Taxonomic and functional analysis of metagenomes

• Author(s): Barbosa, Pedro Santos
• Date: 2013
• Persistent ID: https://hdl.handle.net/1822/27895
• Origin: RepositóriUM - Universidade do Minho
• Document Type: Master thesis
• Language: English
• Contributor(s): Universidade do Minho; Rocha, Miguel; Arrais, Joel Perdiz

Description

Over the years, metagenomics has demonstrated to play an essential role on the study of the microorganisms that live in microbial communities, particularly those who inhabit the human body. Several bioinformatic tools and pipelines have been developed, but usually they only address one question: "Who is there?" or "What are they doing?". This work aimed to develop a computational framework to answer the two questions simultaneously, that is, perform a taxonomic and functional analysis of microbial communities. Merlin, a previously developed software designed for the construction of genome-scale metabolic models for single organisms, was extended to deal with metagenomics data. It has an userfriendly and intuitive interface, not requiring command-line knowledge and further libraries dependencies or installation, as many other tools. The extended version of Merlin can predict the taxonomic composition of an environmental sample based on the results of homology searches, where the proportions of phyla and genera present are discriminated. Regarding the metabolic analysis, it allows to identify which enzymes are present and calculate their abundance, as well as to nd out which metabolic pathways are e ectively present. The performance of the tool was evaluated with samples from the Human Microbiome Project, particularly from the saliva. The taxonomic membership predicted in Merlin was in agreement with other tools, despite some di erences in the proportions. The functional characterization showed a conserved pool of pathways through di erent samples, although Merlin sometimes presented less pathways than expected because the routine is highly dependent on the enzymes annotation. Overall, the results showed the same pattern as reported before: while the pathways needed for microbial life remain relatively stable, the community composition varies extensively among individuals. In the end, Merlin demonstrated to be a reliable standalone alternative to web services for those scientists that have concerns about sharing data.