University of Colorado Boulder, Department of Civil, Environmental, and Architectural Engineering, 1111 Engineering Drive, Boulder, CO, 80309, USA; University of Colorado Boulder, Environmental Engineering Program, 4001 Discovery Drive, Boulder, CO, 80303, USA.
University of Colorado Boulder, Department of Civil, Environmental, and Architectural Engineering, 1111 Engineering Drive, Boulder, CO, 80309, USA; University of Colorado Boulder, Environmental Engineering Program, 4001 Discovery Drive, Boulder, CO, 80303, USA.
Environ Pollut. 2024 Apr 1;346:123647. doi: 10.1016/j.envpol.2024.123647. Epub 2024 Feb 24.
The expanding field of synthetic biology (synbio) supports new opportunities in the design of targeted bioproducts or modified microorganisms. However, this rapid development of synbio products raises concerns surrounding the potential risks of modified microorganisms contaminating unintended environments. These potential invasion risks require new bioinformatic tools to inform the design phase. EcoGenoRisk is a newly constructed computational risk assessment tool for invasiveness that aims to predict where synbio microorganisms may establish a population by screening for habitats of genetically similar microorganisms. The first module of the tool identifies genetically similar microorganisms and potential ecological relationships such as competition, mutualism, and inhibition. In total, 520 archaeal and 32,828 bacterial complete assembly genomes were analyzed to test the specificity and accuracy of the tool as well as to characterize the enzymatic profiles of different taxonomic lineages. Additionally, ecological relationships were analyzed to determine which would result in the greatest potential overlap between shared functional profiles. Notably, competition displayed the significantly highest overlap of shared functions between compared genomes. Overall, EcoGenoRisk is a flexible software pipeline that assists environmental risk assessors to query large databases of known microorganisms and prioritize follow-up bench scale studies.
合成生物学（synbio）领域的不断扩展为靶向生物制品或改良微生物的设计提供了新的机会。然而，synbio 产品的快速发展引发了人们对修饰后的微生物污染意外环境的潜在风险的担忧。这些潜在的入侵风险需要新的生物信息学工具来为设计阶段提供信息。EcoGenoRisk 是一个新构建的用于入侵性的计算风险评估工具，旨在通过筛选具有遗传相似性的微生物的栖息地来预测 synbio 微生物可能在何处建立种群。该工具的第一个模块识别遗传相似的微生物和潜在的生态关系，如竞争、互利共生和抑制。总共分析了 520 个古菌和 32828 个细菌完整组装基因组，以测试该工具的特异性和准确性，并描述不同分类群的酶谱特征。此外，还分析了生态关系，以确定哪些关系会导致共享功能谱之间具有最大的潜在重叠。值得注意的是，竞争显示出比较基因组之间共享功能的显著最高重叠。总的来说，EcoGenoRisk 是一个灵活的软件管道，它可以帮助环境风险评估者查询已知微生物的大型数据库，并优先进行后续的台式规模研究。
