Chapter 2
How does Biotechnology
Operates?
Essam H. Ghanem and Salwa Al-Thawadi
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Operation steps of biotechnology
Process
engineering
Substrate + Microbial Product
cells
▪ Process engineering
▪ Fermentation
▪ Isolation of product or cells
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How does Biotechnology operate?
Principal steps of a
bioengineered
biotechnology
process
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Biomass—renewable energy from plants and
animals
Biomass is organic material that comes from plants and animals, and it is a
renewable source of energy.
Biomass contains stored energy from the sun. Plants absorb the sun's
energy in a process called photosynthesis. When biomass is burned, the
chemical energy in biomass is released as heat. Biomass can be burned
directly or converted to liquid biofuels or biogas that can be burned as
fuels.
Examples of biomass and their uses for energy
•Wood and wood processing wastes—burned to heat buildings, to produce
process heat in industry, and to generate electricity
•Agricultural crops and waste materials—burned as a fuel or converted to
liquid biofuels
•Food, yard, and wood waste in garbage—burned to generate electricity in
power plants or converted to biogas in landfills
•Animal manure and human sewage—converted to biogas, which can be
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burned as a fuel
Microbial biomass (bacteria and fungi)
is a measure of the mass of the living
component of soil organic matter. The
microbial biomass decompose plant
and animal residues and soil organic
matter to release carbon dioxide and
plant available nutrients.
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Raw material (RM)
▪ C-source (substrate)
▪ C-source + O2 produce biomass,
CO2 and water
▪ Economic
▪ Available
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Criteria to select the proper RM
▪ Nature of the raw material.
▪ The targeted end product.
▪ Conditions of the process.
▪ Microorganisms used.
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Upstream processing (USP)
Processing of microorganisms for
optimization of growth and
production
• This includes everything that happens
before and during inoculation of
microorganisms into the main fermenter.
The goal is to prepare the right organism
and conditions for optimal growth and
product formation. 11
Steps of Upstream processing
• Strain selection & improvement: Choosing the right
microbial strain (wild type, mutant, recombinant) with
high productivity.
• Media formulation & sterilization: Supplying carbon,
nitrogen, minerals, growth factors, and vitamins;
sterilizing to prevent contamination.
• Inoculum development: Stepwise scaling up of
culture from small tubes → flasks → seed fermenter →
production fermenter.
• Bioreactor design & sterilization: Preparing the
fermentation vessel with proper aeration, agitation, pH,
and temperature control.
Outcome: A pure, active, and well-prepared microbial
culture ready for fermentation. 12
Fermentation and Biotransformation
▪ Production of targeted cells or
transform substrate or product to
another product. Depends on:
Nature and type of the
microorganism.
The required culture conditions.
The design of the bioreactor.
The targeted end product.
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Fermentation (Bioprocessing /
Bioconversion)
This is the core stage where microorganisms grow and
produce the desired metabolites (primary or secondary),
enzymes, biomass, or recombinant products.
Controlled parameters in fermentation:
Temperature, pH, dissolved oxygen, agitation speed.
Foam control (antifoam agents or mechanical control).
Nutrient feeding strategy (carbon/nitrogen ratio, limiting
substrates).
Outcome: Maximum biomass or product
accumulation under controlled conditions. 14
This involves the recovery, separation,
and purification of the product from the
fermentation broth. It often accounts for
50–80% of total production cost,
especially in pharmaceuticals.
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Upstream Processing (USP)
•Covers everything that happens before the
actual fermentation run begins.
•It’s about preparing the system:
• Strain selection / genetic engineering
• Preparing and sterilizing the media
• Inoculum development (growing seed culture
step by step)
• Bioreactor preparation (sterilization, setting
parameters)
•Goal: Make sure the right microorganism + right
environment are ready for fermentation.
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Fermentation (Bioprocessing step)
•This is the actual production phase inside
the bioreactor.
•Microbes grow, metabolize, and produce the
target product (biomass, enzyme, antibiotic,
recombinant protein, etc.).
•Involves strict control of growth conditions:
aeration, agitation, pH, temperature, feeding,
antifoam.
•Can be batch, fed-batch, or continuous.
Fermentation is the “performance” on the
stage you set up in USP
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Main steps of product recovery:
1.Cell separation: Removing microbial cells from broth
using centrifugation, filtration, or flocculation.
2.Product recovery: Depending on whether the product
is intracellular (enzymes, proteins, DNA) or extracellular
(antibiotics, metabolites).
1.Intracellular: cell disruption (sonication, chemical
lysis, high-pressure homogenization).
2.Extracellular: direct extraction from supernatant.
3.Concentration: Using precipitation, ultrafiltration,
solvent extraction, or adsorption.
Outcome: A purified, stable, and market-ready microbial
product. 18
Purification:
Chromatography (ion exchange, affinity,
size-exclusion), crystallization, distillation,
electrophoresis.
Formulation & packaging: Stabilizing the
product (freeze-drying, adding stabilizers)
and preparing it for storage/market.
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Summary of Biotechnology Operation
▪ Raw materials
▪ Substrates for industrial fermentations.
▪ Upstream processing
▪ Strain improvement
▪ Fermentation and/or biotransformation
▪ Growth
▪ Fermentation
▪ Downstream processing (Product recovery)
▪ Purification
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