Downstream Processing

Downstream processing in microbial fermentation refers to the purification and recovery of the desired product from the fermentation broth. It involves a series of steps to separate and purify the target compound or biomass from other cellular components, contaminants, and byproducts. Creative Biogene has equipment matching different fermentation scales, and the expertise, to develop, test and validate methods for production, recovery, concentration and/or purification of your desired products.

Microbial fermentation downstream processing.Figure 1 Microbial fermentation downstream processing.


The first step is to separate the microbial biomass from the fermentation broth. This can be achieved through methods such as centrifugation, filtration, or sedimentation, depending on the characteristics of the microbial cells and the nature of the fermentation broth.

Cell Disruption

If the desired product is intracellular, the harvested cells need to be disrupted to release the target compound. Cell disruption methods include mechanical methods (such as bead milling, sonication), enzymatic methods (using lytic enzymes), or chemical methods (using detergents or solvents).

Solid-liquid Separation

After cell disruption, solid-liquid separation techniques are employed to separate the soluble components (e.g., proteins, enzymes) from insoluble cellular debris. Filtration or centrifugation can be used to separate the solid and liquid fractions. Clarification techniques such as depth filtration or microfiltration may be applied to further remove any remaining solid particles.


Concentration of the desired product is typically necessary to reduce the volume and increase the concentration for subsequent purification steps. Techniques such as evaporation, ultrafiltration, or precipitation can be used to concentrate the target compound.


Various purification techniques are employed to isolate and purify the target compound from other impurities. These techniques can include chromatography (such as ion exchange, affinity, or size exclusion chromatography), precipitation, crystallization, extraction, or membrane-based separations.

Formulation and Stabilization

Once the target compound is purified, it may undergo formulation processes to enhance its stability, solubility, or shelf life. This can involve formulation in suitable buffers, adjustment of pH, addition of stabilizers or preservatives, or lyophilization (freeze-drying) for long-term storage.

Analysis and Quality Control

Throughout the downstream processing, regular analysis and quality control tests are performed to monitor the purity, identity, and activity of the target compound. Analytical techniques such as HPLC (High-Performance Liquid Chromatography), SDS-PAGE (Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis), spectrophotometry, or mass spectrometry are used to assess the quality and quantity of the product.

Main Methods

Filtration Methods
Ultrafiltration Nanofiltration Reverse Osmosis
Diafiltration Microfiltration Membrane Filtration
Chromatography Methods
Affinity Chromatography (Protein A/G) Hydrophobic Interaction Chromatography Size-Exclusion Chromatography (SEC)
Ion Exchange Chromatography (IEX) Reverse Phase Liquid Chromatography Countercurrent Chromatography (CCC)
Adsorption Chromatography Continuous Chromatography Continuous Annular Chromatography (CAC)

Downstream processing is highly dependent on the specific characteristics of the microbial fermentation and the desired product. Optimization of each step and consideration of factors such as yield, purity, cost, and regulatory requirements are crucial to achieve efficient and economically viable downstream processing. Collaboration with Creative Biogene's experts in downstream processing and process engineering is valuable to develop effective strategies for purification and recovery of microbial fermentation products.

Downstream Processing

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