Non-model microbes offer unique phenotypes that can be beneficial for biomanufacturing, such as the ability to grow on industrial feedstocks, produce various beachhead molecules, or tolerate conditions that can improve process economics (e.g., low pH conditions, increased temperature, etc.).

However, these organisms typically lack the foundational datasets and basic genetic tools required for rational strain development. We specialize in rapidly developing these tools and datasets to enable and enhance Design-Build-Test-Learn (DBTL) cycles for rational strain improvement. 

Evaluation of host development

We have developed a Tier System that organizes, tracks, and prioritizes strain development efforts. Early prioritization is on genetic tool development to create a chassis strain for metabolic engineering that can be utilized in DBTL cycles. More advanced Tiers include omics datasets, fermentation data, more advanced genetic tools, and various metabolic and other models, which facilitate host development goals in further DBTL cycles. Tier system progress for Agile BioFoundry hosts will be tracked and made available to the public through the Host Onboarding Tool website (HObT).

Genetic tool development

Rapid development of genetic tools is critical to enabling rational strain engineering. We have a large — and growing — collection of genetic parts for engineering diverse bacteria and fungi, which can be rapidly adapted to new organisms. We develop and improve transformation methods, demonstrate chromosomal modification methods, characterize gene expression “parts,” and create high throughput tools and protocols. These tools are designed to accelerate bioengineering through the DBTL process.

Datasets

Large datasets provide critical physiological information and serve as the foundation for Learn efforts. We can perform transcriptomics, proteomics, and metabolomics to help understand gene expression and metabolic flux. We have the ability to characterize growth and bioconversion at various scales (spanning microtiter plates to 100s or 1000s of liters). Our advanced genetic tools enable the construction of genome-scale libraries of engineered strains and large libraries of pathway variants that can be used to understand and improve strain performance. As non-model hosts are developed and processed through the Agile BioFoundry’s DBTL cycle, these datasets will be made available through public-facing websites (e.g., HObT) to accelerate development and adoption of these strains by academia and industry.

Currently, onboarded microbes within the Agile BioFoundry include: 

• Aspergillus niger
• Aspergillus pseudoterreus
• Bacillus licheniformis
• Clostridium ljungdahlii
• Clostridium tyrobutyricum
• Corynebacterium glutamicum
• Cupriavidus necator
• Lipomyces starkeyi
• Pichia kudriazevii
• Pseudomonas fluorescens
• Pseudomonas putida
• Rhodobacter sphaeroides
• Rhodosporidium toruloides
• Yarrowia lipolytica
• Zymomonas mobilis