TY - JOUR TI - Functional analysis of microbial genomes and metagenomes DO - https://doi.org/doi:10.7282/T3DV1NTF PY - 2017 AB - Microorganisms are capable of carrying out molecular functionality relevant to a range of human interests, including health, industrial production, and bioremediation. Current microbial taxonomy is phylogeny-guided, i.e., the organisms are grouped based on their evolutionary relationships. Due to horizontal gene transfer, evolutionary relatedness cannot guarantee genome-encoded molecular functional similarity. In this work, we establish a computational framework for comparison of microorganisms based on their molecular functionality. In the fusion (functional-repertoire similarity-based organism network) representation, organisms can be consistently assigned to groups based on a quantitative measure of their functional similarities. The results highlight the specific environmental factor(s) that explain the functional differences between groups of microorganism. We deposit the functional data in fusionDB, mapping bacteria and their functions to available metadata: habitat/niche, preferred temperature, and oxygen use. The web interface further allows mapping new microbial genomes to the functional spectrum of reference bacteria. In the end, we describe mi-faser (microbiome functional annotation of sequencing reads), the meta-genomic/-transcriptomic analysis pipeline combining an algorithm that is optimised to map reads to molecular functions encoded by the read-correspondent genes, and a manually curated reference database of protein functions. With mi-faser, we identify previously unseen oil degradation-specific functions in BP oil-spill data, and reveal the role of gut microbiome in Crohn’s disease pathogenicity, showing that the patient microbiomes are enriched in both the functions that promote inflammation and those that help bacteria survive it. KW - Microbiology and Molecular Genetics KW - Bioinformatics KW - Microbial genomes LA - eng ER -