{rfName}

Indexed in

License and use

Icono OpenAccess

Citations

97

Altmetrics

Analysis of institutional authors

López-Aladid RAuthorFernández-Barat LCorresponding AuthorAlcaraz-Serrano VAuthorBueno-Freire LAuthorVazquez NAuthorPastor-Ibáñez RAuthorPalomeque AAuthorOscanoa PAuthorTorres ACorresponding Author

Share

March 10, 2023
Publications
>
Article
Sí

Determining the most accurate 16S rRNA hypervariable region for taxonomic identification from respiratory samples

Publicated to:Scientific Reports. 13 (1): 3974- - 2023-03-09 13(1), DOI: 10.1038/s41598-023-30764-z

Authors: Lopez-Aladid, Ruben; Fernandez-Barat, Laia; Alcaraz-Serrano, Victoria; Bueno-Freire, Leticia; Vazquez, Nil; Pastor-Ibanez, Roque; Palomeque, Andrea; Oscanoa, Patricia; Torres, Antoni

Affiliations

Cellex Laboratory, CibeRes (Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, 06/06/0028), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. - Author
Hosp Clin Barcelona, Lab Retrovirol & Viral Immunopathogenesis, Grp Genom & Pharmacogen HIV - Author
Hosp Clin Barcelona, Thorax Inst, Dept Pneumol - Author
School of Medicine, University of Barcelona, Barcelona, Spain. - Author
School of Medicine, University of Barcelona, Barcelona, Spain. atorres@clinic.cat. - Author
See more

Abstract

16S rRNA gene profiling, which contains nine hypervariable regions (V1–V9), is the gold standard for identifying taxonomic units by high-throughput sequencing. Microbiome studies combine two or more region sequences (usually V3–V4) to increase the resolving power for identifying bacterial taxa. We compare the resolving powers of V1–V2, V3–V4, V5–V7, and V7–V9 to improve microbiome analyses in sputum samples from patients with chronic respiratory diseases. DNA were isolated from 33 human sputum samples, and libraries were created using a QIASeq screening panel intended for Illumina platforms (16S/ITS; Qiagen Hilden, Germany). The analysis included a mock community as a microbial standard control (ZymoBIOMICS). We used the Deblur algorithm to identify bacterial amplicon sequence variants (ASVs) at the genus level. Alpha diversity was significantly higher for V1–V2, V3–V4, and V5–V7 compared with V7–V9, and significant compositional dissimilarities in the V1–V2 and V7–V9 analyses versus the V3–V4 and V5–V7 analyses. A cladogram confirmed these compositional differences, with the latter two being very similar in composition. The combined hypervariable regions showed significant differences when discriminating between the relative abundances of bacterial genera. The area under the curve revealed that V1–V2 had the highest resolving power for accurately identifying respiratory bacterial taxa from sputum samples. Our study confirms that 16S rRNA hypervariable regions provide significant differences for taxonomic identification in sputum. Comparing the taxa of microbial community standard control with the taxa samples, V1–V2 combination exhibits the most sensitivity and specificity. Thus, while third generation full-length 16S rRNA sequencing platforms become more available, the V1–V2 hypervariable regions can be used for taxonomic identification in sputum. © 2023, The Author(s).

Keywords

BacteriaBacteriumDna sequenceGeneticsHigh throughput sequencingHigh-throughput nucleotide sequencingHumanHumansMicrobiotaMicrofloraRespiratory systemRna 16sRna, ribosomal, 16sSequence analysis, dna

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Scientific Reports due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2023, it was in position 25/134, thus managing to position itself as a Q1 (Primer Cuartil), in the category Multidisciplinary Sciences.

From a relative perspective, and based on the normalized impact indicator calculated from World Citations provided by WoS (ESI, Clarivate), it yields a value for the citation normalization relative to the expected citation rate of: 7.33. This indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: ESI Nov 14, 2024)

This information is reinforced by other indicators of the same type, which, although dynamic over time and dependent on the set of average global citations at the time of their calculation, consistently position the work at some point among the top 50% most cited in its field:

  • Weighted Average of Normalized Impact by the Scopus agency: 4.86 (source consulted: FECYT Feb 2024)
  • Field Citation Ratio (FCR) from Dimensions: 25.77 (source consulted: Dimensions Jul 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-07-16, the following number of citations:

  • WoS: 40
  • Scopus: 35
  • Europe PMC: 2

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-07-16:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 235.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 249 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 11.85.
  • The number of mentions on the social network X (formerly Twitter): 4 (Altmetric).
  • The number of mentions on Wikipedia: 1 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.

Leadership analysis of institutional authors

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (López Aladid, Ruben) and Last Author (Torres Martí, Antoni).

the authors responsible for correspondence tasks have been Fernández Barat, Laia and Torres Martí, Antoni.