Grantee Research Project Results

2024 Progress Report: EcoGenoRisk : Identifying Potential Ecological Risks Posed by a Novel Genome

EPA Grant Number: R840207
Title: EcoGenoRisk : Identifying Potential Ecological Risks Posed by a Novel Genome
Investigators: Mansfeldt, Cresten
Institution: University of Colorado at Boulder
EPA Project Officer: Packard, Benjamin H
Project Period: July 1, 2021 through April 22, 2025
Project Period Covered by this Report: July 1, 2023 through June 30,2024
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:

(1) 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;

(2) Identify environmental habitats that are likely to harbor the susceptible populations; and

(3) 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.

Progress Summary:

Within the reporting period - keeping to the task schedule of deliverables (Figure 1) - the main focus of the coding effort has been to develop the EcoCen or EnCen portion of the code. EnCen extends on the now published HazID framework. EnCen follows a three phase approach of developing a binary library of enzyme functions within metagenome bins, assigning difference scores between metagenome bins, and contextualizing the considered SynBio genome across bins. All three phases are now functional and released on a public GitHub repository and serve as the main data output for a submitted manuscript.

The main results in this reporting period are as follows: (1) a script and public release of EnCen, (2) an automatically updating metagenome database, and (3) a test-run of EnCen on an external dataset.

Future Activities:

The main future research and development activities planned for the next reporting period continue the tasks identified in the timeline (Figure 1). After the current release of EnCen, the developmental effort will switch to RiskQ. The main targeted outputs during this period are the final two papers and the attendance of one conference. John Docter will continue as the lead PhD student.

Journal Articles on this Report : 1 Displayed | Download in RIS Format

Publications Views
Other project views:	All 9 publications	1 publications in selected types	All 1 journal articles

Publications
Type	Citation	Project	Document Sources
Journal Article	Ulanova A, Mansfeldt C. EcoGenoRisk:Developing a computational ecological risk assessment tool for synthetic biology. Environmental Pollution 2024:123647.	R840207 (2023) R840207 (2024)	Full-text: Science Direct- Full Text HTML Exit Abstract: PubMed- Abstract HTML

Supplemental Keywords:

functional classification, phenotypic classification

Relevant Websites:

CMBM-GEM Labs Website Exit

UC Boulder - EcoGenoRisk GitHub Exit

Progress and Final Reports:

Original Abstract

The 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.