Grantee Research Project Results

2022 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, 2021 through June 30,2022
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.

Progress Summary:

Within the reporting period, the main focus of the initial coding effort has been to develop the HazID portion of EcoGenoRisk. HazID has three main functions under development: NicheOverlap, CompetitorFind, and PoisInhibitor. NicheOverlap focuses on the direct displacement by the synbio microorganism overlapping and outcompeting with a given niche. CompetitorFind identifies similar, competing, or mitigating pathways in response to the presence of the synbio microorganism. Finally, PoisInhibitor finds those enzymes that respond negatively to the product of the synbio microorganism.

The main results in this reporting period are as follows: (1) a script for HazID:NicheOverlap, (2) a genome database, (3) an EC number database, (4) a comparison between genomes within the database, and (5) a test of in silico generated synbio genomes.

Future Activities:

The main future research and development activities planned for the next reporting period continue the tasks identified in the timeline (Figure 1). The development of HazID will conclude with the addition of PoisInhibitor and CompetitorFind. The second milestone will be satisfied with the successful implementation of the script for these two sub routines. After passing this milestone, developmental effort will switch to EcoCen and the curation of metagenomes. The main targeted outputs during this time period are two papers and the attendance of two conferences.

Journal Articles:

No journal articles submitted with this report: View all 9 publications for this project

Supplemental Keywords:

functional classification, phenotypic classification

Relevant Websites:

CMBM-GEM Labs 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.