Investigating microbial ecosystems: a computational journey from co-occurrence to metabolic networks
Damien Eveillard - Computational Biology group - Lab. Sciences du Numériques Nantes, Université de Nantes
25th May 2018 at 2pm - IBC Bât 5 room 2.022
Abstract: Recent progresses in metagenomics have promoted a change of paradigm to investigate microbial ecosystems. These ecosystems are today analyzed by emphasizing either their gene content or « who is there and who is not » from a taxonomical viewpoint. However, understanding the interactions between microbial communities and their environment well enough to be able to predict diversity on the basis of physicochemical parameters is a fundamental pursuit of microbial ecology that still eludes us. Such a task must be achieved by dedicated computational approaches or modelings, as inspired from Systems Biology. Nevertheless, direct application of standard cellular systems biology approaches is a complicated task, because (i) communities are complex, (ii) most are described qualitatively, and (iii) quantitative understanding of the way communities interacts with their surroundings remains incomplete.
Within this seminar, we will illustrate how systems biology approaches must be adapted to overcome these points in different manners. First, we will present a network analysis that focus on the global ocean. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve understanding of a biological process such as the carbon export.
Second, we will describe how to integrate heterogeneous omics knowledge. Such an integration will emphasize putative functional units at the community level. Finally, we will illustrate a quantitative modeling from this network. A constraint based modeling will be used to predict microbial community structure and its behaviors based on genome-scale knowledge.