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

FAPROTAX(Functional Annotation of原核生物分类群)是一种流行的数据库和计算工具，用于在微生物组调查中预测细菌和古细菌(原核生物)分类群编码的代谢功能。截至2021年11月，FAPROTAX已在广泛的环境中进行了700项研究。有了这一奖项，FAPROTAX将进行修改，以解决其目前的许多限制，并大幅扩大其适用范围。FAPROTAX2将是在基于实验和基因组证据的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和独特的资源。FAPROTAX2将允许快速洞察微生物群落的代谢功能潜力，而不需要昂贵的元基因组测序或培养。因此，FAPROTAX2将帮助解决与微生物区系有关的多种环境、工业、农业和人类健康问题，如土壤污染物的生物修复、生境恢复和保护、废水处理、垃圾填埋场管理、生物燃料生产、农业土壤改良和治疗人类疾病。作为副产品，拟议的项目还将提供一个涉及数千个原核生物物种的空前全面的代谢表型数据库，从而促进微生物进化的研究，并为从基因组预测原核生物表型的算法提供宝贵的训练/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在标记基因微生物组调查中预测细菌和古生菌(“原核生物”)16S rRNA系统型编码的代谢功能，基于已公布的实验证据(例如，来自培养的)，涵盖环境、工业和医学方面的80种代谢功能。在这笔资金下将完成的具体改进包括纳入更多文献来源的更多实验证据，重新定义代谢功能以与MetaCyc(一个主要的代谢途径数据库)保持一致，纳入来自数千个可用原核生物基因组的表型信息，增加对预测不确定性的支持，以及在根据用户的目标平衡灵敏度和特异度时增加灵活性。拟议的修订，FAPROTAX2，将是在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的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从www.Loucalab.com/ARCHIVE/FAPROTAX网站上获得。该奖项反映了NSF的法定使命，并已通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

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.