Consulting
How a pioneering co-culture fermentation startup leveraged AI-powered simulation to strengthen their core value proposition
Disclosure: The author (Dr. Laurence Yang) serves as Advisor to Allium Bio and holds advisory shares in the company as part of this relationship.

by Laurence Yang

Allium Bio: Innovative Co-Culture Startup
In an industry where bioprocess development relies heavily on trial-and-error experimentation, Allium Bio is pioneering co-culture fermentation systems to make safe, sustainable, and scalable food ingredients to enable the next generation of food products.
Their co-culture platform leverages metabolic synergies between microbes, including algae and fungi, to increase yield and expand ingredient customization.
Yet, to fully wield the potential of co-culture, Allium realized early on that leveraging digital, particularly simulation and AI, could accelerate near-term milestones and strengthen long-term differentiation.
leveraging digital, particularly simulation and AI, could accelerate near-term milestones and strengthen long-term differentiation.
Deciding to leverage AI-powered simulation
In my first conversation with Allium's CEO & Co-Founder Jonathan Ho, his long-term vision and the startup's strong fundamentals stood out.
The team's deep fermentation expertise supported their clear value proposition: delivering safe, sustainable, and scalable food ingredients for next-generation products.
Their technology platform, built on combinatorial co-culture libraries, enabled customized ingredients while achieving higher productivity through synergies between dozens of strains - addressing the industry's economic and sustainable scaling challenges.
Jon's vision for their digital platform aimed to:
  • Optimize microbial co-cultures and media combinations
  • Accelerate development of new ingredients for customers with complex compositions and functional needs
After calculating the tangible ROI of early-stage digital investment, we strategically developed the platform in two phases:
  1. Proof of Concept: 8-week proof of concept with working models and experimental validation
  1. Validated Prototype: 12-week deployment of a web application with case study combining simulation and comprehensive validation
The Key Outcomes
New Capabilities
  • Identify dozens of optimal ingredient/co-culture configurations, enabling yield improvements up to 5.2X (2.8X average)
  • Simulate dynamic co-culture cell biomass with high accuracy (R² = 0.95)
  • Generate time-course exometabolomics predictions at per-minute resolution, equivalent to ~$145k annual experimental value
  • Detect limiting nutrients to optimize feed strategies and media composition for both performance and cost
  • Explore 200 million strain-process combinations through dynamic simulation
A differentiating factor is that the models can be calibrated using a wide variety of data. Even without omics or massive training data the models are highly accurate by leveraging mechanistic (first-principles) knowledge bases.
This advancement accelerates development by predicting optimal strain combinations early and enables rapid optimization of co-culture dynamics, positioning Allium at the forefront of sustainable food ingredient innovation.
Learn more about Allium Bio at https://alliumbio.com
Jonathan Ho - Founder & CEO, Allium Bio
Working with Laurence as an Advisor has been a true partnership experience. From day one, he prioritized understanding our unique challenges at Allium Bio and tailored his insights specifically for our co-culture fermentation needs. His commitment to our success went beyond just helping us implement cutting-edge AI and simulation - he found innovative ways to strengthen our core capabilities, enabling us to explore 200 million strain-process combinations and promising strategies to achieve up to 5.2X yield improvements. His dedication to putting our objectives first has made him an invaluable partner in our mission to deliver safe, sustainable, and scalable ingredients for next-generation food products.
How can you leverage AI-powered simulation?
Are you a cell culture or precision fermentation company trying to improve the following:
  • faster and cost-effective development cycles
  • reliable strain behavior across reactor scales
  • systematic media optimization
  • identify ideal product-strain-process configurations out of millions of combinations
To discover whether AI or simulation can help in your specific situation: