MiCoP: Microbial community profiling method for detecting viral and fungal organisms in metagenomic samples

Nathan Lapierre, Serghei Mangul, Mohammed Alser, Igor Mandric, Nicholas C. Wu, David Koslicki, Eleazar Eskin

    Research output: Contribution to journalArticle

    Abstract

    Background: High throughput sequencing has spurred the development of metagenomics, which involves the direct analysis of microbial communities in various environments such as soil, ocean water, and the human body. Many existing methods based on marker genes or k-mers have limited sensitivity or are too computationally demanding for many users. Additionally, most work in metagenomics has focused on bacteria and archaea, neglecting to study other key microbes such as viruses and eukaryotes. Results: Here we present a method, MiCoP (Microbiome Community Profiling), that uses fast-mapping of reads to build a comprehensive reference database of full genomes from viruses and eukaryotes to achieve maximum read usage and enable the analysis of the virome and eukaryome in each sample. We demonstrate that mapping of metagenomic reads is feasible for the smaller viral and eukaryotic reference databases. We show that our method is accurate on simulated and mock community data and identifies many more viral and fungal species than previously-reported results on real data from the Human Microbiome Project. Conclusions: MiCoP is a mapping-based method that proves more effective than existing methods at abundance profiling of viruses and eukaryotes in metagenomic samples. MiCoP can be used to detect the full diversity of these communities. The code, data, and documentation are publicly available on GitHub at: https://github.com/smangul1/MiCoP.

    Original languageEnglish (US)
    Article number423
    JournalBMC genomics
    Volume20
    DOIs
    StatePublished - Jun 6 2019

    All Science Journal Classification (ASJC) codes

    • Biotechnology
    • Genetics

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