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Tuesday, August 1 • 16:40 - 17:00
EDEN: Evolutionary Dynamics within Environments

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Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions.
Phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data. Calculating the dN/dS ratio for the large-scale sequence data sets that are being generated in metagenomics and comparative microbial genomics is very challenging, due excessive run times of current methods. 
EDEN is the first software for the rapid detection of protein families and regions under positive selection, as well as their associated biological processes, from meta- and pangenome data. It provides an interactive result visualization for detailed comparative analyses. EDEN is available as a Docker installation under the GPL 3.0 license, allowing its use on common operating systems, at http://www.github.com/hzi-bifo/eden
We applied EDEN to 66 samples of the HMP project from six body sites sampled from healthy individuals. Across all body sites, most protein families with significant signs of positive selection in comparison to all other protein families were annotated with transport and binding functions, suggesting the existence of a functional pan-selectome. We also used EDEN to characterize human gut metagenome samples. EDEN determined a significantly higher dN/dS ratio for the protein coding genes from lean individuals compared to overweight and obese individuals, suggestive of a higher functional diversity in the guts of lean individuals.


Speakers

Tuesday August 1, 2017 16:40 - 17:00
Graduate School of Management Building, room 309 Volkhovskiy Pereulok, 3, St. Petersburg, Russia