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

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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.