Wrighton Lab – Microbiome Research Group

Scaling Genomes to Ecosystem Function

Summary: With an emphasis on applying knowledge about microbial communities – who is there and what they are doing – the Wrighton Lab at Colorado State University, led by Dr. Kelly Wrighton, aims to help us better manage ecosystem function. The Wrighton Lab studies a range of ecosystems from soils and rivers, to the human gut, and even deep fractured shale systems. The group synthesizes 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 er al. (2022, preprint) for more information.

Tools in KBase:

GROW logo

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.

Data and analyses in KBase (coming soon)

 

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:

 

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, 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. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Research, 18 Sep 2020; 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/)

System maintenance Aug 16

We will be performing system maintenance on Tuesday, August 16, 2022, from 11am-3pm CDT (9am-1pm PDT).  narrative.kbase.us, compute jobs, and appdev.kbase.us will be unavailable or unstable for parts of this time.

We do not anticipate any interruption to www.kbase.us.