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DRAM for distilling microbial metabolism to automate the curation of microbiome function

Michael ShafferDepartment of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USAMikayla BortonDepartment of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USABridget B. McGivernDepartment of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USAAhmed A. ZayedDepartment of Microbiology, The Ohio State University, Columbus, OH 43210, USASabina Leanti La RosaFaculty of Biosciences, Norwegian University of Life Sciences, Aas 1432, NorwayLindsey SoldenDepartment of Microbiology, The Ohio State University, Columbus, OH 43210, USAPengfei LiuDepartment of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USAAdrienne B. NarroweDepartment of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USAJosué Rodríguez-RamosDepartment of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USABenjamin BolducDepartment of Microbiology, The Ohio State University, Columbus, OH 43210, USAMaría Consuelo GazitúaDepartment of Microbiology, The Ohio State University, Columbus, OH 43210, USARebecca A. DalyDepartment of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USAGarrett J. SmithDepartment of Microbiology, Radboud University, Nijmegen 6525, NetherlandsDean VikDepartment of Microbiology, The Ohio State University, Columbus, OH 43210, USAPhillip B. PopeFaculty of Biosciences, Norwegian University of Life Sciences, Aas 1432, NorwayMatthew B. SullivanDepartment of Microbiology, The Ohio State University, Columbus, OH 43210, USASimon RouxJoint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USAKelly WrightonDepartment of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA

2020en

ABI

Аннотация

Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.

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DOI: 10.1093/nar/gkaa621

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