Service Overview

Chassis Optimization For Metabolic Pathways

Engineer microbial hosts for enhanced production of target compounds through rational metabolic pathway design and gene editing.

Rational pathway design and computational modeling
Precision gene editing (CRISPR) for targeted modifications
Iterative screening and fermentation optimization

Contact Our Scientists

Custom Strain Engineering for Metabolic Production

We combine metabolic modeling, gene editing, and high-throughput screening to develop optimized chassis strains tailored to your target molecule.

Target pathway selection and flux analysis
Custom genetic modification strategy
Production scale-up feasibility assessment

Microbial Hosts (Bacteria, Yeast, Fungus)

CRISPR & Gene Editing

Metabolite QC & Analytics

Our Approach

Comprehensive Metabolic Pathway Engineering

Our chassis optimization service begins with understanding the metabolic landscape of your chosen host and ends with a validated production strain.

Rational Pathway Design

We use genome-scale metabolic models to simulate flux distributions and identify rate‑limiting steps. This in silico analysis guides gene targets for knockout, overexpression, or heterologous pathway integration, reducing trial‑and‑error in the lab.

Genome-scale metabolic model construction
In silico gene knockout/overexpression prediction
Pathway balancing for reduced byproduct formation

Gene Editing & Strain Construction

Our scientists design CRISPR sgRNAs and repair templates for precise, scarless modifications. We transform the constructs into the host, screen for correct edits, and isolate clonal populations for downstream testing.

SgRNA design and off-target analysis
Homology-directed repair (HDR) template design
Transformation and clone screening

Integrated Computational and Experimental Workflow

Modeling and wet‑lab experiments are tightly coupled: each screening round refines the model, enabling data‑driven iteration toward higher titers.

Iterative Design-Build-Test-Learn Cycle

We apply multiple rounds of modification and analysis, adjusting pathway flux and regulatory elements until production targets are met or further improvement plateaus.

Comprehensive Analytical Validation

Every optimized strain is verified by targeted sequencing and metabolite profiling (LC‑MS/GC‑MS). Growth, productivity, and stability are documented in a final report.

What You Get

Service Deliverables

At project completion, you receive a fully characterized and optimized chassis strain along with comprehensive documentation.

Strain Deliverables

Engineered production strain (glycerol stock)
Sequence-confirmed genetic modifications
Parental control strain
QC data package (PCR, sequencing, metabolite analysis)

Data and Reports

Final project report including methodology and results
Metabolite quantification data (LC/MS, GC-MS)
Fermentation performance data (titer, rate, yield)
Strain stability assessment report

Scope of Work

Project Parameters

Each project is scoped case‑by‑case. The table below illustrates typical parameters that are defined during the consultation phase.

Parameter	Typical project scope
Host Organism	Bacteria (E. coli, Bacillus), yeast (S. cerevisiae), or fungus (e.g., A. niger); other organisms upon request.
Target Pathway	Specified by client; supported by literature and in silico modeling.
Genetic Modification Strategy	Gene knockout, knock-in, overexpression, or promoter engineering using CRISPR or homologous recombination.
Screening Method	Microtiter plate or shake-flask screening; high‑throughput if scoped.
Metabolite Analysis	LC-MS, GC-MS, HPLC as per target compound; quantitative and qualitative.
Validation	Genome sequencing (target loci), metabolite profiling, and growth characterization.

Our Process

Chassis Optimization Workflow

A structured, five‑stage pipeline that moves from pathway analysis to deliverable handoff.

Target Pathway Analysis & Modeling

We begin by analyzing the metabolic network of your chosen host, constructing a genome‑scale model to identify flux bottlenecks and prioritize gene targets for modification.

Genetic Modification Design

Based on the model predictions, we design CRISPR sgRNAs and repair templates for precise knockout, knock-in, or overexpression of target genes, with in silico off‑target screening.

Strain Construction & Transformation

The designed constructs are transformed into the host strain. We screen for successful modifications using PCR, sequencing, and selection markers, and isolate homogeneous clones.

Production Screening & Optimization

Engineered strains are cultured under controlled conditions and evaluated for metabolite production. We iterate on design based on screening data to further evaluate yield.

Validation & Deliverable Handoff

Final optimized strains undergo comprehensive QC including full‑genome assessment of edits, metabolite quantification, and fermentation performance assessment. Full data package delivered.

Where It's Used

Applications Across Biotechnology Sectors

Chassis optimization is applied to a wide range of product classes, from small molecules to recombinant proteins.

Production of high‑value drug precursors and active pharmaceutical ingredients

Engineered microbes can produce complex chiral intermediates and secondary metabolites that are difficult to synthesize chemically. We evaluate pathways for APIs such as alkaloids, terpenoids, and non‑ribosomal peptides.

Targeted titers up to gram per liter scale (project‑dependent)
Pathway refactoring for heterologous expression
Fed‑batch fermentation compatibility

High‑yield enzyme and recombinant protein production

By balancing metabolic load and optimizing secretion pathways, we evaluate the production of industrial enzymes (cellulases, lipases) and therapeutic proteins. Gene dosage and promoter tuning are applied iteratively.

Secretion signal optimization
Metabolic burden alleviation
Stable genomic integration for production consistency

Bio‑based production of flavors, fragrances, and cosmetic ingredients

We engineer microbial chassis for sustainable production of natural product analogs, such as vanillin, carotenoids, and fatty acid derivatives. The approach reduces reliance on extraction from natural sources.

Heterologous pathway assembly
Cofactor balancing
Byproduct minimization via knockout of competing reactions

Common Questions

Frequently Asked Questions

Answers to the most common inquiries about chassis optimization projects.

You will receive a purified glycerol stock of the optimized strain, a sequence‑verified parental control, and a comprehensive data package. The data package includes final project methodology, sequencing results, metabolite quantification (LC‑MS/GC‑MS), and fermentation performance metrics (titer, rate, yield). Strain stability data over passaging is also provided.
All genetic modifications are integrated into the chromosome or maintained on stable replicons. We perform serial passaging for at least 20 generations and re‑sequence the target loci to confirm that no mutations or loss of modification occurs. Stability data is reported in the final deliverable.
Yes, we can accept client‑supplied strains. The scope parameter “Host Organism” will include specific handling and confidentiality agreements. We will assess compatibility with our transformation and screening protocols during the consultation phase.
The final strain undergoes targeted genome sequencing of the edited regions to confirm the intended genotype, plus flanking homology arm assessment. Metabolite production is quantified by LC‑MS or GC‑MS, and growth kinetics are measured in defined media. All data is compiled into a traceable QC report.

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