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Analysis of institutional authors

Bars-Cortina, DAuthorRamon, EAuthorGuino, EAuthorObon-Santacana, MCorresponding AuthorMoreno, VCorresponding Author

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November 21, 2024
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Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota

Publicated to: BMC GENOMICS. 25 (1): 730- - 2024-07-29 25(1), DOI: 10.1186/s12864-024-10621-7

Authors:

Bars-Cortina, D; Ramon, E; Rius-Sansalvador, B; Guinó, E; Garcia-Serrano, A; Mach, N; Khannous-Lleiffe, O; Saus, E; Gabaldón, T; Ibañez-Sanz, G; Rodríguez-Alonso, L; Mata, A; García-Rodríguez, A; Obón-Santacana, M; Moreno, V
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Affiliations

Barcelona Inst Sci & Technol, Inst Res Biomed IRB Barcelona - Author
Bellvitge Biomed Res Inst IDIBELL, Oncobell Program, Lhospitalet De Llobregat 08908 - Author
Bellvitge Univ Hosp, Gastroenterol Dept, Lhospitalet De Llobregat 08907 - Author
Consortium Biomed Res Epidemiol & Publ Hlth CIBERE - Author
Ctr Invest Biomed Red Enfermedades Infecciosas CIB - Author
Karolinska Inst, Dept Clin Sci Intervent & Technol - Author
Moises Broggi Hosp, Digest Syst Serv - Author
Univ Barcelona UB, Doctoral Programme Biomed - Author
Univ Barcelona UB, Fac Med & Hlth Sci, Dept Clin Sci, Inst Complex Syst UBICS, Lhospitalet De Llobregat 08908 - Author
Univ Toulouse, IHAP, INRAE, ENVT - Author
Viladecans Hosp IDIBELL, Digest Syst Serv, Endoscopy Unit - Author
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Abstract

BackgroundGut dysbiosis has been associated with colorectal cancer (CRC), the third most prevalent cancer in the world. This study compares microbiota taxonomic and abundance results obtained by 16S rRNA gene sequencing (16S) and whole shotgun metagenomic sequencing to investigate their reliability for bacteria profiling. The experimental design included 156 human stool samples from healthy controls, advanced (high-risk) colorectal lesion patients (HRL), and CRC cases, with each sample sequenced using both 16S and shotgun methods. We thoroughly compared both sequencing technologies at the species, genus, and family annotation levels, the abundance differences in these taxa, sparsity, alpha and beta diversities, ability to train prediction models, and the similarity of the microbial signature derived from these models.ResultsAs expected, the results showed that 16S detects only part of the gut microbiota community revealed by shotgun, although some genera were only profiled by 16S. The 16S abundance data was sparser and exhibited lower alpha diversity. In lower taxonomic ranks, shotgun and 16S highly differed, partially due to a disagreement in reference databases. When considering only shared taxa, the abundance was positively correlated between the two strategies. We also found a moderate correlation between the shotgun and 16S alpha-diversity measures, as well as their PCoAs. Regarding the machine learning models, only some of the shotgun models showed some degree of predictive power in an independent test set, but we could not demonstrate a clear superiority of one technology over the other. Microbial signatures from both sequencing techniques revealed taxa previously associated with CRC development, e.g., Parvimonas micra.ConclusionsShotgun and 16S sequencing provide two different lenses to examine microbial communities. While we have demonstrated that they can unravel common patterns (including microbial signatures), shotgun often gives a more detailed snapshot than 16S, both in depth and breadth. Instead, 16S will tend to show only part of the picture, giving greater weight to dominant bacteria in a sample. Therefore, we recommend choosing one or another sequencing technique before launching a study. Specifically, shotgun sequencing is preferred for stool microbiome samples and in-depth analyses, while 16S is more suitable for tissue samples and studies with targeted aims.
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Keywords

16sActinobacteriaArticleBacteriaBacteroidesBacteroides fragilisBacteroidetesBifidobacteriaceaeBifidobacteriumColonoscopyColorectal cancerColorectal neoplasmsComparative studyComparisonControlled studyDna extractionDysbiosisEscherichia coliEubacteriumFaecalibacteriumFecesFemaleFirmicutesGastrointestinal microbiomeHumanHumansIntestine floraMachine learningMaleMetagenomeMetagenomicsMicrobial communityMicrobial diversityMicrobiomeNonhumanParvimonas micraPrevotellaProteobacteriaPyrosequencingQuality controlRisk assessmentRna 16sRna, ribosomal, 16sRuminococcusScoring systemSensitivity and specificitySequence analysis, dnaShigella sonneiShotgunShotgun sequencingStreptococcus thermophilusSupport vector machineTrainingWhole-genome shotgun

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal BMC GENOMICS due to its progression and the good impact it has achieved in recent years, according to the agency Scopus (SJR), it has become a reference in its field. In the year of publication of the work, 2024 there are still no calculated indicators, but in 2023, it was in position , thus managing to position itself as a Q1 (Primer Cuartil), in the category Biotechnology.

Independientemente del impacto esperado determinado por el canal de difusión, es importante destacar el impacto real observado de la propia aportación.

Según las diferentes agencias de indexación, el número de citas acumuladas por esta publicación hasta la fecha 2026-04-04:

  • WoS: 43
  • Scopus: 46
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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 2026-04-04:

  • 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: 87.
  • 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: 87 (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: 5.

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.
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Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: France; Sweden.

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 (BARS CORTINA, DAVID) and Last Author (Moreno Aguado, Victor Raul).

the authors responsible for correspondence tasks have been OBON SANTACANA, MIREIA and Moreno Aguado, Victor Raul.

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