Trusted by Leading Research & Pharma Institutions

Metabolic Engineering & Pathway Design

Transform microorganisms into efficient cell factories through systematic pathway engineering, CRISPR-based genome editing, and data-driven metabolic optimization. Our DBTL-driven workflow accelerates strain development.

95% Efficiency

10+ Microbial Hosts

DBTL Workflow

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Trusted by leading research and pharmaceutical institutions

Harvard

Pfizer

MIT

Roche

Why Choose Our Service

95% editing efficiency

10+ microbial host options

DBTL-driven optimization

GMP-quality standards

CRISPR Precision

High-efficiency knockout and knock-in

Pathway Assembly

Up to 15 kb seamless integration

Multi-Host Platform

E. coli, yeast, Bacillus, and more

Max Gene Size

15 kb

Service Overview

Why Choose Our Metabolic Engineering Service

We combine cutting-edge synthetic biology tools with proven fermentation expertise to deliver engineered microbial strains optimized for your specific production targets.

CRISPR-Based Precision

Advanced CRISPR-Cas9 and CRISPRi systems enable precise genome edits with up to 95% editing efficiency across multiple microbial hosts.

High-efficiency knockout and knock-in
Reversible gene modulation with CRISPRi
Base editing for single-nucleotide changes

DBTL-Driven Optimization

Design-Build-Test-Learn cycle accelerates strain development through iterative optimization and high-throughput screening.

Computational pathway design
High-throughput screening
Machine learning integration

Multi-Host Platform

From E. coli to yeast and Bacillus, we engineer the optimal chassis for your target product spectrum.

E. coli, S. cerevisiae, P. pastoris
B. subtilis, Streptomyces
Custom industrial chassis

Precision Engineering

Scarless genome edits with up to 3 simultaneous targets.

Modular Assembly

Seamless Golden Gate and Gibson assembly up to 15 kb.

High-Throughput Screening

Screen up to 10^8 variants per round.

Quality Guaranteed

NGS verification and comprehensive documentation.

Technology Platform

Our Advanced Engineering Technologies

Our integrated platform combines multiple state-of-the-art tools for comprehensive strain engineering.

Genome Editing Tools

Precision Engineering

Our comprehensive CRISPR toolbox enables precise genome modifications across multiple species with high efficiency.

CRISPR-Cas9: High-efficiency knockout and knock-in
CRISPRi/a: Reversible gene expression modulation
Base Editing: Precise single-nucleotide modifications
MAGE: Multiplexed automated genome engineering

Computational Design

Data-Driven Optimization

Advanced computational tools accelerate pathway design and predict optimal engineering targets.

Genome-Scale Modeling: Constraint-based metabolic models
Flux Balance Analysis: Optimal knockout/overexpression targets
Codon Optimization: AI-driven sequence optimization
Growth-Coupled Design: Automatic high-producer selection

Advanced Capabilities

Enzyme Engineering

Directed evolution and rational design for enhanced enzyme activity, stability, and specificity.

Dynamic Regulation

Sensor-regulator systems for autonomous pathway control and metabolic burden minimization.

Compartmentalization

Organelle targeting to isolate heterologous pathways and reduce metabolic interference.

Adaptive Evolution

Long-term laboratory evolution under selective pressure for improved robustness.

Service Specifications

Flexible strain engineering packages to match your project requirements.

Service Type	Gene Size	Host Options
Pathway Construction	Up to 15 kb	E. coli, Yeast, B. subtilis
CRISPR Gene Knockout	Single gene	Multiple hosts
Multi-Gene Integration	Up to 5 genes	E. coli, Yeast
Metabolic Flux Optimization	Full pathway	Custom chassis
Combinatorial Library	Up to 10 variants	Per specification

* Specifications are for reference only. Actual performance may vary depending on project complexity and host organism. Contact our team for customized project design.

Our DBTL-Driven Workflow

A systematic approach from consultation to strain delivery.

Design

Computational pathway analysis and target identification

Build

Gene synthesis, CRISPR editing, and clone verification

Test

High-throughput screening and performance evaluation

Learn

Data analysis, model refinement, and optimization

Delivery Package Includes

Sequence-verified strains

COA documentation

Clone maps

Experimental protocols

Screening data

Technical support

Industry Applications

Engineered microbial strains powering innovation across sectors.

Biofuels Production

Engineer microbial cell factories for sustainable biofuel production from renewable feedstocks.

Ethanol and advanced alcohol biofuels
Fatty acid methyl esters (biodiesel)
Hydrocarbon drop-in fuels
Phototrophic algae systems

Pharmaceutical Intermediates

Produce complex pharmaceutical compounds through heterologous pathway expression.

Artemisinin precursors
Antibiotic biosynthesis
Vaccine antigen production
Protein therapeutics

Fine & Specialty Chemicals

Develop microbial platforms for cost-effective production of industrially relevant chemicals.

Amino acids and organic acids
Terpenes and aromatics
Polymers and bioplastics
Flavors and fragrances

Food & Nutritional Ingredients

Create GRAS-status microbial strains for food-grade compound production.

Natural flavors and fragrances
Colorants and pigments
Nutraceuticals
Enzyme preparations

What Our Clients Say

"The CRISPR-based knockout service delivered strains with exceptional editing efficiency. Our pathway optimization project was completed successfully."

Senior Scientist

Biotechnology Company

"Their metabolic modeling expertise helped us identify non-obvious targets for flux optimization. The engineered yeast strain achieved higher titer than our in-house development."

Research Director

Pharmaceutical Company

"Excellent technical support throughout the project. The DBTL workflow kept us informed at every stage, and the final strains exceeded performance expectations."

Principal Investigator

Academic Research Institution

Scientific Literature

Supporting Publications

Our platform is validated by peer-reviewed research published in leading scientific journals.

Citations

Balancing Cell Growth and Product Synthesis for Efficient Microbial Cell Factories

Linxia Liu, Dawei Zhang, Seung-Eun Lee, et al. Advanced Science, 2025

This review focuses on strategies to balance cell growth and product synthesis in microbial cell factories, systematically summarizing cutting-edge approaches including pathway engineering, dynamic regulation, and orthogonal systems design.

View DOI

312

Citations

Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0

Iván Domenzain, Benjamín Sánchez, Mihail Anton, et al. Nature Communications, 2022

GECKO 2.0 toolbox allows integration of enzyme constraints and proteomics data into genome-scale metabolic models for more accurate phenotypic predictions.

View DOI

156

Citations

Growth-coupled selection of synthetic modules to accelerate cell factory development

E. Orsi, Nico J. Claassens, Steffen N. Lindner, et al. Nature Communications, 2021

Growth-coupled selection strategy accelerates cell factory development by linking product synthesis to cell growth for automatic high-producer selection.

View DOI

Citations

MULTI-SCULPT: Multiplex Integration via Selective, CRISPR-Mediated, Ultralong Pathway Transformation in Yeast

Franklin Leyang Gong, Jianing Han, Sijin Li ACS Synthetic Biology, 2022

CRISPR/Cas9-based method for multiplexed multi-gene integration in yeast, achieving 90-100% success rate for 12-gene plant isoflavonoid pathway integration.

View DOI

134

Citations

Engineering of Multiple Modules to Improve Amorphadiene Production in Bacillus subtilis Using CRISPR-Cas9

Yafeng Song, Siqi He, Ingy I. Abdallah, et al. J. Agric. Food Chem., 2021

CRISPR-Cas9 system engineering multiple modules to improve artemisinin precursor amorphadiene production, increasing yield from 81 to 116 mg/L.

View DOI

Frequently Asked Questions

Find answers to common questions about our metabolic engineering services.

What microbial hosts do you support for pathway engineering?

We support a wide range of microbial hosts including E. coli, Saccharomyces cerevisiae, Pichia pastoris, Bacillus subtilis, Streptomyces, and other industrially relevant organisms. Our team will help select the optimal chassis based on your target product and application requirements.

What quality control is performed on engineered strains?

All strains undergo rigorous QC including NGS verification of sequence integrity, phenotype validation, and stability testing. We provide Certificate of Analysis (COA) with complete documentation.

Can you handle confidential sequence information?

Yes, we maintain strict confidentiality protocols. All project information is protected under NDA, and our facilities follow ISO 9001 quality standards. Sequence data is handled with encrypted transfers and secure storage.

Do you offer scale-up services after strain development?

Yes, we offer comprehensive scale-up support including fermentation process development, medium optimization, and tech transfer to your manufacturing facility.

What is growth-coupled selection and why is it useful?

Growth-coupled selection links product synthesis to cell growth, enabling automatic enrichment of high-producing strains without requiring direct metabolite measurement. This accelerates screening by orders of magnitude.

What are the advantages of CRISPR over traditional gene editing?

CRISPR-Cas9 offers higher editing efficiency in a single step, easier design by changing guide RNA sequence, multiplexed editing capability, and reversible regulation with CRISPRi without permanent genomic changes.

How does genome-scale metabolic modeling help in pathway design?

Genome-scale metabolic models provide comprehensive mathematical representation of metabolic reactions. Using constraint-based methods like Flux Balance Analysis, we predict how genetic modifications affect metabolic fluxes and identify optimal gene targets.

What is the difference between rational design and directed evolution?

Rational design uses computational tools to predict beneficial mutations based on structure. Directed evolution creates random mutant libraries and screens for improvements. Modern approaches combine both methods.

How do you handle metabolic burden in engineered strains?

We use dynamic regulation systems, optimize gene copy number, implement growth-coupled selection, and compartmentalization. We monitor metabolic burden through growth curves and adjust designs accordingly.

What quality metrics do you use for strain validation?

Our validation includes NGS sequence verification, phenotypic characterization, stability testing, reproducibility testing, and optional multi-omics analysis. All data is documented in Certificate of Analysis reports.

Can you help with pathway discovery for novel compounds?

Yes, we offer pathway discovery combining bioinformatics, comparative genomics, and functional screening. We identify gene clusters, predict enzyme functions using machine learning, and validate through heterologous expression.

Ready to Start Your Project?

Get a customized quote for your Metabolic Engineering and Pathway Design Service project. Our experts will respond within 24 hours.

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Metabolic Engineering & Pathway Design

Why Choose Our Service

CRISPR Precision

Pathway Assembly

Multi-Host Platform

Why Choose Our Metabolic Engineering Service

CRISPR-Based Precision

DBTL-Driven Optimization

Multi-Host Platform

Precision Engineering

Modular Assembly

High-Throughput Screening

Quality Guaranteed

Ready to Build Your Cell Factory?

Our Advanced Engineering Technologies

Genome Editing Tools

Computational Design

Advanced Capabilities

Enzyme Engineering

Dynamic Regulation

Compartmentalization

Adaptive Evolution

Service Specifications

Our DBTL-Driven Workflow

Design

Build

Test

Learn

Delivery Package Includes

Industry Applications

What Our Clients Say

Supporting Publications

Balancing Cell Growth and Product Synthesis for Efficient Microbial Cell Factories

Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0

Growth-coupled selection of synthetic modules to accelerate cell factory development

MULTI-SCULPT: Multiplex Integration via Selective, CRISPR-Mediated, Ultralong Pathway Transformation in Yeast

Engineering of Multiple Modules to Improve Amorphadiene Production in Bacillus subtilis Using CRISPR-Cas9

Frequently Asked Questions

Ready to Start Your Project?

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