Microbial Community Modelling

Network analysis of microbial ecosystems

The arrival of high-throughput sequencing has resulted in an unprecedented amount of publicly available data. This allows, for the very first time, the study of microbial interaction patterns at a global scale by simultaneously analyzing hundreds of samples with bioinformatics tools. Understanding the rules that regulate the assembly of microorganisms is the first step required for the rational engineering of synthetic microbial communities, a feat that would help in such diverse fields as bioremediation, biomining, medicine, biotechnology, or responses to marine acidification and global warming.

This project aims to identify potential associations between groups of microbial strains by analyzing their co-variation patterns along a large set of well-characterized samples. The project will have the following stages:

1) Processing of raw 16S rRNA amplicon sequencing datasets in order to characterize the microbial diversity present on every sample.

2) Determination of the potential interactions between the detected microbial strains.

3) Construction of an interaction network. Identification of clusters of significantly associated strains, and the key microbes that connect the different clusters together.

4) Relating the topology of the interaction network to the physico-chemical parameters recorded at the different sampling points.