Microbial ecoSystems Laboratory
Scaling Genomes to Ecosystem Function
With an emphasis on applying knowledge about microbial communities – who is there and what they are doing – the Microbial ecoSystems Laboratory at Colorado State University, led by Dr. Kelly Wrighton, aims to help us better manage ecosystem function. The lab studies a range of ecosystems from soils and rivers, to the human gut, and even deep fractured shale systems. Then, they synthesize predictive models around microbial community stability and the impact of changing conditions through a combination of technologies that study environmental genomes and chemistry, and laboratory validations.
Collaborative Development Projects
Distilling and Refining Annotation of Metabolism (DRAM)
Developers: Lead – Michael Shaffer, PhD (https://github.com/shafferm); Rory Flynn (https://github.com/rmFlynn)
Source Code: GitHub Repository: DRAM
A tool for annotating genomes, metagenomic assembled genomes (MAGs), and VirSorter-identified viral contigs (DRAM-v). See Shaffer et al. (2020) and Shaffer et al. (2023) for more information.
Tools in KBase:
- Annotate and Distill Genomes with DRAM: Annotates isolate genomes and metagenome assembled genomes (MAGs) and provides an interactive functional summary per genome. (Released)
- Annotate and Distill Assembles with DRAM: Annotates metagenome assemblies and provides an interactive functional summary per assembly. (Released)
- Annotate and Distill Viral Assemblies with DRAM: Annotates viral assemblies and provides an interactive functional summary per assembly. (Released)
Genome Resolved Open Watershed (GROW)
Lead Scientist: Mikayla Borton, PhD
The Genome Resolved Open Watershed (GROW) was selected as a Community Science Program (CSP) by the Joint Genome Institute (JGI). Entitled “Microbial Genomes Across the World’s Rivers”, the proposal aims to create the GROW (Genome Resolved Open Watershed) Database by leveraging distributed research networks to understand watershed systems.
The GROW database is available via the KBase GROW Organization – https://narrative.kbase.us/#org/grow. To join, create a KBase account at www.kbase.us, navigate to the KBase Organizations (Orgs) and search for GROW in “all Orgs”, then request to join. Once your request has been accepted, you will have access to all GROW data available in KBase.
Summary and links to access GROW US River Systems samples and data in KBase at https://kbase.us/n/109073/41. Please cite as: Borton, et al. (2022) GROWdb US River Systems – Samples. [Data set]. DOE Systems Biology Knowledgebase. doi:10.25982/109073.30/1895615.
Multiscale Microbial Dynamics Modeling – 2020 EMSL Summer School
Every summer, the Environmental Molecular Sciences Laboratory (EMSL) User Research Facility, based at the Pacific Northwest National Laboratory (PNNL), hosts a course for early career researchers. In 2020, the course was online to accommodate restrictions imposed by the global pandemic, so course lectures were streamed live and recorded. More information on the entire course can be found on the KBase 2020 Microbial Dynamics Summer School website.
Wrighton Lab course lectures:
- Metagenomics 101, by Dr. Kelly Wrighton
- Inferring Biogeochemical Function from Genomes (with DRAM tutorial), by Drs. Mikayla Borton and Michael Shaffer
Additional Information
Meet the Members
Principle Investigator: Kelly Wrighton
Lead Contributors: Mikayla Borton, Michael Shaffer, Rory Flynn
Project Team: Bridget McGivern, Josue Rodriguez-Ramos, Ikaia Lelweiwi, Katherine Kokkinias, Djennyfer Ferreira, Lady Grant, Angela Oliverio, Jared Ellenbogen, Rebecca Daly, Rory Flynn, Rich Wolfe, Hannah Lucero, Christopher Chorpenning, Levi Johnson
Resources
Shaffer M, Borton MA, Bolduc B, Ghadermazi P, Edirisinghe JN, Faria JP, Miller CS, Chan SH, Sullivan MB, Henry CS, and Wrighton KC. (2023). kb_DRAM: Annotating and functional profiling of genomes with DRAM in KBase. Bioinformatics 39:4. doi: 10.1093/bioinformatics/btad110
Shaffer M, Borton MA, McGivern BB, Zayed AA, Leanti La Rosa S, Solden LM, Liu P, Narrowe AB, Rodríguez-Ramos J, Bolduc B, Gazitúa MC, Daly RA, Smith GJ, Vik DR, Pope PB, Sullivan MB, Roux S, Wrighton KC. (2020). DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Research 48:16. doi: 10.1093/nar/gkaa621
Goldman AE, Chu RK, Danczak RE, Daly RA, Fansler S, Garayburu-Caruso VA, Graham EB, McCall ML, Ren H, Renteria L, Resch CT, Tfaily M, Tolic N, Torgeson JM, Toyoda JG, Wells J, Wrighton KC, Stegen JC. WHONDRS Consortium T (2020): WHONDRS Summer 2019 Sampling Campaign: Global River Corridor Sediment FTICR-MS, NPOC, and Aerobic Respiration. River Corridor and Watershed Biogeochemistry SFA Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS). doi: 10.15485/1729719 (SFA)
Toyoda JG, Goldman AE, Chu RK, Danczak RE, Daly RA, Garayburu-Caruso VA, Graham EB, Lin X, Moran JJ, Ren H, Renteria L, Resch CT, Tfaily M, Tolic N, Torgeson JM, Wells J, Wrighton KC, Stegen JC. WHONDRS Consortium T (2020): WHONDRS Summer 2019 Sampling Campaign: Global River Corridor Surface Water FTICR-MS, NPOC, and Stable Isotopes.Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS). doi: 10.15485/1603775 (SFA)
Genome Insider Podcast Episode: River Microbiomes From Around The World (https://jgi.doe.gov/genome-insider-episode-3-river-microbiomes-from-around-the-world/)
