Strain Metabolic Profiling Services

The Strain Metabolic Profiling Service utilizes advanced analytical chemistry, specifically metabolomics, to provide a detailed snapshot of the internal chemical state of a microbial strain. By identifying and quantifying intracellular and extracellular metabolites, we gain crucial insight into metabolic bottlenecks, flux distribution, and the impact of genetic modifications on the cell’s physiology.

CD Biosynsis offers both Targeted and Untargeted Metabolomics using highly sensitive mass spectrometry (LC-MS and GC-MS). This service is indispensable for metabolic engineering, allowing researchers to quickly confirm whether a pathway intervention (e.g., gene knock-out or overexpression) resulted in the predicted changes in intermediate concentrations. Metabolic profiling identifies hidden roadblocks and provides the quantitative evidence needed for rational, iterative strain design, moving beyond simple titer measurements to true bioprocess optimization.

Highlights

Core benefits of utilizing our Metabolic Profiling Service:

• Metabolic Roadblock Identification: Precisely locates the accumulation of intermediate metabolites, pinpointing bottlenecks in biosynthetic pathways.
• Flux Confirmation: Provides quantitative evidence of how genetic edits alter carbon flow, validating the success of a metabolic engineering strategy.
• Untargeted Discovery: Capable of identifying novel or unexpected byproducts and stress-related metabolites.
• Bioprocess Monitoring: Used for real-time analysis of nutrient depletion or the onset of overflow metabolism during fermentation.

Profiling Methods

Advanced analytical techniques for comprehensive metabolite analysis:

Targeted Metabolomics (LC-MS/GC-MS)

Quantitative analysis of specific known metabolite panels (e.g., amino acids, TCA cycle intermediates, organic acids) with high accuracy.

Untargeted Metabolomics

Broad screening to detect and semi-quantify hundreds of known and unknown compounds for discovery and systems biology.

Isotope Tracing and Fluxomics

Using labeled carbon substrates (e.g., 13C glucose) to track metabolic fate, calculate flux, and reveal pathway activity.

Extracellular Analysis

Quantifying secreted products, byproducts, and consumed nutrients in the fermentation broth for yield calculations.

Key Features & Applications

Key technical features and the utility of metabolic profiling data:

Rapid Quenching Protocol

Immediate cell collection and quenching to preserve the true intracellular metabolite concentrations for accurate measurement.

Mass Spectrometry Expertise

Dedicated instruments (LC-MS/MS, GC-MS/MS) and libraries for high-confidence identification and separation of complex metabolite mixtures.

Data Visualization and Flux Analysis

Delivery of clear heatmaps, principal component analysis (PCA), and pathway maps highlighting significant metabolic changes.

Host Compatibility

Proven protocols for preparing and analyzing metabolites from diverse hosts including E. coli, Yeast, Algae, and Fungi.

Bioprocess Troubleshooting

Rapid identification of causes for titer drop, byproduct formation, or poor conversion efficiency during fermentation.

Workflow

Our systematic workflow for accurate strain metabolic profiling:

• Strain Cultivation: Strains are grown under defined bioprocess conditions (e.g., in bioreactors or controlled flasks).
• Rapid Quenching and Sampling: Cells are instantly quenched (e.g., with cold methanol solution) to stop enzymatic activity, and samples are collected for both intracellular and extracellular analysis.
• Metabolite Extraction: Intracellular metabolites are extracted using optimized solvent protocols, and extracellular media is pre-processed.
• LC-MS/GC-MS Analysis: Samples are analyzed on high-resolution mass spectrometers for separation and quantification of targeted metabolites.
• Data Processing and Bioinformatics: Raw data is processed, normalized, and subjected to statistical analysis (e.g., fold change, t-tests, PCA) to highlight metabolic differences.
• Reporting and Interpretation: Delivery of a detailed report, including pathway visualizations and actionable insights for strain engineering.

We provide essential assurance for high-quality metabolic profiling outcomes:

• Quenching Fidelity: Guaranteed effective quenching protocols to ensure measured metabolite levels accurately reflect the cellular state.
• Quantitative Accuracy: Use of internal standards and rigorous calibration to ensure accurate quantification of targeted metabolites.
• Comprehensive Coverage: Ability to screen hundreds of known primary metabolites and pathway intermediates per sample.
• Actionable Insights: Expert interpretation of metabolic data to guide the next phase of the strain engineering cycle.