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International Conference on Practical Applications of Computational Biology & Bioinformatics

PACBB 2019: Practical Applications of Computational Biology and Bioinformatics, 13th International Conference pp 8–15Cite as

Proposal of a New Bioinformatics Pipeline for Metataxonomics in Precision Medicine

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Part of the book series: Advances in Intelligent Systems and Computing ((AISC,volume 1005 ))

Abstract

Microbes are found all over the human body and they have a direct impact on the immune system, metabolism and homeostasis. The homeostatic balance of the intestinal microflora can be broken under certain conditions, a situation known as dysbiosis, which can lead to disease, including certain types of cancer, or even affect a patient response to a therapeutic treatment. Metataxonomics pursues the identification of the bacteria species that are present in biological samples of interest, through the sequencing of the 16S rRNA gene, a highly conserved genetic marker that is present in most prokaryotes. Interactions between the microbiota and the human host are being very relevant in the expansion of precision medicine and cancer research, to better predict the risk of disease and to implement bacteria-directed therapeutics. In order to take metataxonomics to the clinic, efficient bioinformatics pipelines are required, that are flexible and portable, and that are able to classify groups of biological samples according to microbiome diversity. With this objective in mind, we propose a new bioinformatics pipeline to analyze biological samples obtained through NGS of the 16S rRNA gene, doing all the required quality checks and computational calculations. The results obtained with this pipeline are aimed to be interpreted together with host DNA exome or RNA-Seq studies and clinical data, to improve the knowledge about the potential reasons that could lead to disease or to a worst patient treatment response.

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Acknowledgments

The SING group thanks the CITI (Centro de Investigación, Transferencia e Innovación) from the University of Vigo for hosting its IT infrastructure. This work was partially supported by the Consellería de Educación, Universidades e Formación Profesional (Xunta de Galicia) under the scope of the strategic funding ED431C2018/55-GRC Competitive Reference Group, and by the Plataforma de Bioinformática from the Instituto de Salud Carlos III (PT17/0009/0011).

Author information

Authors and Affiliations

  1. Bioinformatics Unit, Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), C/Melchor Fernández Almagro, 3, 28029, Madrid, Spain

    Osvaldo Graña-Castro & Fátima Al-Shahrour

  2. Department of Computer Science, ESEI, University of Vigo, Campus As Lagoas, 32004, Ourense, Spain

    Osvaldo Graña-Castro, Hugo López-Fernández, Florentino Fdez-Riverola & Daniel Glez-Peña

  3. The Biomedical Research Centre (CINBIO), Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain

    Hugo López-Fernández, Florentino Fdez-Riverola & Daniel Glez-Peña

  4. SING Research Group, Galicia Sur Health Research Institute (ISS Galicia Sur), SERGAS-UVIGO, Vigo, Spain

    Hugo López-Fernández, Florentino Fdez-Riverola & Daniel Glez-Peña

Authors
  1. Osvaldo Graña-Castro
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  2. Hugo López-Fernández
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  3. Florentino Fdez-Riverola
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  4. Fátima Al-Shahrour
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  5. Daniel Glez-Peña
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Corresponding author

Correspondence to Osvaldo Graña-Castro .

Editor information

Editors and Affiliations

  1. Edificio Politécnico, Escuela Superior de Ingeniería Informática,Campus Universitario As Lagoas , Ourense, Spain

    Florentino Fdez-Riverola

  2. Department de Informática, Universidade do Minho, Braga, Portugal

    Miguel Rocha

  3. Faculty of Bioengineering and Technology, Universiti Malaysia Kelantan, Kelantan, Malaysia

    Mohd Saberi Mohamad

  4. Department of Computer Science and Software Engineering Leader, Data Science Research Group, College of Information Technology (CIT) United Arab Emirates University (UAEU), Al Ain, United Arab Emirates

    Nazar Zaki

  5. IBSAL/BISITE Research Group, University of Salamanca, Salamanca, Salamanca, Spain

    José A. Castellanos-Garzón

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Graña-Castro, O., López-Fernández, H., Fdez-Riverola, F., Al-Shahrour, F., Glez-Peña, D. (2020). Proposal of a New Bioinformatics Pipeline for Metataxonomics in Precision Medicine. In: Fdez-Riverola, F., Rocha, M., Mohamad, M., Zaki, N., Castellanos-Garzón, J. (eds) Practical Applications of Computational Biology and Bioinformatics, 13th International Conference. PACBB 2019. Advances in Intelligent Systems and Computing, vol 1005 . Springer, Cham. https://doi.org/10.1007/978-3-030-23873-5_2

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