The 4 main modes of bioreactor operation have different PROS and CONS. Each mode defines how cells and substrates (nutrients) interact over time, and each has distinct implications for productivity, control, and scalability. Thus, selection of the mode of operation is critical for the desired production end goal and biomanufacturing design process constraints. Click HERE and HERE for videos describing the modes of operation.

1) Batch Process

Definition: All nutrients and cells are added at the start. The culture runs without further input until nutrients are depleted or inhibitory byproducts accumulate.
Key Features:

Closed system (no addition or removal during the run).
Simple setup, easy to control.
Growth follows a typical curve: lag → exponential → stationary → decline.

Advantages:

High reproducibility.
Well-suited for small-scale production and research.

Limitations:
-Limited productivity due to nutrient depletion and waste buildup.
-Not ideal for long-term or high-density cultures.

2) Repeated (Serial) Batch Process

Definition: A sequence of batch runs where part of the culture is harvested and replaced with fresh medium, while retaining some cells as inoculum.
Key Features:

Extends culture life by refreshing nutrients.
Maintains cells in active growth phase longer than a single batch.

Advantages:

Higher productivity compared to single batch.
Useful for maintaining cultures without continuous operation.

Limitations:
-Still subject to fluctuations in nutrient and waste levels.
-The cells can be subject to genetic mutational drift after a certain amount of passages.
-Labor-intensive compared to continuous systems.

3) Fed-Batch Process

Definition: Starts like a batch, but nutrients are added gradually during the run without removing culture volume.
Key Features:

Prevents nutrient depletion.
Controls substrate concentration to avoid significant overflow of metabolic product build-up (i.e. lactate and NH4 in mammalian cells, ethanol in yeast).

Advantages:

Most widely used in industrial biomanufacturing (i.e. CHO cells for monoclonal antibodies).
Enables high cell densities and product titers.

Limitations:
-Still accumulates waste products.
-Requires careful feeding strategy design (stoichiometric balances, metabolic modeling, automation engineering).

4) Perfusion (Continuous) Process

Definition: Fresh medium is continuously supplied while spent medium (containing product and waste) is removed, often with cell retention devices. The working volume in the vessel is kept constant and at steady state throughout the duration of the bioreactor run.
Key Features:

Maintains steady-state conditions.
Cells can be kept in exponential growth indefinitely.

Advantages:

Very high productivity and product quality consistency.
Ideal for long-term cultures and sensitive biologics.

Limitations:
-Complex to design and operate.
-Higher costs and technical challenges (cell retention, sterility, mixing).
-The cells can be subject to genetic mutational drift over time.

There are two common modes of running a perfusion bioreactor system: 1) Tangential flow filtration (TFF), and 2) alternating tangential flow filtration (ATF).

The two common modes of running a perfusion bioreactor system.

Tangential Flow Filtration (TFF)

Principle:
Medium flows tangentially across a filter membrane (the cell retention device). The cross-flow prevents clogging, while permeate (cell-free medium containing product and waste) passes through the membrane. Cells are retained in the bioreactor.
Key Features:

Uses hollow-fiber or flat-sheet membranes.
Continuous removal of product and waste.
Retains cells and sometimes large biomolecules.

Advantages:

Well-established, robust technology.
Scalable to large bioreactors.
Effective for high-density cultures.

Limitations:
-Membrane fouling over time.
-Requires careful control of transmembrane pressure.
-Shear stress can affect sensitive mammalian cells.

Alternating Tangential Flow Filtration (ATF)

Principle:
A refinement of TFF. Instead of constant tangential flow, ATF uses a diaphragm pump to alternate flow direction across the filter (the cell retention device). This back-and-forth motion reduces fouling and shear stress.
Key Features:

Alternating flow keeps the membrane surface clear.
Cells remain in the bioreactor, while clarified medium is removed.
Often used with hollow-fiber modules.

Advantages:

Lower fouling compared to standard TFF.
Gentler on cells (reduced shear).
Enables very high cell densities (CHO cultures >100 million cells/mL).
More stable long-term perfusion runs.

Limitations:
-More complex equipment (pump + control system).
-Higher cost compared to simple TFF.
-Requires optimization of cycle frequency and pressure.

An interesting bioreactor process, which deserves its own classification (away from the main 4 modes of operation) is the plug flow reactor (PFR)-type bioreactor.

A plug flow reactor (PFR)-type bioreactor is a tubular system where liquid components (cells and nutrients) move in a “plug” fashion with minimal back-mixing, enabling precise control of residence time and reaction conditions. Liquid circulation in a PFR is promoted by pumps or gas convection. A specialized form of a PFR is the hollow fiber bioreactor (HFBR). In an HFBR system, the hollow fiber filter column is the bioreactor vessel itself, where cells can either grow while circulating through the column, or grow attached to the column. The hollow fiber in the HFBR column still has capillary pores small enough for cell retention and exchange of nutrients and metabolic waste.

The use of HFBR bioreactors is common in the biopharma industry for mimicking an environment similar to the flow of cells in the bloodstream, in terms of flow conditions (ideal for growing immune system cells and red blood cells).

The HFBR bioreactors are also good for separating exosomes from stem cells in exosome production runs in the biopharma industry.

Bioreactor Modes of Operation

2026

Bioreactor Modes of Operation

Bioreactor Mixing Modes

2026