Thermo Fisher Scientific supports Amyris to optimize the bioproduction of sustainable squalane

Significance of the topic

Biotechnological production of squalane addresses pressing environmental and ethical concerns associated with traditional sourcing from shark liver oil. Converting renewable feedstock (sugarcane) into high-value emollients via engineered yeast reduces pressure on marine ecosystems and aligns with market demand for cruelty-free, sustainable ingredients. Real-time analytical monitoring of fermentation is essential to ensure process efficiency, product quality and reproducibility at industrial scale.

Objectives and overview of the case study

This case study describes how Amyris uses engineered Saccharomyces cerevisiae and precision fermentation of sugarcane-derived feedstock to produce farnesene, which is subsequently processed to squalane. The primary objective is to optimize bioproduction throughput and product quality by integrating online gas analysis to monitor culture health and carbon balance during multi-stage fermentations, particularly during the terminal "master fermentation".

Methodology

The process employs multi-step fermentation with genetically modified yeast strains that convert sugarcane sucrose into farnesene. Key control points include maintaining yeast stability and maximizing yield across fermentation stages. Critical process variables monitored are ethanol, dissolved oxygen (indirectly via gas composition and oxygen consumption), and carbon dioxide evolution to evaluate metabolic state and substrate utilization. Online analysis of both sparge (inlet) and exhaust (outlet) gases enables non-invasive tracking of growth kinetics and respiratory metrics without compromising sterility.

Used instrumentation

The primary analytical tool described is the Thermo Scientific Prima PRO Process Mass Spectrometer for online gas composition analysis. The instrument provides continuous measurements of key gaseous species (e.g., O2, CO2, ethanol vapor) used to:

• Calculate respiratory quotient (RQ = CO2 evolution / O2 uptake) to infer metabolic state and efficiency.
• Detect deviations in the carbon balance that may indicate formation of unwanted by-products or process upsets.
• Support near-real-time adjustments to aeration, feed rates or other operational parameters.

Main results and discussion

Online mass spectrometry enabled actionable real-time insight into the fermentation, with specific advantages observed:

• Respiratory patterns (RQ) allowed discrimination between aerobic and anaerobic metabolism and provided an indicator of substrate utilization and culture health.
• Monitoring ethanol levels signalled shifts to fermentative metabolism and helped guide process corrections to restore aerobic conditions when required.
• Comparative measurement of inlet and outlet gas streams produced an accurate, non-invasive assessment of oxygen uptake and carbon dioxide evolution, facilitating calculation of carbon balances and early detection of ‘‘missing’’ carbon associated with by-product formation.
• Real-time data supported operational interventions during the master fermentation, improving stability and maximizing farnesene yield.

The integration of online gas analysis reduced the risk of undetected process deviations and improved reproducibility between production batches.

Benefits and practical applications

Implementing online process mass spectrometry in farnesene/squalane bioproduction yields multiple practical benefits:

• Environmental and ethical: replaces shark-derived squalene, avoiding detrimental impacts on shark populations.
• Quality control: real-time detection of metabolic shifts and by-product formation supports consistent product quality.
• Process optimization: enables tighter control of aeration and feeding strategies to maximize yield and productivity.
• Scale-up support: provides quantitative process signatures (RQ, gas fluxes) useful for scaling from lab to commercial fermenters.

Industries that can apply these advantages include cosmetic ingredient manufacturing, sustainable chemistry, and larger-scale biomanufacturing where real-time process analytical technologies (PAT) are desired.

Future trends and potential applications

Key future directions and opportunities for this approach include:

• Deeper PAT integration: combining online mass spectrometry with additional sensors (e.g., Raman, NIR, dissolved oxygen probes) and advanced control algorithms for closed-loop process control.
• Advanced data analytics: use of multivariate and machine-learning models to translate gas signatures into predictive KPIs for yield, impurity profiles and early fault detection.
• Expanded analyte scope: coupling mass spectrometry with soft ionization or tandem MS to monitor a broader range of volatile and semi-volatile metabolites and impurities in real time.
• Lifecycle and sustainability assessment: quantifying environmental footprint improvements and aligning production metrics with corporate sustainability goals and regulatory expectations.
• Synthetic biology advancements: further strain engineering to improve carbon conversion efficiency and reduce unwanted by-products, simplifying monitoring and downstream processing.

Conclusion

Online process mass spectrometry is a valuable PAT tool for optimizing biotechnological production of farnesene-derived squalane. Continuous gas composition monitoring enables rapid detection of metabolic shifts, accurate carbon balancing, and improved control of fermentation processes—contributing to higher yields, consistent product quality and a sustainable alternative to shark-derived squalane. The approach supports industrial scalability and aligns with market and regulatory trends favoring environmentally responsible and cruelty-free ingredients.

Reference

Thermo Fisher Scientific. Case study: Thermo Fisher Scientific supports Amyris to optimize the bioproduction of sustainable squalane. Thermo Fisher Scientific, 2024.