Topic Area: 15b. Understanding the Microbiome

Formatted Title:

EcoGenoRisk: High Performance Computing for Synthetic Biology Invasion and Cross Biome Functional Modeling

Background/Objectives:

Microbial communities can be regarded as the fundamental units of the environment. Introducing non-native functions into native communities alters these fundamental units with the potential for negative outcomes in community structure and nutrient cycling. Synthetic biological (synbio) products pose a unique challenge for mitigating these risks, as select synbio products maintain the ability to actively replicate within the environment, compounding the mass and locations required to manage, as well as the potential to negatively impact environmental and human health. Understanding where a synbio product will establish and how the functional profile of the biome will shift is necessary for maximizing the benefits of introducing synbio products while minimizing negative impacts.

Approach/Activities:

EcoGenoRisk has been developed to model, investigate, and prevent adverse effects from synbio products. EcoGenoRisk is a Python-based bioinformatic ecological risk assessment tool that determines the likelihood of environmental establishment of a full synthetic microbial cell into the environment and the impact a release event may have on community function. Leveraging high performance computing and the Joint Genome Institute’s Integrated Microbial Genomes and Microbiomes (IMG) database, EcoGenoRisk uses a functional similarity search and one-hot encoding method to efficiently identify the most susceptible organism and biome to synbio displacement. Once identified, EcoGenoRisk screens for relevant synbio survival and stress response enzymes, as well as taxonomic similarity to established organisms in the biome. Cumulatively, all model outputs provide the user with data to inform the location and likelihood of synbio establishment.

Cresten Mansfeldt

Affiliation

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EcoGenoRisk: High Performance Computing for Synthetic Biology Invasion and Cross Biome Functional Modeling