DRAM for distilling microbial metabolism to automate the curation of microbiome function
2020/07/22 by Michael Shaffer, Mikayla Borton, Bridget B. McGivern +15 · 43 citations
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Genomics and Phylogenetic Studies #Bacteriophages and microbial interactions #Gut microbiota and health
paper · pdf · doi:10.1093/nar/gkaa621
openalex publication_date 2020/07/22 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/31
Abstract
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.
Cited by
- Minisyncoccus archaeiphilus gen. nov., sp. nov., a mesophilic, obligate parasitic bacterium and proposal of Minisyncoccaceae fam. nov., Minisyncoccales ord. nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. formerly referred to as Candidatus Patescibacteria or candidate phyla radiation
- Novel Methanosarcinaceae species Methanohalophilus methylutens sp. nov., Methanolobus methylotrophicus sp. nov., and Methanococcoides guerreronegronense sp. nov. from Guerrero Negro hypersaline microbial mats in accordance with the SeqCode
- Viromics approaches for the study of viral diversity and ecology in microbiomes
- Metagenomic time series reveals a Western English Channel viral community dominated by members with strong seasonal signals
- Aerobic soil bacteria adapt to hypoxia by hybridizing fermentation with carbon storage
- A call for caution in the biological interpretation of viral auxiliary metabolic genes
- Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly
- New insights into the microbiome of the deep-sea sponge Inflatella pellicula and the secondary metabolic potential of metagenome-assembled genomes and the wider microbiome
- Geochemistry shapes microbial diversity and selected functional traits in flowback and produced waters from hydraulically fractured formations
- A molecular inventory of the faecal microbiomes of 23 marsupial species
- Current Understanding of Taxonomy and Ecology of the Phylum <i>Minisyncoccota</i>
- Environmental selection constrains metabolic network architecture despite taxonomic turnover in anaerobic digestion communities
- Pushing the upper temperature limit of methanotrophy in continental hydrothermal ecosystems, active biological methane oxidation in hot springs of Yellowstone National Park
- Microbial starch degradation in arid soil: Community dynamics, environmental influences, and archaeological implications
- Minimizing decompression and warming during deep seawater collection increases abundance and activity of autochthonous bacteria and archaea
- From soil to sea: unravelling the metabolic versatility and social dynamics of Myxococcota bacteria from different Danish environments
- Genomic analysis of the widely distributed Acidobacteriota members reveals their overlooked metabolic roles
- Diversity of DNA viruses in the atmosphere of sub-Antarctic South Georgia
- Cattle manure suppresses methane consumption and enhances denitrification-associated nitrous oxide production in farm dams
- Diversity and ecological roles of hidden viral players in groundwater microbiomes
- Resilient Antarctic soil bacteria consume trace gases across wide temperature ranges
- Viruses Facilitate Energy Acquisition Potential by Their Bacterial Hosts in Rhizosphere of Grafted Plants
- Expansion, restructuring and characterization of the Legionellaceae family
- Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions
- The MiDAS global genome catalog: 53,501 long-read MAGs representing all core prokaryotic genera in the global activated sludge microbiome
- Functional gut microbiota dynamics of generalist and specialist bacteria in association with chicken growth
- The hidden role of rhizospheric viruses in promoting nitrogen fixation in soils
- Lactobacillus and Limosilactobacillus MAGs from alcoholic fermentation in sugarcane biorefineries
- A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics
- Host–virome associations in the weathering crust of a rapidly retreating temperate Alpine glacier
- Human gut microbiota subspecies carry implicit information for in-depth microbiome research
- Delivery Mode Impacts Gut Bacteriophage Colonization During Infancy
- Host Range Breadth Correlates with Genic Diversity in Honeybee Phages
- Seasonality of lake microbial denitrification and its sensitivity to climate warming
- Quantitative stable isotope probing (qSIP)-informed metagenomics identifies viruses infecting chemoautotrophs
- Global genomic diversity of temperate P2-like viruses
- Forest Disturbance Drives Changes in the Functional Traits of Soil Bacteria: A Metagenomic Study of Kauri ( Agathis australis ) Forest Ecosystems
- Prime osservazioni sulla subirrigazione a goccia dei frutteti
- CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning
- eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
- Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats
- The Microflora Danica atlas of Danish environmental microbiomes
- Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism
- Metagenomic spaces: a framework to study the effect of microbiome variation on animal ecology and evolution
Related