Grantee Research Project Results
Final Report: EcoGenoRisk : Identifying Potential Ecological Risks Posed by a Novel Genome
EPA Grant Number: R840207Title: EcoGenoRisk : Identifying Potential Ecological Risks Posed by a Novel Genome
Investigators:
Institution:
EPA Project Officer:
Project Period: July 1, 2021 through April 22, 2025
Project Amount: $337,616
RFA: Assessment Tools for Biotechnology Products (2020) RFA Text | Recipients Lists
Research Category: Safer Chemicals , Chemical Safety for Sustainability
Objective:
The primary objective of this proposal is to develop and deploy the Python-based EcoGenoRisk, a bioinformatic tool with three aims for the software to deliver:
- Identify those genomes within public databases that negatively respond to the product, display the most similarity genetically to the synbio organism, and/or harbor similar or competing pathways to define susceptible populations;
- Identify environmental habitats that are likely to harbor the susceptible populations; and
- Quantify both the likelihood of the synbio microorganism to arrive in the susceptible habitat and the extent of structural or functional disruption experienced by the resident microbial community.
Conclusions:
The EcoGenoRisk project developed and publicly released a Python-based bioinformatic platform to anticipate ecological risks posed by engineered microorganisms. Designed to support both regulators and innovators in synthetic biology, the tool integrates genomic and metagenomic data from global repositories to identify susceptible microbial populations, assess vulnerable environments, and evaluate potential ecological disruptions from synthetic organisms. Over the course of the project, two major modules were completed and released: HazID, which predicts competitive or susceptible organisms through genome-to-genome functional comparisons, and EnCen, which extends this framework to environmental metagenomes to identify at-risk habitats. Together, these modules establish the first computational system capable of systematically predicting functional overlap and ecological displacement risk between engineered and natural microorganisms. Despite early termination of the final RiskQ module due to programmatic changes, the project achieved its core objectives, producing open-source code, automatically updating databases, peer-reviewed publications, and training opportunities for graduate and master’s students. EcoGenoRisk now provides a transparent resource to inform safe biotechnology design, ecological stewardship, and proactive risk assessment for agencies, industry, and the research community.
References:
Publications:
Docter, John, and Cresten Manfeldt. “Environmental Census: Modeling Synthetic Biology Ecological Risk with Metagenomic Enzymatic Data and High-Performance Computing”. Submitted to ACS Synthetic Biology and under review.
Presentations:
Mansfeldt, C. EcoGenoRisk: Bioinformatic Mining of Expanding Genomic Databases to Predict Ecological Hazards and Risks. Environmental Protection Agency Region 8. October 24, 2024. Denver, CO.
Docter., J and Mansfeldt, C. Computing Environmental Synthetic Biology Risk. Poster Presentation. April 25, 2024. Front Range Microbiome Symposium, Fort Collins, CO, USA.
Docter., J and Mansfeldt, C. Environmental Census: Computing Environmental Synthetic Biology Risk. Poster Presentation. June 19, 2024. American Society of Microbiology, Atlanta, GA, USA.
Mansfeldt, C. Anticipating the Future Impact of Synthetic Biology on Aquatic Sciences. Poster Presentation. June 27, 2024. Gordon Research Conference: Water, Holderness, NH, USA.
Mansfeldt, C, and Ulanova, A. Predicting the Risks Associated with Synthetic Biology to Wastewater. Poster Presentation. September 10-13, 2023. International Water Association Microbial Ecology and Water Engineering Conference, Brisbane, Australia.
Mansfeldt, C., Burn After Reading: The Increasing Need for Uniting Surveillance with Treatment in Wastewater Management. Oral Presentation. June 19-23, 2023. AEESP Conference, Boston, Massachusetts.
Ulanova, A. and Mansfeldt, C. Computational Tool for Synthetic Organism Risk Assessment: HazID. June 28-30, 2022. Association of Environmental Engineering and Science Professors Conference. St. Louis, MO.
Mansfeldt, C. AEESP 2022 Early Career Spotlight: Cresten Mansfeldt. June 28-30, 2022. Association of Environmental Engineering and Science Professors Conference. St. Louis, MO.
Mansfeldt, C, and Ulanova, A. Insurance against everything being everywhere: Managing and Monitoring Microbiomes Susceptible to Invasion. June 19-24, 2022. Front
Range Microbiome Symposium: Fort Collins, CO. Gordon Research Conference: Microbiology of the Built Environment: Waterville Valley, NH.
Mansfeldt, C, and Ulanova, A. Database-driven microbial risk and benefit analyses. April 13, 2022. Front Range Microbiome Symposium: Fort Collins, CO.
Journal Articles:
No journal articles submitted with this report: View all 9 publications for this projectSupplemental Keywords:
functional classification, phenotypic classificationRelevant Websites:
Creative Microbial Bio Maintenance for Greener Environments and Municipalities (CMBM-GEM) research team webpage Exit
EcoGenoRisk GitHub webpage Exit
Progress and Final Reports:
Original AbstractThe perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Conclusions drawn by the principal investigators have not been reviewed by the Agency.