Reference-free comparison of microbial communities via de Bruijn graphs

Serghei Mangul, David Koslicki

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    3 Scopus citations

    Abstract

    Microbial communities inhabiting the human body exhibit significant variability across different individuals and tissues, and are suggested to play an important role in health and disease. High-throughput sequencing offers unprecedented possibilities to profile microbial community composition, but limitations of existing taxonomic classification methods (including incompleteness of existing microbial reference databases) limits the ability to accurately compare microbial communities across different samples. In this paper, we present a method able to overcome these limitations by circumventing the classification step and directly using the sequencing data to compare microbial communities. The proposed method provides a powerful reference-free way to assess differences in microbial abundances across samples. This method, called EMDeBruijn, condenses the sequencing data into a de Bruijn graph. The Earth Mover's Distance (EMD) is then used to measure similarities and differences of the microbial communities associated with the individual graphs. We apply this method to RNA-Seq data sets from a coronary artery calcification (CAC) study and shown that EMDeBruijn is able to differentiate between case and control CAC samples while utilizing all the candidate microbial reads. We compare these results to current reference-based methods, which are shown to have a limited capacity to discriminate between case and control samples. We conclude that this reference-free approach is a viable choice in comparative metatranscriptomic studies.

    Original languageEnglish (US)
    Title of host publicationACM-BCB 2016 - 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics
    PublisherAssociation for Computing Machinery, Inc
    Pages68-77
    Number of pages10
    ISBN (Electronic)9781450342254
    DOIs
    StatePublished - Oct 2 2016
    Event7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM-BCB 2016 - Seattle, United States
    Duration: Oct 2 2016Oct 5 2016

    Publication series

    NameACM-BCB 2016 - 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

    Conference

    Conference7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM-BCB 2016
    CountryUnited States
    CitySeattle
    Period10/2/1610/5/16

    All Science Journal Classification (ASJC) codes

    • Software
    • Health Informatics
    • Biomedical Engineering
    • Computer Science Applications

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  • Cite this

    Mangul, S., & Koslicki, D. (2016). Reference-free comparison of microbial communities via de Bruijn graphs. In ACM-BCB 2016 - 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (pp. 68-77). (ACM-BCB 2016 - 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics). Association for Computing Machinery, Inc. https://doi.org/10.1145/2975167.2975174