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Table 2. Controlled Cultivation and Sample Processing Technology Development Roadmap (acronyms)

Technology Objectives

Research, Design, and Development

Demonstration: Pilots, Modular Deployment

Integration and Production Deployment

Facility Outputs

Controlled Cell Growth, Analysis

Flexible, highly instrumented and monitored cultivation systems

Online metabolite monitoring

Sample preparation, characterization, stabilization

Sample archiving, tracking

User environments

Community outreach, education

Define and determine:

  • Appropriate parameters, culture variability
  • Workflow processes
  • Scale factors
  • Hardware, software, instrumentation

Develop:

  • Reactor and instrumentation, interfaces, sampling methods
  • Reactor-based growth models, simulations
  • Searchable sample archive
  • Isotope labeling
  • High-throughput cultivation, isolation of community members

Pilot:

  • High-throughput controlled cell growth, processing
  • Methods for large sample collection
  • Online analytical systems for high-throughput metabolite measurements
  • Experiment and sample database
  • Automation, standardization, protocols

Develop methods:

  • Commensal cocultures
  • Extremophiles
  • Biofilms and structures
  • Sample receipt and delivery

Establish high-throughput pipeline based on defined products, standards, protocols, costs

Scale up parallel processes for multiple organisms

Process automated, reproducible samples

Scale up user-access protocols for sample receipt, growing, delivery

Coordinated high-quality analyses of microbial samples for nucleic acids, proteins, metabolites, and others as needed

Detailed cultivation and sampling parameters

Efficient, high-capacity, annotated biosample archives

User environment for access, protocols, process

To develop and incorporate the necessary technologies and methods into a high-throughput production environment, a phased process will be followed as described in this roadmap. The process includes research, design, and development; modular and pilot-scale deployment; and final integration and scaleup into operational procedures.