Innovative Ingredients: Precision fermentation, proteins, feeds. Functional ingredients. High value sugars
As the global population grows and pressure on natural resources intensifies, new approaches to food production are vital.
The UQ Biosustainability Hub is advancing fermentation-based manufacturing to complement traditional farming and fisheries. Precision fermentation is a technology that uses microbes as production platforms to manufacture specific food ingredients such as proteins and functional compounds, in controlled systems, .
Using precision fermentation and microbial biotechnology, we can produce high-value ingredients including animal feed, dairy proteins and natural sweeteners, with great efficiency. These technologies reduce reliance on land and water while significantly lowering the environmental footprint of producing food and ingredients.
Biohub Innovative Ingredients Projects
Strategic capabilities, innovative ingredients
Chief Investigator(s): Esteban Marcellin, Birgitta Ebert, Yosephine Gumulya, Huadong Peng
Background and Need
Precision fermentation infrastructure remains limited in Australia, with most facilities operating at small scale and lacking integration across strain engineering, bioprocessing and analytical capabilities. This gap restricts the ability of industry to develop and scale new fermentation-derived products domestically. There is therefore a need to establish a nationally coordinated precision fermentation capability that integrates infrastructure, expertise and industry engagement to support development of new sustainable food, feed and industrial bioproducts.
Project Aim
The project aims to establish UQ as the national home of precision fermentation by integrating infrastructure, technical capability, and industry engagement to support scalable biomanufacturing development.
Approach and Key Activities
The project focuses on developing integrated precision fermentation capability across strain engineering, fermentation scale-up and downstream analysis. Instrumented bioreactor platforms are deployed to support development from laboratory to pilot scale. Analytical capabilities including metabolomics and proteomics are applied to characterise strain performance and optimise processes. Industry collaboration programs are established to support translation of new fermentation technologies, while training activities are implemented to develop workforce capability and establish nationally coordinated precision fermentation expertise.
Expected Outcomes
The project will deliver an integrated precision fermentation platform operating at multiple scales, validated workflows supporting strain-to-process development, and established industry partnerships supporting technology translation. Additional outputs include trained personnel, operational demonstration projects and datasets supporting development of commercially relevant fermentation processes.
Impact and Significance
This project establishes national capability for precision fermentation, supporting development of sustainable protein, ingredient and biomaterial industries in Australia.
The outcomes benefit industry partners by enabling domestic technology development, reduce reliance on overseas infrastructure and position Australia as a leader in precision fermentation innovation and industrial biomanufacturing.
- Adaptive laboratory evolution
- Bioprocess optimisation
- Bioreactor engineering
- Computational biology & AI
- Gas fermentation
- Metabolic modelling
- Multi-omics analysis
- Precision fermentation
- Process scale-up & pilot plant
- Synthetic biology & strain engineering
Demonstrating “the Hyper-Fermentation Advantage” for the production of target molecules using robust microbial cell factories
Chief Investigator(s): Axayacatl Gonzalez, Esteban Marcellin, Huadong Peng
Background and Need
Modern biomanufacturing relies heavily on fed-batch fermentation, which is limited by stop-start operation, downtime and high energy and resource consumption. These constraints reduce productivity and increase costs, limiting scalability and sustainability. Hyper-fermentation offers a continuous, high-efficiency alternative, but its adoption is constrained by limited mechanistic understanding and lack of validated industrial data. Addressing this gap is critical to enable scalable, low-cost and sustainable biomanufacturing in Australia.
Project Aim
To generate mechanistic and quantitative evidence validating hyper-fermentation as a superior continuous biomanufacturing platform, enabling scalable, efficient and reproducible production of proteins and high-value biomolecules.
Approach and Key Activities
The project will combine strain engineering, comparative fermentation studies and multi-omics analysis to benchmark hyper-fermentation against conventional fed-batch processes. A reference yeast strain will be engineered to produce a comparable protein, enabling direct performance comparison with Cauldron’s proprietary system. Key activities include bioprocess characterisation, population dynamics analysis and identification of metabolic bottlenecks. Process optimisation will be conducted through controlled variation of operating parameters, followed by long-term continuous fermentation trials to assess stability, scalability and productivity across different strains and conditions.
Expected Outcomes
The project will deliver a validated dataset demonstrating the performance advantages of hyper-fermentation, an engineered reference strain for benchmarking and optimised process conditions for continuous production. Additional outputs include mechanistic insights into productivity and stability, identification of process bottlenecks and reproducible protocols supporting industrial-scale implementation and commercialisation of continuous fermentation technologies.
Impact and Significance
This project will accelerate adoption of continuous biomanufacturing in Australia, reducing production costs, energy use and waste while increasing productivity. It benefits industry by de-risking scale-up and enabling commercial deployment of hyper-fermentation. Broader impacts include strengthening sovereign biomanufacturing capability, attracting investment and positioning Australia as a global leader in sustainable, high-efficiency precision fermentation technologies.
Metagen – lipopeptide bioprocess optimisation
Chief Investigator(s): Laurin Walther, Axayacatl Gonzalez, Tim McCubbin
Background and Need
Lipopeptides such as surfactin, iturin and fengycin offer strong antimicrobial and biocontrol properties, yet their large-scale adoption is limited by low yields, high production costs and inconsistent product quality. Current fermentation processes lack integration between systems biology, analytics and process engineering, restricting optimisation and scalability. There is a clear need for robust, reproducible and cost-efficient precision fermentation platforms to enable sustainable production and reduce reliance on synthetic agrochemicals.
Project Aim
To develop an integrated precision fermentation platform for scalable, cost-effective, and reproducible production of lipopeptides using Bacillus spp., supported by systems biology, advanced analytics and process optimisation.
Approach and Key Activities
The project will combine systems biology, analytical development, and bioprocess engineering to optimise lipopeptide production. Multi-omics characterisation (metabolomics, proteomics, genomics) will identify metabolic drivers of productivity. LC-MS/MS workflows will be developed for accurate quantification and profiling of lipopeptides. A geometry-informed lab-scale fermentation platform will enable controlled comparison of batch, fed-batch and continuous processes, alongside media optimisation. These insights will inform scale-up strategies, including bioreactor design and control parameters, culminating in validated protocols and tech-transfer packages for industrial deployment.
Expected Outcomes
The project will deliver a validated precision fermentation process for lipopeptide production, robust analytical pipelines for product quantification and a reproducible scale-down model for optimisation. Additional outputs include optimised media and operating conditions, engineering guidelines for scale-up, and tech-transfer packages supporting rapid industrial adoption and commercialisation of lipopeptide-based bioproducts.
Impact and Significance
This project will enable sustainable, large-scale production of lipopeptides, supporting Australian agriculture to reduce reliance on synthetic chemicals while improving crop protection and biosecurity.
It strengthens national capability in precision fermentation and biomanufacturing, drives innovation through NCRIS infrastructure, and positions Australia as a leader in high-value, bio-based products addressing global challenges such as antimicrobial resistance and food security.
- Bioprocess optimisation
- Bioreactor engineering
- Metabolic modelling
- Multi-omics analysis
- Precision fermentation
Production of rare sugars by engineering Bacillus subtilis
Chief Investigator(s): Axayacatl Gonzalez, Esteban Marcellin, Tim McCubbin
Background and Need
Australia’s sugar industry is heavily reliant on raw sugar exports, limiting value capture and long-term competitiveness. At the same time, increasing health concerns around sugar consumption are driving demand for low-calorie alternatives. Current rare sugar production methods are inefficient, costly, and environmentally intensive. There is a clear need for sustainable, scalable technologies that enable domestic production of high-value sugar alternatives while supporting industry diversification and reducing environmental impact.
Project Aim
To develop a robust microbial cell factory using precision fermentation to efficiently convert fructose into rare sugars, enabling scalable, cost-effective and sustainable production for the Australian sugar industry.
Approach and Key Activities
The project will apply systems and synthetic biology to engineer microbial strains capable of efficiently converting fructose into rare sugars. Key activities include metabolic pathway optimisation, strain engineering, and fermentation process development using industrial feedstocks from MSF Sugars.Process conditions will be optimised to maximise yield and productivity, while eliminating the need for complex substrates. Downstream processing strategies will also be developed to ensure product purity and scalability, supporting translation from laboratory to pilot and industrial scale.
Expected Outcomes
The project will deliver a validated microbial cell factory for rare sugar production, an optimised fermentation process using industrial feedstocks, and a scalable production framework.
Additional outputs include techno-economic assessments, proof-of-concept demonstration at pilot scale, and intellectual property supporting commercialisation of sustainable rare sugar manufacturing in Australia.
Impact and Significance
This project will benefit the Australian sugar industry by enabling diversification into high-value, health-oriented products, increasing revenue and global competitiveness. It supports national priorities in sustainable food manufacturing and innovation, while reducing environmental impact. Broader benefits include job creation, investment attraction, and strengthening collaboration between industry and research institutions, positioning Australia as a leader in precision fermentation.
Project Luna – Eclipse Ingredients
Chief Investigator(s): Axayacatl Gonzalez, James Behrendorff (QUT), Nidhi Bansal (AGFS), Jolieke van der Pols (QUT)
Background and Need
Efficient screening and benchmarking of microbial strains under controlled fermentation conditions is critical for advancing industrial bioprocess development. However, variability in experimental setups and limited access to parallel, instrumented systems often constrain robust comparison of strain performance. There is a need for standardised, high-throughput fermentation platforms that generate reproducible datasets to support strain selection, process optimisation and downstream scale-up in industrial biotechnology applications.
Project Aim
To systematically evaluate the fermentation performance of 48 yeast strains under controlled bioreactor conditions to generate reproducible data supporting strain selection and process optimisation.
Approach and Key Activities
The project will conduct controlled fermentations of 48 yeast strains using instrumented bioreactor systems following protocols defined by Eclipse Ingredients. Experiments will be performed in batch or fed-batch modes over up to 144 hours. Regular sampling will monitor biomass growth, substrate consumption, and protein production using analytical tools such as LabChip XL. Experimental design, including replication and media composition, will be guided by industry input. Data generated will be benchmarked against existing datasets to enable comparative analysis and support optimisation of fermentation performance across strains.
Expected Outcomes
The project will deliver a comprehensive dataset on yeast strain performance, including growth kinetics, metabolite profiles and protein titres. Outputs include comparative benchmarking of strains, validated fermentation protocols and data packages supporting strain selection and process optimisation. These results will inform further development, scale-up strategies and potential industrial deployment.
Impact and Significance
This project strengthens Australia’s biomanufacturing capability by enabling data-driven strain selection and optimisation. It supports industry partners by reducing development risk and accelerating process scale-up. Broader impacts include fostering collaboration between academia and industry, improving experimental reproducibility and contributing to efficient development of fermentation-based products across food, biotechnology and ingredient manufacturing sectors.
- Bioprocess optimisation
- Bioreactor engineering
- Precision fermentation
Biosensor assisted synthetic co-culture setup
Chief Investigator(s): Huadong Peng, Esteban Marcellin
Background and Need
High-value aromatics used in food, pharmaceutical and chemical industries are still produced mainly through petroleum-based synthesis or plant extraction. This is often unsustainable, low-yielding, difficult to standardise and vulnerable to supply limitations. Microbial production offers a renewable alternative, but progress is hindered by long biosynthetic pathways, metabolic burden and slow design-build-test-learn cycles.New engineering strategies are needed to enable efficient, scalable and robust fermentation-based production of these important molecules.
Project Aim
This project aims to develop biosensor-guided modular yeast co-cultures for more efficient, stable and scalable production of high-value aromatic compounds, including melatonin and the alkaloid alstonine.
Approach and Key Activities
The project will combine synthetic biology, metabolic engineering and modelling to divide complex aromatic pathways between “sender” and “receiver” yeast strains. GPCR-based biosensors will be introduced to detect pathway intermediates and products, support screening and enable dynamic regulation within co-cultures. Modular strain construction will focus on melatonin and alstonine pathways, alongside development of an alkaloid biosensor. Design-of-experiments, precursor feeding studies, fluorescence-based screening and predictive co-culture modelling will be used to identify bottlenecks, optimise population balance and improve production performance before scale-up.
Expected Outcomes
Expected outcomes include engineered yeast sender and receiver strains, validated GPCR biosensors for pathway monitoring and screening, optimised co-culture conditions for melatonin and alstonine production and a predictive model linking biosensor outputs with co-culture performance. The project is also expected to generate new knowledge, at least one high-impact publication and potential intellectual property for future translation.
Impact and Significance
This project will benefit industrial biotechnology by providing new tools for sustainable microbial production of valuable aromatics currently sourced from fossil chemistry or plants. It will support greener manufacturing, more reliable supply chains and faster development of microbial cell factories. Researchers, industry partners and society will benefit from improved access to scalable, renewable production technologies for medically and commercially important aromatic molecules.
- Precision fermentation
- Synthetic biology & strain engineering
Designing a programmable food ingredient library via precision fermentation in Yarrowia lipolytica
Chief Investigator(s): Huadong Peng, Esteban Marcellin
Background and Need
Raspberry ketone (RK) is a high-value aroma compound used in food, fragrance and nutraceutical industries, yet its natural supply relies on costly plant extraction. Microbial production via precision fermentation offers a sustainable alternative, but most efforts target single compounds in isolated strains. Scaling to deliver multiple bioactive ingredients simultaneously while maintaining stable strain ratios and consistent product profiles remains an unresolved challenge for the food manufacturing sector.
Project Aim
To build on engineered Yarrowia lipolytica strains producing aroma compound and other bioactive compounds, developing a co-culture fermentation system integrated with 3D food printing to create a functionally enhanced food prototype.
Approach and Key Activities
Engineer stains for Raspberry Ketone producing in Y. lipolytica strains alongside strains engineered for betanin and ergothioneine, a co-culture system will be developed. Inoculation timing and strain ratios will be optimised to minimise population drift and ensure reproducible multi-compound output. The fermentation broth will then be formulated into a 3D-printable food matrix, with printing parameters tuned to preserve bioactive compound stability and achieve acceptable texture and structure.
Expected Outcomes
A stable co-culture fermentation system producing at least three bioactive food ingredients simultaneously; validated ratio-control strategies ensuring reproducible output; and a 3D-printed food prototype incorporating the fermentation-derived compounds, demonstrating a pipeline from engineered microorganism to functional food prototype.
Impact and Significance
This work establishes a modular platform linking precision fermentation with additive food manufacturing. It benefits food producers seeking scalable, natural-ingredient supply chains and provides a generalisable framework for multi-strain co-culture design. The approach reduces reliance on synthetic additives and plant-extracted compounds, supporting more sustainable and flexible food production.
- Precision fermentation
- Synthetic biology & strain engineering
Engineering acetate tolerance, assimilation and lipid biosynthesis pathway in Yarrowia lipolytica
Chief Investigator(s): Huadong Peng
Background and Need
Natural lipid sources are limited and costly, partly due to competing demand in food processing and oleochemical industries (Pereira et al., 2021). Microbial lipids offer substantial potential to meet this growing demand (Jin et al., 2015), including structured lipids like 1,3-dioleoyl-2-palmitoyl-glycerol (OPO) for human milk fat substitutes (Bhutada et al., 2022). However, efficiency and cost-effectiveness remain tightly coupled to microbial chassis and feedstock choice. Acetate is a low-cost substrate, but its cytotoxicity and low uptake efficiency limit lipid yields and industrial feasibility (Gao et al., 2017; Dulermo & Nicaud, 2011).
Project Aim
The aim of this project is the metabolic engineering of lipid biosynthesis and acetate assimilation in Yarrowia lipolytica, with the goal of enhancing lipid accumulation, including both bulk and OPO and acetate utilization.
Approach and Key Activities
A push-pull metabolic engineering strategy will be used to redirect carbon flux toward fatty acid and TAG biosynthesis. Selected genes involved in precursor supply, chain elongation and lipid storage will be overexpressed, and competing pathways will be reduced (gene knockout) to maximize carbon allocation to lipids (Qiao et al., 2017). Genetic modifications will be introduced using the EasyCloneYALI and EXPRESSYALI systems (Holkenbrink et al., 2018). Following this, adaptive laboratory evolution will be performed to evolve acetate-tolerant strains. The strains will then be screened for key performance indicators including growth, lipid content, and acetate consumption.
Expected Outcomes
This strategy is expected to deliver engineered Y. lipolytica strains that can grow well on acetate and accumulate high levels of bulk TAGs and OPO with palmitic acid stereospecifically positioned at the sn-2 position (Bhutada et al., 2022), supported by defined process conditions and reproducible analytics, thereby addressing acetate cytotoxicity and limited productivity of current strains.
Impact and Significance
This work establishes a microbial chassis that can convert low-cost, non-food substrates into lipid products. Microbial oil production offers numerous advantages over traditional plant-based sources, including adaptability to diverse feedstocks, reduced land requirements, rapid process turnover and greater scalability (Blazeck et al., 2014). The engineered strains have potential applications in biofuel production, oleochemicals and human milk fat substitutes for infant nutrition.
- Precision fermentation
- Synthetic biology & strain engineering
Engineering Yarrowia lipolytica to produce tryptophan derived therapeutics
Chief Investigator(s): Huadong Peng
Background and Need
Psychedelics have garnered sustained attention within mental health research and treatment. Psilocybin is one of the promising candidates among them and has been granted Breakthrough Therapy status by the U.S. FDA. To meet its increasing demand in both current clinical studies and future large-scale manufacturing, achieving high-titre yields and high-purity levels of psilocybin is essential; thus, developing a cost-effective, sustainable production strategy is an urgent necessity.
Project Aim
This project aims to facilitate the de novo biosynthesis of psilocybin and its derivatives in microbial cell factories by implementing diverse synthetic biology strategies.
Approach and Key Activities
This project includes three key activities: (1) performing modular metabolic engineering to establish Yarrowia lipolytica as a microbial biomanufacturing platform for the de novo production of psilocybin, enabling a cost-effective and sustainable microbial production of psilocybin.
(2) developing a biosensor-assisted workflow to facilitate the rapid, high-throughput screening of superior production strains, accelerating the iterative design-build-test-learn (DBTL) cycle.
(3) applying enzyme and metabolic engineering strategies to enable psilocybin derivatisation, further exploring the therapeutic potential of psilocybin and its derivatives.
Expected Outcomes
Achievement of high-titre psilocybin production in Y. lipolytica by integrating a heterologous biosynthetic pathway and subsequent metabolic fine-tuning. Construction of a yeast biosensor responsive to psilocybin and establishment of a biosensing workflow for the relative quantification of psilocybin from microbial production. Employment of advanced enzyme engineering to facilitate the precise in vivo production of diverse psilocybin.
Impact and Significance
This project seeks to establish a sustainable Y. lipolytica-based biomanufacturing platform for the production of psilocybin and its derivatives, as well as an optimised compound identification workflow to accelerate the DBTL cycle during the strain engineering. This microbial production strategy overcomes the limitations of traditional extraction and chemical synthesis of psilocybin and facilitates clinical research into these high-value therapeutic compounds.
- Bioprocess optimisation
- Precision fermentation
- Synthetic biology & strain engineering
Engineering Yarrowia lipolytica to produce tryptophan derived pigments
Chief Investigator(s): Huadong Peng
Background and Need
Indigoid compounds such as indigo and indirubin are widely used as dyes and exhibit promising biological activities. However, current chemical synthesis is energy-intensive and generates hazardous waste, raising environmental concerns. While microbial platforms offer a sustainable alternative, they are currently limited by low titers and a lack of precise control over pathway branching. Therefore, there is a pressing need for sustainable, biologically based platforms that enable scalable and tunable production of structurally diverse indigoid compounds with enhanced industrial and functional potential.
Project Aim
To engineer a tunable Yarrowia lipolytica platform for indigo biosynthesis system to enhance production titres and enable controlled pathway branching and functionalisation towards indirubin and halogenated derivatives.
Approach and Key Activities
This project will optimise indigo biosynthesis by engineering promoter systems to enhance expression of key pathway enzymes and improve metabolic flux. It will then investigate how metabolite supplementation influences gene expression and pathway performance using transcriptomic analysis. These strategies will be integrated to establish a controllable system linking transcriptional regulation, metabolic context and biosynthetic output.
Expected Outcomes
The project will deliver an optimised yeast-based indigo production system with improved titres and stability. It will provide mechanistic insights into how gene expression, metabolite availability, and gene interactions influence pathway flux and product distribution. Additionally, it will enable controlled production of higher-value derivatives, including indirubin and halogenated indigo compounds.
Impact and Significance
This research provides a sustainable and efficient biosynthetic route for the production of indigo, reducing the environmental burden associated with conventional chemical synthesis. It benefits the pharmaceutical and biomanufacturing industries by enabling scalable and controllable production of high-value indigoid compounds. Additionally, it offers a generalisable framework for the biosynthesis and selective regulation of structurally related natural products.
- Precision fermentation
- Synthetic biology & strain engineering
Engineering acetate tolerance, assimilation and lipid biosynthesis pathway in Yarrowia lipolytica
Chief Investigator(s): Huadong Peng, Axayacatl Gonzalez, Tim McCubbin
Background and Need
Sustainable lipid production is constrained by reliance on sugar-based feedstocks and limited process efficiency, increasing costs and competition with food resources. Acetate represents a low-cost, abundant carbon source, but its toxicity and poor cellular uptake restrict industrial use. Additionally, current microbial lipid production lacks the flexibility to generate high-value tailored lipids. There is a need for robust microbial platforms capable of efficiently converting acetate into valuable lipid products at scale.
Project Aim
To engineer a robust microbial platform capable of efficiently converting acetate into high-value lipids through integrated strain engineering, adaptive evolution and bioprocess optimisation.
Approach and Key Activities
The project will combine adaptive laboratory evolution (ALE), metabolic engineering and bioprocess optimisation to enhance acetate utilisation and lipid production. ALE in controlled turbidostats will improve acetate tolerance and uptake. Targeted genetic modifications will increase acetyl-CoA flux, lipid biosynthesis, and reducing power while minimising competing pathways.The platform will be further engineered to produce high-value lipids such as OPO and omega-3 fatty acids. Iterative design-build-test-learn cycles will optimise fermentation parameters, including C/N ratio, feeding strategies and aeration, ensuring robust and scalable production performance.
Expected Outcomes
The project will deliver acetate-tolerant microbial strains with enhanced lipid productivity, validated metabolic engineering strategies and optimised fermentation processes. Outputs include strains capable of producing both bulk and high-value lipids, improved process conditions for stable operation and a scalable framework for converting low-cost substrates into commercially relevant lipid products.
Impact and Significance
This project enables sustainable, cost-effective lipid production by valorising low-cost acetate, reducing dependence on agricultural feedstocks. It benefits industries in nutrition, food, and biotechnology by enabling production of high-value lipids such as human milk fat substitutes and omega-3 oils. Broader impacts include advancing Australia’s precision fermentation capabilities, supporting circular bioeconomy strategies and strengthening competitiveness in global bio-based manufacturing.
Profitable upcycling of genetically modified biomass from precision fermentation
Chief Investigator(s): Esteban Marcellin, Neha Lal, Damian Hine
Background and Need
The rapid expansion of precision fermentation in food, medical and manufacturing sectors is expected to generate increasing volumes of genetically modified spent microbial biomass (GMSMB). Current industrial practice relies on sterilisation and landfill disposal, creating significant operational costs and long-term sustainability concerns. Although spent biomass contains valuable macronutrients, most existing research focuses on non-genetically modified materials, leaving a gap in viable upcycling pathways suitable for genetically modified biomass under Australian regulatory and industrial conditions.
Project Aim
The project aims to identify and validate economically viable and regulatory-compliant strategies for upcycling genetically modified spent microbial biomass into value-added products suitable for Australian industry.
Approach and Key Activities
The project evaluates multiple GMSMB upcycling strategies, including conversion into biofertiliser, animal feed, biogas and component-derived value-added products. A techno-economic analysis is conducted to compare the financial feasibility of each option against current sterilisation and landfill disposal costs. The most promising pathway is then assessed through life cycle analysis to evaluate environmental sustainability. Experimental validation studies are performed to assess product effectiveness and safety. Engagement with industry stakeholders supports evaluation of regulatory alignment and facilitates translation of validated solutions into practical industrial applications.
Expected Outcomes
The project will deliver a validated and economically assessed pathway for upcycling genetically modified spent microbial biomass. Additional outputs include techno-economic and life cycle datasets, experimentally validated processing strategies and industry-informed implementation frameworks supporting adoption within the Australian biotechnology sector.
Impact and Significance
This project supports development of a circular bioeconomy within the precision fermentation sector by transforming waste biomass into valuable resources. The outcomes reduce disposal costs, improve sustainability performance and provide industry with practical strategies to manage increasing volumes of genetically modified biomass while maintaining regulatory compliance and economic viability.
- Bioprocess optimisation
- Bioreactor engineering
- Metabolic modelling
- Multi-omics analysis
- Precision fermentation
Precision fermentation for scalable production of bovine lactoferrin
Chief Investigator(s): Yosephine Gumulya, Huadong Peng
Background and Need
Current bovine lactoferrin supply relies largely on extraction from dairy streams, which limits yield, consistency and scalability. Existing production routes also offer limited control over glycosylation and process performance, making it difficult to meet growing market demand. A precision fermentation platform is needed to deliver reliable, scalable and commercially viable lactoferrin production for food and nutrition industries, while reducing dependence on resource-intensive animal-based supply chains.
Project Aim
To develop a scalable precision fermentation platform for bovine lactoferrin by engineering yeast strains with improved expression, glycosylation, stability and productivity under lab-scale bioreactor conditions.
Approach and Key Activities
The project will first establish proof-of-concept bovine lactoferrin production in yeast through host evaluation, vector construction, transformation, and confirmation of expression, secretion and glycosylation. It will then build a high-throughput automated strain engineering platform to generate multiplex libraries and identify metabolic bottlenecks. Engineered strains will be optimised to reduce by-products and improve yield, supported by machine learning-based selection of top performers. Finally, leading strains will be validated for expression conditions, genetic stability and productivity in flask and 1.2 L bioreactor systems, with benchmarking under scaled bioreactor conditions.
Expected Outcomes
Expected outputs include a validated yeast host for bovine lactoferrin production, engineered vector and strain libraries, an automated high-throughput engineering platform, identified metabolic bottlenecks, improved strains with reduced by-products, optimised induction and culture conditions, confirmed strain stability over extended passaging and benchmarked lab-scale bioreactor performance with target lactoferrin yields and consistent glycosylation profiles.
Impact and Significance
This project will benefit dairy, food and nutrition industries by enabling a more sustainable and scalable route to bovine lactoferrin production. It will support commercial translation of precision fermentation, strengthen sovereign biomanufacturing capability and reduce reliance on conventional dairy extraction.
The resulting platform could improve ingredient security, process consistency and long-term environmental sustainability.
- Bioprocess optimisation
- Multi-omics analysis
- Precision fermentation
- Synthetic biology & strain engineering
Engineering robust microbial hosts for precision fermentation
Chief Investigator(s): Yosephine Gumulya, Mark Turner, Esteban Marcellin
Background and Need
Precision fermentation offers a promising solution to rising global food demand, yet most microbial hosts are not optimised for industrial-scale production. They lack the ability to maintain performance under multiple fluctuating stresses encountered during scale-up. Existing engineering approaches are low-throughput and strain-specific, limiting scalability. Industry requires versatile, high-performing microbial cell factories to enable efficient, sustainable and economically viable food production.
Project Aim
The project aims to develop a high-throughput, modular platform for reprogramming microbial gene regulatory networks to generate robust, high-performing cell factories for precision fermentation.
Approach and Key Activities
This project integrates protein engineering, synthetic biology and machine learning to engineer microbial robustness. Ancestral transcription factors will be reconstructed and diversified through mutagenesis to create libraries capable of globally rewiring gene regulatory networks. These libraries will be introduced into multiple microbial hosts and subjected to selection under industrially relevant stresses. Comparative transcriptomics and machine learning will identify key regulatory mechanisms driving adaptation. Iterative cycles of engineering and selection will generate strains with enhanced resilience, productivity and suitability for large-scale precision fermentation.
Expected Outcomes
The project will deliver a modular platform for gene regulatory network engineering, a library of broadly acting transcription factors and a collection of robust microbial strains with improved fermentative traits. It will also generate detailed maps of stress-responsive regulatory networks and identify key genes enabling adaptation to industrial conditions, supporting future strain engineering.
Impact and Significance
This project will accelerate the development of industry-ready microbial hosts, enabling scalable and cost-effective precision fermentation. It will support sustainable food production, reduce reliance on traditional agriculture, and strengthen Australia’s leadership in biotechnology.
- Precision fermentation
- Synthetic biology & strain engineering