Starting from upstream to downstream processing including purification
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Bioprocess PrinciplesBioprocess Principles
Dr. S Venkat Kumar B.Tech., M.E., Ph.D
Bioprocess Development
Bioprocessing is an essential part of many food,
chemical and pharmaceutical industries
Bioprocess operations make use of microbial,
animal, plant cells and component of cells such as
enzyme to manufacture new products and destroy
harmful wastes.
Bioprocesses have been developed for an
enormous range of commercial products from
relatively cheap materials
The products are industrial alcohol and organic
solvents, to expensive speciality chemicals such as
antibiotics, therapeutic proteins and vaccines
Industrially-usefulenzymes and living cells
such as bakers and brewers yeast are also
commercial products of bioprocessing
Definition
Fermentation is the chemical transformation of
organic substances into simpler compounds by the
action of enzymes, complex organic catalysts, which
are produced by microorganisms such as molds,
yeasts, or bacteria.
Enzymes act by hydrolysis, a process of breaking
down or predigesting complex organic molecules to
form smaller (and in the case of foods, more easily
digestible) compounds and nutrients.
Fermentation results in the production of energy in
the form of two ATP molecules, and produces less
energy than the aerobic process of cellular
respiration
Introduction to fermentation
Fermentation is a metabolic process that converts
sugar to acids, gases or alcohol. It occurs in yeast
and bacteria.
More broadly, fermentation is the foaming ( Un-
healthy ) that occurs during the manufacture of wine
and beer, a process at least 10,000 years old. The
frothing results from the evolution of carbon dioxide
gas, though this was not recognized until the 17th
century.
French chemist and microbiologist Louis Pasteur in
the 19th century used the term fermentation in a
narrow sense to describe the changes brought about
by yeasts and other microorganisms growing in the
absence of air (anaerobically); he also recognized
that ethyl alcohol and carbon dioxide are not the only
products of fermentation.
The first solid evidence of the living nature of yeast
appeared between 1837 and 1838 when three
publications appeared by C. Cagniard de la Tour, T.
Swann, and F. Kuetzing, each of whom
independently concluded as a result of microscopic
investigations that yeast was a living organism
that reproduced by budding.
In 1860 Louis Pasteur demonstrated that bacteria
cause souring in milk, a process formerly thought to
be merely a chemical change
His work in identifying the role of microorganisms in
food spoilage led to the process of pasteurization.
In 1877 the era of modern medical bacteriology
Began when Koch (a German physician; 1843- 1910)
and Pasteur showed that the anthrax bacillus caused
the infectious disease anthrax.
This epic discovery led in 1880 to Pasteur's general
germ theory of infectious disease, which postulated
for the first time that each such disease was caused
by a specific microorganism.
Koch also made the very significant discovery of a
method for isolating microorganisms in pure
culture.
Stage 1 (Pre 1900)
Organism Mixed culture, pure yeast culture
Products Alcohol, vinegar
Vessels Wooden barrels with manual stirring
and trickling generators
Process Batch
Process controlThermometer, heat exchangers,
hydrometer
Quality control Nil
Stage 2 (1900 – 1940)
Organism Pure culture
Products Bakers yeast, glycerol, citric acid,
acetone/ butanol, lactic acid
Vessels Steel vessel with mechanical
stirring and air sparger
Process Batch and fed batch
Process controlTemperature control, pH
electrode
Quality control Nil
Stage 3 (1940 onwards)
Organism Pure culture - wild type and strain
improved
Products Penicillin and other antibiotics, amino
acids, nucleotides, and enzymes
Vessels True aseptic fermentor
Process Batch, fed batch and continuous
culture
Process controlSterilizable oxygen and pH
electrodes, control loops
Quality control Very important
Stage 4 (1964 onwards)
Organism Genetically modified strain
Products Single cell protein using
hydrocarbon
Vessels Pressure jet and pressure cycle
vessels
Process Batch, fed batch and continuous
with recycle
Process controlComputerized control loops
Quality control Very important
Stage 5 (1979 onwards)
Organism Recombinant strains
Products Monoclonal antibodies and
recombinant proteins
Vessels Animal cell reactors
Process Continuous perfusion and
immobilized cell culture for
animal cell process
Process controlComputerized control loops
Quality control Very important
Aerobic Cellular Respiration
•Aerobic means “with air”. This type of
respiration needs oxygen for it to occur,
so it is called aerobic respiration.
Glucose + Oxygen -> Carbon dioxide + Water + Energy
•The chemical equation is:
C
6H
12O
6 + 6O
2-> 6CO
2 + 6H
2O + 2900 kj
•3 stages: -glycolysis
-citric acid cycle
-electron transport chain
Stages of Aerobic Cellular Respiration
•In glycolysis, a net of 2 molecules of
ATP, or chemical energy, are produced.
•The citric acid cycle produces another 2
molecules of ATP
•The electron transport chain produces 28
molecules of ATP.
•Oxygen is used in aerobic cellular
respiration as the final electron acceptor
in the electron transport chain, which is
part of why it's able to create so much
ATP.
But what happens when
oxygen doesn't exist?
Anaerobic Cellular Respiration
In anaerobic cellular respiration, the only step
of this process that occurs is glycolysis.
What is Fermentation?
•It is a process by which the living cell is
able to obtain energy through the
breakdown of glucose and other simple
sugar molecules without requiring
oxygen.
•Fermentation results in the production
of energy in the form of two ATP
molecules, and produces less energy
than the aerobic process of cellular
respiration .
Alcoholic fermentation of glucose
C
6H
12O
6 → 2 C
2H
5OH + 2 CO
2
glucoseethanolcarbon dioxide
Glucos
e
Glycolysis Pyruvic
Acid
Acetaldehyd
e
Ethyl
Alcohol
CO
2
NAD
H
NAD
H
NAD
+
NAD
+
Alcoholic Fermentation
ATP
ATP
Lactic Acid Fermentation
•In lactic acid fermentation, the
pyruvic acid from glycolysis is
reduced to lactic acid by NADH,
which is oxidized to NAD
+. This
commonly occurs in muscle cells.
Lactic acid fermentation allows
glycolysis to continue by ensuring
that NADH is returned to its
oxidized state (NAD
+).
Lactic Acid Fermentation
The range of fermentation process
There are five major groups of commercially
important fermentations:
(i)Those that produce microbial cells (or
biomass) as the product.
(ii)Those that produce microbial enzymes.
(iii)Those that produce microbial metabolites.
(iv)Those that produce recombinant products.
(v)Those that modify a compound which is
added to the fermentation the transformation
process.
THE COMPONENT PARTS OF A
FERMENTATION PROCESS
(i)The formulation of media to be used in culturing
the process organism during the development of
the inoculum and in the production fermenter.
(ii)The sterilization of the medium, fermenters and
ancillary equipment.
(iii)The production of an active, pure culture in
sufficient quantity to inoculate the production
vessel
(iv)The growth of the organism in the production
fermenter under optimum conditions for product
formation.
(v)The extraction of the product and its purification.
(vi)The disposal of effluents produced by the
process.
Types of Fermentation
1. Based on process
Batch, Fed batch
Continuous
Continuous with recycle
2. Based on Oxygen
Aerobic fermentation
Anaerobic fermentation
3. Based on nature of substrate and moisture content
Submerged or liquid state fermentation
Solid substrate fermentation
BATCH FERMENTATION:
A batch fermentation is a closed culture system, because of
limited amount of sterilized nutrient medium is introduced
into the fermenter.
The medium is inoculated with a suitable microorganism and
incubated for a definite period for fermentation to proceed
under optimal physiological conditions.
Oxygen in the form of air, an antifoam agent and acid or
base, to control the pH, are being added during the course of
fermentation process
During the course of incubation, the cells of the
microorganism undergo multiplication and pass through
different phases of growth and metabolism due to which
there will be change in the composition of culture medium,
the biomass and metabolites.
The fermentation is run for a definite period or until the
nutrients are exhausted. The culture broth is harvested and
the product is separated.
BATCH FERMENTATION:
Batch culture is suitable to harvest the secondary
metabolites of micro-organisms
It includes the following 5 steps:
1.Medium added
2.Fermentor sterilized
3.Inoculum added
4.Fermentation followed to completion
5.Culture harvested.
Characteristics of a batch
fermentation system
Simplest fermentor operation
Sterilisation can be performed in the reactor.
All nutrients are added before inoculation.
Maximum levels of C and N are limited by inhibition of
cell growth.
Biomass production limited by C/N load and
production of toxic waste products.
Advantages
Used where end product required in more quantities at
a given period of time. Useful where the shelf life of the
end product is short.
Useful specifically for the product produced only at the
stationary phase
The possibility of contamination and mutation is very
less.
Simplicity of operation
Disadvantages
• For every fermentation process, the fermenter and
other equipment are to be cleaned and sterilized.
•Yield is low
CONTINUOUS FERMENTATION
It is a continuous process where the nutrient is
continuously added to the fermenter at a fixed rate.
The organisms are continuously maintained at
logarithmic stage.
The products are recovered continuously. The
fermenters in this type are called “ flow through’’
fermentation.
Continuous culture is important in industrial
processes to harvest the primary metabolites of
micro-organisms as their product
Advantages
•The fermenter is continuously used with little
or no shutdown time and chemostat is
achieved
•Only little quantity of initial inoculum is
needed and there is no need of additional
inoculum.
•It facilitates maximum and continuous
production of the desired product.
Disadvantages of continuous
fermentation
Complete sterilization is difficult.
More prone to contamination.
Possibility of wastage of nutrient medium because of
continuous withdrawal for product isolation.
The process becomes more complex and difficult to
accomplish when the desired products are antibiotics
rather than a microbial cells.
FED BATCH FERMENTATION
•This fermentation is intermediate of both batch and
continuous fermentation. In this process substrate is
added periodically in instalments as the fermentation
progresses, due to which the substrate is always at an
optimal concentration.
•This is essential as some secondary metabolites are
subjected to catabolite repression by high concentration
of either glucose, or other carbohydrate or nitrogen
compounds present in the medium.
•For this reason, the critical elements of the nutrient
medium are added in low amount in the beginning of the
fermentation and these substrates continue to be added
in small doses during the production phase. This method
is generally employed for the production of penicillin.
Characters of fed batch fermentation.
Initial medium concentration is relatively low. Medium
constituents are added continuously or in increments.
Controlled feed results in higher biomass and product
yields.
Fermentation is still limited by accumulation of toxic
end products.
Finally the products are harvested in one stroke.
Merits
•Production of high cell densities due to extension of
working time (particularly growth associated
products).
•Control over the production of by-products or
catabolite repression effects due to limited provision
of substrates solely required for product formation.
Demerits
•It requires a substantial amount of skilled operator
for the set-up of fermentation and development of
the process.
•More chance of contamination
•Product inhibition
SOLID STATE FERMENTATION
The growth of microorganisms on moist solid
substrate particles in the absence or mere absence
of visible liquid water between the particles.
Particles are a solid culture substrate such as rice or
wheat bran saturated with water and inoculated with
(mold, yeast, bacteria) in controlled room
temperature.
It is more cost effective (smaller vessels, lower water
consumption, reduced waste water treatment costs,
lower energy consumption, and less contamination
problems).
Potentially many high value products such as extra-
cellular enzymes, primary metabolites, and
antibiotics could be produced in SSF.
Liquid state /Solid state fermentation
Characteristics of solid state fermentation
1) The substrate may require preparation or pre-
treatment like, Chopping or grinding-reduce particle
size.
2)Microorganism is usually a filamentous fungus
requiring aerobic condition.
3)The Inoculum is mixed into substrate to
fermentation.
4)Cooking or chemical hydrolysis. Pasteurization or
sterilization-reduce contaminants.
Examples of Solid State Fermentation
Cultivation of mushrooms such as Agaricus,
Pleurotus on sawdust or hay
Production of cheese by the fermentation of milk by
Penicillium roqueforti
Production of Sauerkraut by the fermentation of
cabbage by lactic acid bacteria
Production of organic acids from molasses by
Aspergillus niger
Production of enzymes such as alpha-amylase by
Aspergillus niger
Advantages of SSF
Requires only simple nutrient media as the substrate
Requires very less technology or instrumentation
Capital investment required is very low
Energy expenditure will be low
Sterilization of the media is not required
Chance of microbial contamination is very less
Purification of products is very easy
Yield is usually very high
Low waste water generation
No problem with foaming
Disadvantages of SSF
Only those microbes that can survive in low moisture
can be used in SSF
Precise monitoring and accurate regulation of the
fermentation process is not possible with SSF
The growth rate of the microbes is relatively slow
Scale up of the fermentation process is difficult
Bacterial contamination sometimes problematic
Environmental conditions of the microbes cannot be
regulated in SSF
Anaerobic Fermentation
In anaerobic fermentation, a provision for aeration is
usually not needed.
The air present in the headspace of the fermentor
should be replaced by CO
2
, H
2
, N
2
or a suitable
mixture of these.
The fermentation usually liberates CO
2 and H
2
Recovery of products from anaerobic fermenters
does not require anaerobic conditions. .
Aerobic Fermentation
The main feature of aerobic fermentation is the
provision for adequate aeration.
In addition, these fermenters may have a mechanism
for stirring and mixing of the medium and cells.
Aerobic fermenters may be either of the
(i) stirred tank type in which mechanical motor
driven stirrers are provided or
(ii) of air lift type in which no mechanical stirrers are
used and the agitation is achieved by the air bubbles
generated by the air supply.
An ideal producer or economically important strain should
have the following characteristics
1. It should be pure, and free from phage.
2. It should be genetically stable, but amenable to genetic
modification.
3. It should produce both vegetative cells and spores;
species producing only mycelium are rarely used.
4. It should grow vigorously after inoculation in seed stage
vessels.
5. Should produce a single valuable product, and no toxic
by-products.
6. Product should be produced in a short time, e.g., 3 days.
7. It should be amenable to long term conservation.
8. The risk of contamination should be minimal under the
optimum performance conditions
Isolation of Microorganisms - The first step in
developing a producer strain is the isolation of
concerned microorganisms from their
natural habitats
Microorganisms can be obtained as pure cultures from
organization, which maintain culture collections,
Example:
American Type Culture Collection (ATCC).Rockville,
Maryland, U.S.A.,
Commonwealth Mycological Institute (CMI), Kew, Surrey,
England,
Fermentation Research Institute (FERM), Tokyo, Japan
Research Institute for Antibiotics (RIA), Moscow
National Collection of Industrial Microorganisms
(NCIM), National Chemical Laboratory, Pune,
Maharashtra, India.
Microbial Type Culture Collection (MTCC) and Gene
Bank, Institute of Microbial Technology, Chandigarh,
India
https://jcm.brc.riken.jp/en/abbr_e
The microorganisms of industrial importance are,
generally, bacteria, actinomycetes, fungi and
algae
These organisms occur virtually
everywhere, e.g., in air, water, soil, surfaces of
plants and animals, and plant and animals
tissues
But most common sources of industrial
microorganisms are soils, lake and river mud
Medium
All micro-organisms require water,
sources of energy, carbon, nitrogen,
mineral elements and possibly
vitamins plus oxygen if aerobic.
On a small scale it is relatively simple
to prepare a medium containing pure
compounds, but the resulting medium,
although supporting satisfactory
growth, may be unsuitable for use in a
large scale process.
Criteria for good medium
Maximum yield of product
Maximum rate of product formation
Minimum yield of undesirable products
Minimal problems during media making and
sterilization
Minimal problems during fermentation process
Should be of consistent quality and readily available
throughout the year
The constituents of a medium must satisfy the
elemental requirements for cell biomass and
metabolite production and there must be an
adequate supply of energy for biosynthesis and cell
maintenance.
The first step to consider is an equation based on the
stoichiometry for growth and product formation.
Thus for an aerobic fermentation:
Carbon and energy source + nitrogen source+ O
2 + other
requirements →biomass + products + CO
2
+ H
2
O + heat
Medium requirements
Carbon source
- Energy and product formation
Nitrogen source
- Energy and amino acid supplement
Minerals
- Growth and metabolism
Growth factors
- Synthesis of cell components
Water
Factors influencing the choice of
carbon sources
Rate at which carbon source is metabolized
Type of product to be produced
Cost of the product
Purity of the carbon source
Methods of media preparation
Government legislation
Carbon sources
Saccharine materials
- Molasses, fruit juices, cheese whey
Starchy materials
- Cereals, roots and tubers
Cellulosic materials
- wood molasses, sulfite waste liquor
Hydrocarbons and vegetable oils
Saccharine materials
Molasses
-Byproduct of the cane and beet sugar industry
-It is rich in sucrose (95% of total sugar)
-Rich in biotin, pantothenic acid, thiamine,
phosphorous and sulphur
-Beet molasses is deficient in biotin but
contain betaine (organic nitrogen source)
-It is mainly used for production of high volume
low price products like ethanol, SCP
Fruit juices
- Contain soluble sugars, ex- grape juice contain
glucose and fructose
Cheese whey
- Straw colored liquid produced as a byproduct of
cheese making
Starchy materials
Cereals (ex- wheat, rice, maize, etc)
-Contains soluble carbohydrate in large quantity than
proteins, fats, crude fiber and minerals
-Barley grains partially germinated and heat treated to
give malt, which is used for brewing beers
-Corn steep liquor, by product after starch extracted
from maize
Roots and tubers (ex- potato, tapioca, etc)
- Contains starch, which requires pretreatment to bring
about the conversion to fermentable sugar
Cellulosic materials
Sulfite waste liquor
- It is a dilute sugar solution having 2% of total
sugar
- In the manufacture of paper pulp, wood is
subjected for hydrolysis by calcium bisulfite
under heat and pressure, at the end the spent
liquid left is known as sulfite waste liquor
- It is necessary to remove free sulfur dioxide or
sulfurous oxide present in the medium before
fermentation
Wood molasses
-Acid hydrolysis of wood cellulose result in production
of wood molasses with 65 to 85% of fermentable
sugars
-Among sugars hexoses and pentoses are more
predominant
Hydrocarbons and vegetable oils
Vegetable oils
-Examples like olive, maize, cotton seed, linseed,
soya bean, etc.
-Contains fatty acids, oleic, linoleic and linolenic
acid.
-Contains 2.4 times the energy of glucose
-It has volume advantages
-It has antifoaming property
-On energy basis to sugars it could be cheaper
and economic
Hydrocarbon and derivatives
-Methane, methanol and n- alkanes for the
production of SCP
-On an weight basis n- alkanes have
approximately twice the carbon and three time
the energy content of the same weight of sugar
-Initially they are impure hence more down stream
steps and effluent treatments are required
-But it can be refined to obtain pure products
Inorganic nitrogen sources
Ammonia is used as pH control as well as
nitrogen source
Ammonium sulfates will produce acidic
conditions as the ammonium ions is utilized
and the free acid is liberated.
Ammonium nitrates initially will produce acid
drift as the ammonium ions are utilized then
there is an alkaline drift as the nitrates is used
as an alternative nitrogen source
Organic nitrogen sources
Corn steep liquor
-the used steep water resulting from the steeping of
corn during the manufacturing of starch, gluten and
other corn products
-Used in the production of penicillin
Soya bean meal
-The material left after the deoiling of the soya bean
seeds
-It is more complex nitrogenous source than corn
steep liquor
-Used in the production of streptomycin
Distillers soluble
-In the manufacture of alcohol from grains or maize,
alcohol is distilled from fermented grain or maize
leaving the residue, which is further processed to
produce distillers soluble
-It is also rich is B complex vitamins
Best nitrogen sources for some
secondary metabolites
Minerals
All micro-organisms require certain mineral elements
for growth and metabolism
In many media, magnesium, phosphorus, potassium,
sulphur, calcium and chlorine are essential
components, and because of the concentrations
required, they must be added as distinct components
Others such as cobalt, copper, iron, manganese,
molybdenum and zinc are also essential but are usually
present as impurities in other major ingredients
Trace elements influencing primary and
secondary metabolism
Chelators
Gaunt et al. (1984) demonstrated that when the medium of Mandels
and Weber was autoclaved, a white precipitate of metal ions
formed, containing all the iron and most of the calcium, manganese
and zinc present in the medium
The problem of insoluble metal phosphate(s) may be eliminated by
incorporating low concentrations of chelating agents such as
ethylene diamine tetra acetic acid (EDTA), citric acid,
polyphosphates, etc., into the medium
These chelating agents preferentially form complexes with the
metal ions in a medium. The metal ions then may be gradually
utilized by the microorganism were able to show that the
precipitate was eliminated
It is important to check that a chelating agent does
not cause inhibition of growth of the micro-
organism which is being cultured
In many media, particularly those commonly used
in large scale processes, there may not be a need to
add a chelating agent as complex ingredients such
as yeast extracts or proteose peptones will
complex with metal ions and ensure gradual
release of them during growth
Growth factors
Some micro-organisms cannot synthesize a full
complement of cell components and therefore
require preformed compounds called growth factors
The growth factors most commonly required are
vitamins, but there may also be a need for specific
amino acids, fatty acids or sterols
Many of the natural carbon and nitrogen sources
used in media formulations contain all or some of
the required growth factors
Inducers
Majority of the enzymes produced are inducible,
hence substrates are inducers and the products are
inducible
Example- starch for amylase
- pectin for pectinase
- fatty acid for lipase
Inhibitors
When certain inhibitors are added to fermentations,
more of a specific product may be produced, or a
metabolic intermediate which is normally
metabolized is accumulated.
Bromide when added chlortetracycline production is
inhibited and tetracycline is increased
Penicillin when added increases the production of
glutamic acid by increasing the cell wall
permeability of Micrococcus glutamicus
Sodium bisulphite when added as inhibitor in
ethanol production from glucose, acetaldehyde an
intermediate in the above process is repressed and
there by glycerol production increases
Precursors
Some chemicals, when added to certain fermentations,
are directly incorporated into the desired product.
Addition of corn-steep liquor increased the yield of
penicillin from 20 units/cm
3
to 100 units/cm
3
. Corn-steep
liquor was found to contain phenylethylamine which was
preferentially incorporated into the penicillin molecule to
yield benzyl penicillin (Penicillin G).
Addition of phenyl acetic acid related products gives
penicillin G and phenoxy acetic acid gives penicillin V
Other examples chloride for chlortetracycline and
cyanide for vitamin B12
Water
Water is the major component of all fermentation media, and
is needed in many of the ancillary services such as
heating, cooling, cleaning and rinsing
Clean water of consistent composition is therefore required in
large quantities from reliable permanent sources
When assessing the suitability of a water supply it is
important to consider pH, dissolved salts and effluent
contamination
The mineral content of the water is very important in
brewing, and most critical in the mashing process
Antifoaming agents
Foam may be due to some component in the medium or
some factors produced by the microorganism
Mainly due to the proteins in the medium
Foaming causes both physical and biological problems
like
- Removal of cells
- Lower mass and heat transfer rates
- Invalid process data due to interference at sensing
electrodes
- Deposition of cells in the upper part of the fermenter and
problems of sterile operation
- Exit air filter becoming wet and there is a danger of
microbial infection
Foaming is encountered by
-Avoiding using of materials which causes foam
-Modification of some of the physical parameters(pH,
temp,aeration and agitation)
-Antifoaming agents
-Mechanical foam breakers
1.Should disperse readily and have fast action on an existing
foam.
2. Should be active at low concentrations.
3. Should be long acting in preventing new foam formation.
4. Should not be metabolized by the microorganism.
5. Should be non-toxic to the micro-organism.
6. Should be non-toxic to humans and animals.
7. Should not cause any problems in the extraction and purification
of the product.
8. Should not cause any handling hazards.
9. Should be cheap.
10. Should have no effect on oxygen transfer.
11. Should be heat sterilizable
Complex media
Media that contain some ingredients of unknown
chemical composition are complex media
A single complex medium may me sufficiently rich
and complete to meet the nutritional requirements of
many different microorganisms
101
Fermenter
DOWNSTREAM
PROCESSING
Culture
fluid
Cell
separation
Biomass
Cell free
supernatant
Product
extraction
Product
purification
Product packaging
Effluent treatment
Production
fermenter
Medium raw material
Medium FORMULATION
Medium STERILIZATION
Stock
culture
Shake
flask
Seed
fermenter
Flow sheet of a multipurpose fermenter and its
auxiliary equipment