Improving FAPROTAX, a popular tool for predicting metabolic phenotypes in microbiome surveys

改进 FAPROTAX，一种在微生物组调查中预测代谢表型的流行工具

• 批准号: 2135169
• 负责人: Stilianos Louca
• 金额: $ 38.72万
• 依托单位: University of Oregon Eugene
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-02-01 至 2025-01-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2135169&HistoricalAwards=false
• 关键词: Improving; FAPROTAX; popular; tool; predicting

FAPROTAX (Functional Annotation of Prokaryotic Taxa) is a popular database and computational tool for predicting the metabolic functions encoded by bacterial and archaeal (`prokaryotic') taxa in microbiome surveys. FAPROTAX has been used in 700 studies (as of November 2021) in a broad spectrum of environments. With this award, FAPROTAX will be revised to resolve many of its current limitations and substantially expand its applicability scope. FAPROTAX2 will be the only tool for conducting broad phenotypic predictions in microbiome surveys based on both experimental and genomic evidence, thus providing a valuable and unique resource for microbiome research. FAPROTAX2 will allow rapid insight into the metabolic functional potential of microbial communities without the need for expensive metagenomic sequencing or culturing. Hence, FAPROTAX2 will help tackle a multitude of environmental, industrial, agricultural and human health issues related to the microbiota, such as the bioremediation of soil pollutants, habitat restoration and conservation, wastewater treatment, landfill management, biofuel production, agricultural soil enhancement, and treating human diseases. As a side-product, the proposed project will also deliver an unprecedentedly comprehensive database of metabolic phenotypes across thousands of prokaryotic species, thus facilitating investigations of microbial evolution and providing valuable training/testing data for algorithms that predict prokaryotic phenotypes from genomes. This project will also provide student training in bioinformatics, programming, database design and management, and microbiology. FAPROTAX predicts the metabolic functions encoded by bacterial and archaeal (“prokaryotic”) 16S rRNA phylotypes in marker-gene microbiome surveys, based on published experimental evidence (e.g., from cultures) across thousands of taxa, covering 80 metabolic functions of environmental, industrial and medical interest. The specific improvements to be completed under this funding include incorporation of additional experimental evidence from more literature sources, redefinition of metabolic functions to be consistent with MetaCyc (a major metabolic pathway database), inclusion of phenotypic information from thousands of available prokaryotic genomes, added support for calculating prediction uncertainties, and increased flexibility when balancing sensitivity versus specificity, depending on the user's objectives. The proposed revision, FAPROTAX2, will be the only tool for conducting broad phenotypic predictions in marker-gene microbiome surveys based on both experimental and genomic evidence. These improvements will improve the ability to study the metabolic functions of microbial communities and their role in ecosystem processes. The final results of the project will be accessible from www.loucalab.com/archive/FAPROTAX.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

Faprotax（原核分类群的功能注释）是一种流行的数据库和计算工具，用于预测微生物组调查中细菌和档案（“原核生物”）分类群编码的代谢功能。 Faprotax已在各种环境中使用了700项研究（截至2021年11月）。有了该奖项，Faprotax将进行修订，以解决其当前的许多限制并大大扩大其适用性范围。 Faprotax2将是基于实验和基因组证据进行微生物组调查中进行广泛表型预测的唯一工具，从而为微生物组研究提供了宝贵而独特的资源。 Faprotax2将可以快速深入了解微生物群落的代谢功能潜力，而无需昂贵的宏基因组测序或文化。因此，Faprotax2将有助于解决与微生物群有关的多种环境，工业，农业和人类健康问题，例如土壤污染物的生物修复，栖息地恢复和保护，废水处理，垃圾填充治疗，垃圾填充管理，生物燃料管理，生物燃料的生产，农业土壤和人类疾病。作为副产品，该拟议的项目还将提供成千上万种原核生物的代谢表型的前所未有的全面数据库，从而开发了微生物进化的投资，并为预测来自基因组的原核表型的算法提供有价值的培训/测试数据。该项目还将为学生提供生物信息学，编程，数据库设计和管理以及微生物学培训。 Faprotax预测由细菌和古细菌（“原核”）16S rRNA系统型编码的标记 - 基因微生物组调查中的rRNA系统型，基于已发表的实验证据（例如，来自培养物）的已发表证据（例如，来自培养物），涵盖80个环境，工业，工业，工业和医疗利益的代谢功能。在这笔资金下将要完成的具体改进包括库存更多的文献来源的其他实验证据，重新定义与Metacyc（一个主要的代谢途径数据库）一致的代谢功能，包括数千个可用的原始基因组中的表型信息，对稳定性的启发性依赖性的稳定性逐渐增强，从而增加了可用的原点基因组的添加支持，并支持求解的求解，并依赖于灵活性。拟议的修订版Faprotax2将是基于实验和基因组证据的标记 - 基因微生物组调查中进行广泛表型预测的唯一工具。这些改进将提高研究微生物群落代谢功能及其在生态系统过程中的作用的能力。该项目的最终结果将可以从www.loucalab.com/archive/faprotax.this奖中访问，该奖项反映了NSF的法定任务，并使用基金会的智力优点和更广泛的影响审查标准，通过评估诚实地认为通过评估。