Microbial Biotechnology Community

Bioeconomies are economies based on renewable resources from the land and sea, such as crops, fish, forests and animals. The bioeconomy in the EU is worth an estimated €2 trillion and employs 9% of the workforce. Microbial biotechnology designs and builds new strains of microbes that can produce chemical building blocks, food supplements, novel medicines and fuels to replace fossil fuels. As such, biotechnology can play a huge role in the bioeconomy and can help tackle climate change, achieve a clean environment, foster industrial innovation, and ensure food security.

However, a formal framework for microbial biotechnology to manage and manipulate strains, samples, knowledge, data and metadata is still lacking. The Design - Build - Test - Learn (DBTL) cycle provides a conceptual framework for the development of tailor-made microbes and biological systems. The ELIXIR Microbial Community takes the DBTL cycle as a starting point for defining its four key objectives.

Goals of the Community

To build scalable microbial Genome-Scale Metabolic Models (GSMMs)

  • The Microbial Biotechnology Community will support the use of advanced Genome-Scale Metabolic Models (GSMMs) to predict the effects of genetic manipulations on cellular phenotypes such as production of a specific compound or protein.
  • The Community will integrate advanced GSMMs computational models in the DBTL cycle by developing a consolidated cell model or metabolic reaction network resource that will (1) provide species-specific genome-scale metabolic networks and models, and (2) the necessary data to facilitate the design of microbial engineering projects.
  • The specific actions include:
    • Improve representation of microbial reference enzymes and metabolic reactions in ELIXIR databases and services
    • Expand descriptions of enzymatic activities to include a definition of the chemical transformations involved
    • Develop an open-source community-supported evaluation suite for metabolic models testing
    • Develop tools for microbial community description, modelling and design
    • Develop user interfaces for visual manipulation of advanced genome-scale models and designs methods
    • Define a catalogue of natural and synthetic bio-bricks
    • Develop a semantic framework for integration of heterogeneous models, data and algorithms

To develop a knowledge-based infrastructure for biotechnology

  • The Community will develop a FAIR repository of experimental data in microbial biotechnology to (1) facilitate the development of biotechnology experimental implementations and (2) encourage the reporting of experimental data.
  • As most applications in microbial biotechnology first design microbial strains that are then engineered and characterised, such a repository will support design of new microbial strains and contribute to the annotation of genome-scale metabolic networks.
  • To promote reproducibility and reuse of these experimental data, the repository will capture complete design information and complete metadata for the different Build-Test-Learn stages.
  • The specific actions include:
    • Compile and maintain a list of data repositories and tools available to the Microbial Biotechnology Community and register them in ELIXIR registries (FAIRsharing, bio.tools).
    • Establish workflows between a limited number of interoperable tools and resources to support metadata integration across the different steps in the DBTL cycle.
    • Identify a set of tools and conventions for metadata collection against control- and data-driven workflows for the different steps in the DBTL cycle.
    • Align the Community practices in workflows, data and metadata management with the current ELIXIR activities in ELIXIR Interoperability, Compute and Tools Platforms by supporting the use of Common Workflow Language, BioContainers, identifiers.org or Ontology Lookup Service.
    • Adopt ELIXIR Core Data Resources and ELIXIR Deposition Databases for long-term public pooling of final models, data and workflows.
    • Build a new data repository for reaction rules that will gather both positive and negative results.

To develop a unified semantic ontology for microbial biotechnology

  • To increase the tools interoperability, support dataset integration within and across the DBTL cycle(s), and increase the potential of data-mining approaches, the Community will develop shared semantic standards for the representation of data and knowledge in microbial biotechnology.
  • By implementing RDF data models, the Community will demonstrate how existing ELIXIR Node resources can be integrated to provide a unified access to data to end-users.
  • The specific actions include:
    • Map between languages that describe the designs, build processes, models, entities and experimental data in the DBTL cycle and promote their convergence where possible. Register these standards in FAIRsharing.
    • Import Genome-scale metabolic networks and biochemical pathways from major resources into a common semantic namespace of chemical compounds, reactions, cellular compartments and proteins.
    • Support the provenance annotation of models, designs, build information and experimental data.

To develop training and community engagement in in microbial biotechnology

  • To address the lack of a European catalogue of available training materials in microbial biotechnology and to support European coordination in training activities relevant to microbial biotechnology, the Community will collaborate with the ELIXIR Training Platform and TeSS in facilitating access to high-quality training and public engagement.
  • The specific actions include:
    • Compile a catalogue of online courses related to Microbial Biotechnology; provide link to these in the ELIXIR Training portal (TeSS).
    • Organise developer hackathons to support the technical activities defined in the technical goals of the Community (see above).
    • Organise end-user competitions on a series of pathway and strain designs, or metabolite identification in microbial strains.
    • Organise public outreach events as part of existing networks and projects in microbial biotechnology.

Commissioned Services

The Microbial Biotechnology Community will be involved in a number of short-term, technical projects called Commissioned Services. The first such project helped establish the Community, and ran from January 2017 to June 2018:

This webinar gave an overview of the results of the study:

Leadership

Vincent Fromion
Vincent Fromion
(ELIXIR France)
Vitor Martins dos Santos
Vitor Martins dos Santos
(ELIXIR Netherlands)
John Hancock
John Hancock
(ELIXIR Services and Communities Coordinator, ELIXIR Hub)

Find out more