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（原核类群功能注释）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古菌（“原核”）类群编码的代谢功能。FAPROTAX 已在 700 项研究中使用（截至 2021 年 11 月）。凭借该奖项，FAPROTAX 将进行修订，以解决其当前的许多局限性并大幅扩展其适用范围。 FAPROTAX2 将是基于实验和基因组证据在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宝贵且独特的资源，FAPROTAX2 将允许快速了解微生物群落的代谢功能潜力，而无需其他技术。因此，FAPROTAX2 将有助于解决与微生物群相关的多种环境、工业、农业和人类健康问题，例如土壤的生物修复。污染物、栖息地恢复和保护、废水处理、垃圾填埋场管理、生物燃料生产、农业土壤改良和人类疾病治疗作为副产品，拟议项目还将提供涵盖数千种原核物种的代谢表型的前所未有的综合数据库，从而促进微生物进化的研究，并为从基因组预测原核表型的算法提供有价值的训练/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方面的培训。 FAPROTAX 根据已发表的数千个分类群的实验证据（例如来自培养物），预测标记基因微生物组调查中细菌和古菌（“原核”）16S rRNA 系统发育型编码的代谢功能，涵盖环境、工业和环境的 80 种代谢功能。这笔资金将完成的具体改进包括纳入来自更多文献来源的额外实验证据、重新定义代谢功能以与 MetaCyc 保持一致（a）主要代谢途径数据库），包含来自数千个可用原核基因组的表型信息，增加了对计算预测不确定性的支持，并根据用户的目标增加了平衡敏感性与特异性时的灵活性。拟议的修订版 FAPROTAX2 将是唯一的工具。基于实验和基因组证据在标记基因微生物组调查中进行广泛的表型预测，这将提高研究微生物群落的代谢功能及其在生态系统过程中的作用的能力。该项目可从 www.loucalab.com/archive/FAPROTAX 访问。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力优点和更广泛的影响审查标准进行评估，被认为值得支持。