Fungal Metabolic Engineering

Engineer fungal Cell Factories for Enhanced Production of Biofuels, Organic Acids, and Pharmaceuticals

We provide custom fungal metabolic engineering services to modify metabolic pathways in filamentous fungi and yeasts for optimized yields of target compounds.

Custom strain engineering in filamentous fungi and yeasts
Pathway design, gene editing (CRISPR-Cas9), and flux optimization
Fermentation process development and scale-up support

Request a Project Consultation

Comprehensive Fungal Metabolic Engineering Services

Leverage our proven platform for rational engineering of fungal metabolism — from host selection and genetic modification to production strain delivery with quality data.

End-to-end service: design, build, test, learn
Experienced with Aspergillus niger, Saccharomyces cerevisiae.
QC via HPLC, GC-MS, and targeted metabolite analysis

Custom Pathway Design

Gene Editing & Overexpression

Fermentation Optimization

Our Approach

We apply metabolic engineering principles to rewire fungal pathways for overproduction of high-value compounds. Our approach integrates established genetic tools and fermentation know-how to deliver engineered strains with defined product yield and titer targets.

Deliverables

What You Receive

Each project delivers a validated engineered strain, detailed process data, and a project report including methods, QC, and datasets to support your downstream development.

Strain & Data Deliverables

Engineered fungal strain(s) – validated genotype and phenotype
Fermentation process protocol and production data
QC analytical results (HPLC, GC-MS) for target product
Project report including strain design, methods, and conclusions

Optional Add‑Ons

Stability assessment over multiple passages
Scale‑up to pilot‑scale fermentation
Purification process development
Metabolic flux analysis results

Service Scope

Parameter	Typical project scope
Host Organism	Filamentous fungi (Aspergillus niger, A. nidulans) or yeasts (Saccharomyces cerevisiae, Pichia pastoris) – other strains upon request
Genetic Engineering Method	CRISPR-Cas9, homologous recombination, episomal expression – scoped per target
Pathway Engineering Complexity	Single gene to multi‑gene pathway assembly – defined in SOW
Analytical Methods	HPLC, GC-MS, LC-MS – defined in statement of work
Fermentation Scale	Shake flask studies to 5‑L bioreactor; larger scale evaluated per project
Product Purity Target	Defined in statement of work based on target compound
Product Yield/Titer Target	Defined in statement of work based on target compound and host biology

Workflow

How We Deliver Your Project

We follow a structured design‑build‑test‑learn workflow adapted to each fungal metabolic engineering goal.

1. Host Selection & Target Analysis

We evaluate your target compound and desired pathway, then select the most suitable fungal host (filamentous or yeast) and perform initial literature and genomic analysis to define engineering targets.

2. Pathway Design & Genetic Constructs

Our team designs gene expression cassettes, CRISPR guide RNAs, and homologous repair templates; constructs are assembled and verified by sequencing.

3. Strain Engineering & Transformation

We transform fungal protoplasts or spheroplasts with the designed constructs, apply selective markers, and confirm integration by PCR and sequencing.

4. Fermentation & Process Optimization

Engineered strains are cultured under controlled conditions; we test media, feeding strategies, and inducer regimes to evaluate yield in shake flasks or bioreactors.

5. Product Recovery & QC Documentation

Fermentation broth is harvested, and target product is quantified by HPLC or GC-MS. A final report includes strain documentation, process parameters, and analytical data.

Applications

Supported Product Classes

Our fungal metabolic engineering platform is suited for a broad range of industrially relevant compounds.

Citric, Succinic, Itaconic Acids

We engineer filamentous fungi for high‑titer organic acid production, leveraging native overproduction capacity and rational pathway optimization.

Aspergillus niger citric acid pathways
Fed‑batch fermentation for acid accumulation
Product isolation and purity analysis

Ethanol, Higher Alcohols, Biodiesel Precursors

Metabolic engineering of yeast for biofuel production from renewable feedstocks, including optimization of ethanol tolerance and yield.

S. cerevisiae ethanol pathway rewiring
Xylose utilization pathway integration
Fed‑batch fermentation to high cell density

Ergot Alkaloids, Statins, Terpenoids

Heterologous expression of complex biosynthetic pathways in fungal hosts for production of medicinal compounds.

Aspergillus nidulans platform for alkaloids
P450 and tailoring enzyme co‑expression
Scale‑up to bioreactor production

FAQ

Frequently Asked Questions

Common inquiries about our fungal metabolic engineering service.

We routinely engineer filamentous fungi such as Aspergillus niger and A. nidulans, as well as yeasts including Saccharomyces cerevisiae and Komagataella phaffii (Pichia pastoris). Other species can be accommodated after feasibility assessment.
We confirm all modifications by PCR, Sanger sequencing, and, when needed, whole‑genome sequencing. Integration copy number and stability are evaluated during the project.
Outcomes are highly project‑dependent—they depend on target biology, pathway complexity, and host genetics. We set realistic acceptance criteria with you in the statement of work and report results transparently.
Yes, we can develop processes up to pilot‑scale bioreactors as a scoped add‑on. Larger scales are evaluated on a case‑by‑case basis and may involve technology transfer to your facility.

Scientific Literature

References

Wang G, Kell DB, Borodina I. Harnessing the yeast Saccharomyces cerevisiae for the production of fungal secondary metabolites. Essays in biochemistry. 2021;65(2):277-291. View on PubMed
Behera BC. Citric acid from Aspergillus niger: a comprehensive overview. Critical reviews in microbiology. 2020;46(6):727-749. View on PubMed
Baptista SL, Costa CE, Cunha JT, et al. Metabolic engineering of Saccharomyces cerevisiae for the production of top value chemicals from biorefinery carbohydrates. Biotechnology advances. 2021;47:107697. View on PubMed
Eldarov MA, Mardanov AV. Metabolic Engineering of Wine Strains of Saccharomyces cerevisiae. Genes. 2020;11(9). View on PubMed

Ready to Start Your Project?

Get a customized quote for your Engineer fungal Cell Factories for Enhanced Production of Biofuels, Organic Acids, and Pharmaceuticals project. Our experts will respond within 24 hours.

No obligation

24h response

Expert consultation