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The U.S. Department of Energy (DOE) Systems Biology Knowledgebase (KBase) is a software and data platform designed to help researchers predict and understand biological function.
This newsletter contains information about KBase’s newest features, user documentation, upcoming workshops and events, social media pages, and more.
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Metabolic Reconstruction and Modeling Microbial Electrosynthesis in KBase
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Microbial electrosynthesis is a renewable energy and chemical production platform that relies on microbial taxa to capture electrons from a cathode and fix carbon. The metabolic capacity of multispecies microbial communities on electrosynthetic biocathodes remains unknown. In a recent article published in
Scientific Reports, researchers used KBase to create metabolic models of the primary community members (
Acetobacterium, Sulfurospirillum and
Desulfovibrio) from an electrosynthetic biocathode. The research revealed that
Acetobacterium were the primary carbon fixer and a keystone member of the community, while
Desulfovibrio were essential conduits for electron flow from the electrode into the electrosynthetic community. The molecular discoveries and metabolic modeling techniques deployed in this research may serve as a foundation for future examination and development of electrosynthetic microbial communities.
View Narrative for this Publication
Marshall CW, Ross DE, Handley KM, Weisenhorn PB, Edirisinghe JN, Henry CS, et al. Metabolic Reconstruction and Modeling Microbial Electrosynthesis. Scientific Reports. 2017;7. doi:10.1038/s41598-017-08877
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Summer 2017 Publications
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Check out some of the latest publications from scientists using KBase to enable their research. Visit our Publications page to see examples of how biologists are using KBase to support discovery across a variety of subdisciplines.
- Hamilton JJ, Garcia SL, Brown BS, Oyserman BO, Moya-Flores F, Bertilsson S, et al. Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI. Pollard KS, editor. mSystems. 2017;2: e00091-17. doi:10.1128/mSystems.00091-17
- Gilmore SP, Henske JK, Sexton JA, Solomon KV, Seppälä S, Yoo JI, et al. Genomic analysis of methanogenic archaea reveals a shift towards energy conservation. BMC Genomics. 2017;18. doi:10.1186/s12864-017-4036-4
- Jensen PA, Zhu Z, van Opijnen T. Antibiotics Disrupt Coordination between Transcriptional and Phenotypic Stress Responses in Pathogenic Bacteria. Cell Reports. 2017;20: 1705–1716. doi:10.1016/j.celrep.2017.07.062
- Crofts TS, Wang B, Spivak A, Gianoulis TA, Forsberg KJ, Gibson MK, et al. Draft Genome Sequences of Three β-Lactam-Catabolizing Soil Proteobacteria. Genome Announcements. 2017;5: e00653-17. doi:10.1128/genomeA.00653-17
- Nicholls C, Kump A, Ford S, Gonser R, Cho KH. Draft Genome Sequence of Streptococcus pyogenes Strain M3KCL. Genome Announcements. 2017;5: e00610-17. doi:10.1128/genomeA.00610-17
- Wu X, Deutschbauer AM, Kazakov AE, Wetmore KM, Cwick BA, Walker RM, et al. Draft Genome Sequences of Two Janthinobacterium lividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center. Genome Announcements. 2017;5: e00582-17. doi:10.1128/genomeA.00582-17 – Link to Publication
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Protocol for Genome Assembly and Annotation
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A new protocol in
Current Protocols in Microbiology demonstrates an example workflow for taking a comparative and iterative approach to assembly and annotation of prokaryotic genomes using KBase. This approach can be used by microbiologists seeking to perform isolate analysis in a rapid and reproducible fashion. There is also a tutorial Narrative in KBase that replicates the workflow described in the protocol. KBase users can copy this Narrative to run the workflow on their own prokaryotic sequencing reads.
Allen B, Drake M, Harris N, Sullivan T. Using KBase to Assemble and Annotate Prokaryotic Genomes. Current Protocols in Microbiology. Hoboken, NJ, USA: John Wiley & Sons, Inc.; 2017. p. 1E.13.1-1E.13.18. doi:10.1002/cpmc.37 – Link to Publication
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Summer Meetings and Conferences
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KBase scientists presented their work and conducted workshops at a variety of conferences this summer.
- At ASPB Plant Biology 2017, KBase scientists presented a talk, two posters, and gave demonstrations at a booth with the DOE Joint Genome Institute (JGI).
- Chris Henry of Argonne National Labory (ANL) gave an talk at Metabolic Pathway Analysis 2017 titled “Progressing towards a deep integration of chemistry and biology to discover new protein functions, pathways, and ecological principles,” while José Pedro Lopes Faria of ANL discussed improving automated metabolic model reconstruction using KBase.
- Janaka Edirisinghe from ANL presented a talk at the 2017 International Conference on Systems Biology titled “Automated pathway curation and improving metabolic model reconstruction based on phylogenetic analysis of pathway conservation.”
- Robert Cottingham, Co-PI of KBase at Oak Ridge National Laboratory, presented a KBase demo showing bioinformatics researchers how to integrate their open-source tools into the KBase App Catalog and data environment at the 2017 ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB).
- Bill Reihl from Lawrence Berkeley National Lab spoke at JupyterCon about KBase's Narrative Interface, built on the Jupyter Notebook, is the front end to a scalable object store, an execution engine, a distributed compute cluster, and a library of analysis tools packaged as Docker images.
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Testimonials Page
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| Visit our Testimonials page to read in their own words how scientists are using KBase to enable their research and support discovery. If you would like to submit a testimonial, please contact us. |
| Newsletter #5 |
September 20, 2017 |
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