Augmenting metagenomic-wide association studies by grouping species that share functional potential or ecological role.

  • Rasmussen, Simon (Project Participant)

    Project Details

    Description

    Association studies between the constituents of the human microbiome and human phenotypes are challenged by the complexity and redundancy of the microbiome. Thus, if multiple microbial species contribute to the same effect it may cripple the associations unless the group of contributing species can be identified. Here, we suggest to develop several protocols for identifying groups of species with potential overlapping functional or ecological roles. These protocols will group species based on their taxonomy, functional potential or possession of orthologous proteins and thereby reduce the combinatorics problem of identifying species contribute to a given effect. We obtain this by using ourbreakthrough method “identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes” (Nielsen et al., Nature biotechnology 2014), that will enable us to describe and group more than 1500 species identified from 3000 human microbiome samples.
    The concept will be tested on multiple different data sets and different phenotypes, including novel serum metabolomics and lipidomics data sets. The objective will be to produce software implementations and a method article that describe and benchmark the concept. Furthermore, we aim at producing novel biological discoveries about the microbiome ecology and its effect on human health.
    AcronymThe functional species concept
    StatusFinished
    Effective start/end date01/02/201731/01/2020

    Keywords

    • Microbiome, systems biology, bioinformatics, association studies.