papers in PubMed, 4 citations in OpenAlex.

  1. Article
  2. 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

5 authors at 1 institution in 1 country.

Amaia Leunda-EsnaolaDepartment of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940, Leioa, Spain.
Evgeni BuninResearch Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain.
Pablo ArrufatDepartment of Plant Biology and Ecology, Faculty of Sciences and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain.
Peter B PearmanDepartment of Plant Biology and Ecology, Faculty of Sciences and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain. peter.pearman@ehu.es.
Vladimir R KaberdinDepartment of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940, Leioa, Spain. vladimir.kaberdin@ehu.eus.
University of the Basque Country · ES

Funding

Erasmus Mundus Joint Master Degree ECT+ scholarship, European Union EMJMD 2019-1485Gobierno Vasco IT1487-22Gobierno Vasco IT1657-22Gobierno Vasco PRE_2022_2_0171Ministerio de Ciencia e Innovación PID2020-118028GB-I00Ministerio de Ciencia e Innovación TED2021-132109BC21
6 · The paper itself

Abstract

Although the 16S rRNA gene is frequently used as a phylogenetic marker in analysis of environmental DNA, this marker often fails to distinguish closely related species, including those in the genus Vibrio. Here, we investigate whether inclusion and analysis of 23S rRNA sequence can help overcome the intrinsic weaknesses of 16S rRNA analyses for the differentiation of Vibrio species. We construct a maximum likelihood 16S rRNA gene tree to assess the use of this gene to identify clades of Vibrio species. Within the 16S rRNA tree, we identify the putative informative bases responsible for polyphyly, and demonstrate the association of these positions with tree topology. We demonstrate that concatenation of 16S and 23S rRNA genes increases the number of informative nucleotide positions, thereby overcoming ambiguities in 16S rRNA-based phylogenetic reconstructions. Finally, we experimentally demonstrate that this approach considerably improves the differentiation and identification of Vibrio species in environmental samples.

Indexed as

PhylogenyRNA, Ribosomal, 16SVibrioGenetic VariationRNA, Ribosomal, 23SrRNA OperonRNA, Ribosomal, 16SRNA, Ribosomal, 23S16S and 23S ribosomal genesEvolutionInformative basesPhylogenetic marker

Identifiers

PMID38688963
PMCPMC11061105
OpenAlexW4396518994

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.