Biofuels SFA

Tools and functionality to support a systems biology approach to understanding interactions in bioenergy-relevant microbial communities

The Systems Biology Approach to Interactions and Resource Allocation in Bioenergy-Relevant Microbial Communities (a.k.a. Biofuels) Science Focus Area (SFA), led by Dr. Rhona Stuart at Lawrence Livermore National Laboratory (LLNL), is focused on the community systems biology of microbial consortia that are closely associated with bioenergy-relevant plants and algae. The SFA focuses on linking microscale impacts of single cells on system scale processes, applying quantitative isotope tracing of elemental exchanges and various ‘omics-based approaches. The project also utilize constraint-based genome-scale metabolic modeling to predict and test interactions within microbial communities.

Biofuels had improved the quality of genome annotations to improve draft metabolic models within KBase, by developing tools for importing, comparing, and merging metabolic annotations. These tools expedite the curation process during model building and produce the high-quality, multi-evidenced curated models needed to investigate the complex interactions within microbial communities.

Longer term, the team seeks to engage with KBase to interpret and integrate data streams to further goals around understanding and predicting ecological, biophysical, and biochemical dynamics of multi-taxa communities, as well as the metabolite fluxes that regulate trophic interactions.

Collaborative Development Projects

Starting Fall 2021 – Probabilistic Annotation and Ensemble Metabolic Modeling

Improving Draft Metabolic Models:

Create annotation tools that accept multiple lines of evidence to determine an optimal consensus annotation from data like EC numbers, KEGG, and MetaCyc reaction identifiers.

Functionality and Tools

• Import Annotations From Staging (Released)
  • Provides a way to upload third-party annotations like EC and KEGG into KBase
• Bulk Import Annotations From Staging (Released)
  • Provides a way to upload third-party annotations to add to an existing genome into KBase in bulk
• Compare Metabolic Annotations (Released)
  • Compare and contrast the metabolic annotations from multiple sources
• Merge Metabolic Annotations (Released)
  • Generate a consensus annotation by combining multiple annotation sources

Additional Information

Meet the Members

SFA Manager: Henry Shaw¹
SFA Principal Investigator: Rhona Stuart¹
KBase Contact: Chris Henry^2,3
Lead Developers: Patrik D’haeseleer¹, Jeffrey Kimbrel¹
Project Team: Ali Navid¹, Ben Bowen⁴
Affiliations: ¹Lawrence Livermore National Laboratory, ²Argonne National Laboratory, ³KBase, ⁴Lawrence Berkeley National Laboratory

Resources

• LLNL SFA Project Website – “A Systems Biology Approach to Interactions and Resource Allocation in Bioenergy-Relevant Microbial Communities”
• Functional Annotation Tools (14 April 2021) – KBase tutorial webinar