Reference-free comparison of microbial communities via de Bruijn graphs

Serghei Mangul, David Koslicki*

*Corresponding author for this work

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

4 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

Keywords

  • CAC
  • Coronary artery calcification
  • De Bruijn graph
  • Earth Mover's Distance
  • Metagenomics
  • Metatranscriptomics
  • Microbiome
  • Reference-free

ASJC Scopus subject areas

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

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