Industrial Microbiology - Use of microbes to obtain a product or service of economic value constitutes industrial microbiology.

Any
process mediated by or involving microorganisms in which a product of economic value is obtained is called fermentation (Casida, Jr.,
1968). The terms industrial microbiology and fermentation are virtually synonymous in their scope, objectives and activities.
The microbial product may be microbial cells (living or dead), microbial biomass, and components of microbial cells, intracellular or
extracellular enzymes or chemicals produced by the microbes utilizing the medium constituents or the provided substrate.
The services generated by microorganisms range from the degradation of organic wastes, detoxification of industrial wastes and toxic
compounds, to the degradation of petroleum to manage oil spills, etc. Industrial microbiology also encompasses activities like production
of biocontrol agents, inoculants used as biofertilizers, etc.
Obviously, the scope and activities of industrial microbiology are too extensive to be covered in any detail in a book like this scope;
therefore, the coverage in this chapter remains generalized and rather elementary.
The activities in industrial microbiology begin with the isolation of microorganisms from nature, their screening for product formation,
improvement of product yields, maintenance of cultures, mass culture using bioreactors, and usually end with the recovery of products and
their purification.

Microbial Products of Potential Importance -

Product / Activity Examples

Products
1. Amino acids L-glutarnic acid, L-lysine
2. Antibiotics Streptomycin, penicillin, tetracyc1ines, polymyxin
3. Beverages Wine, beer, distilled beverages
4. Biodegradable plastic β-polyhydroxybutyrate
5. Enzymes Amylase, proteases, pectinases, invertase, cellulase
6. Flavouring agents Monosodium glutamate, nucleotides
7. Foods Cheese, pickles, yoghurt, bread, vinegar
8. Gases CO2, H2,CH4
9. Organic acids Lactic, citric, acetic, butyric, fumaric
10. Organic solvents Acetone, ethanol, butanol, amyl alcohol
11. Others Glycerol, fats, steroids, gibberellins
11 a. Vitamins B12, riboflavin, A
12. Recombinant proteins Insulin, interferon, subunit vaccines
13. Substrates A wide range of compounds used for chemical syntheses of valuable products.
Cells/Biomass
14. Biomass Food and feed yeast, other organisms used as single cell protein (SCP)
15. Cells Biofertilizers, biocontrol agents, bacterial insecticides, mycorrhyzae
16. Vaccines A variety of viral and bacterial vaccines
Activities
Biotransformation Steroids, antibiotics D-sorbitol
Degradation Disposal of biological and industrial wastes, detoxification of toxic compounds, petroleum
Solubilization/accumulation Improved recovery of oil and metals, discovery of new oil reserves, removal of toxic metals

.
Microbes History - Microbes have been employed for product generation, e.g., wines, bread, etc., since thousands of years, but these
activities were purely art. The science of industrial microbiology is only about 150 years old. The first observations of microorganisms by
Leeuwenhoek were published in 1677.
The experiments of Spallanzani in 1799 and of Schwan in 1837 not only disproved the idea of spontaneous generation of microorganisms,
but also provided a means of sterilization of liquids (by heat) and air (by heat), respectively.
Schwan's findings also suggested that alcoholic fermentation was due to a fungus or mold, i.e., yeast, and inoculation resulted in quicker
fermentation. But microbiology is widely considered to have begun in 1857 when Pasteur reported his studies on lactic acid fermentation,
including the microscopic features of the microorganisms and a suitable medium for the process; the scientific basis of industrial
microbiology began with this paper.
In 1860, Pasteur reported the first synthetic medium for microorganisms, and used it to study alcohol fermentation. In 1861, Pasteur
showed that growth and physiology of yeast (and hence the accumulation of fermentation product, alcohol) differs depending on the
presence or absence of °2' This phenomenon is known as Pasteur effect and is applicable to other microorganisms as well.
In 1878, Lister described the dilution technique for obtaining the first pure microbial culture of lactic acid bacterium. A simpler and more
effective technique for obtaining pure cultures from isolated separate colonies developed on solidified medium was described by Robert
Koch in 1881; this technique is widely followed even today.

In 1876, Cohn showed that bacterial spores have a high level of heat resistance and developed the technique of 'intermittent sterilization'
for their inactivation. In 1897, Buchner demonstrated alcohol fermentation by cell-free yeast juice; he suggested that a proteinaceous
enzyme was responsible for fermentation.
Wildiers demonstrated in 1901 that yeast required growth factors (vitamins) for growth, especially at low inoculum levels; vitamins are
used in fermentation even today. In 1929, Alexander Fleming accidentally discovered penicillin produced by Penicillium growing as
contaminant in a Petri plate of Staphylococcus.
Fleming developed the technique for assay of antibacterial activity of penicillin using bacteria and showed its low toxicity to man and
animals. This was followed by an intensive search for antibiotics during the Second World War leading to the discovery of streptomycin,
chloramphenicol, tetracyclines, etc.
Later developments have resulted in the use of metabolically blocked mutants of microorganisms, which accumulate large amounts of
metabolic intermediates.

Isolation and Screening of Microorganisms - The success of an industrial fermentation process chiefly depends on the microorganism
strain used. 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. Alternatively, microorganisms can be obtained as pure cultures from organisation, which maintain culture collections, e.g.,
American Type Culture Collection (ATCC).
Rockville, Maryland, U.S.A., Commonwealth Mycological Institute (CMI), Kew, Surrey, England, Fermentation Research Institute
(FERM), Tokyo, Japan, U.S.S.R. Research Institute for Antibiotics (RIA), Moscow, U.S.S.R., etc.

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, and lake and river mud.
Often the ecological habitat from which a desired microorganism is more likely to be isolated will depend on the characteristics of the
product desired from it, and of process development. For example, if the objective is to isolate a source of enzymes, which can withstand
high temperatures, the obvious place to look will be hot water springs.
A variety of complex isolation procedures have been developed, but no single method can reveal all the microorganisms present in a
sample. Many different microorganisms can be isolated by using specialized enrichment techniques, e.g., soil treatment (UV irradiation, air
drying or heating at 70120°C, filtration or continuous percolation, washings from root systems, treatment with detergents or alcohols,
preinoculation with toxic agents), selective inhibitors (antimetabolites, antibiotics, etc.), nutritional (specific C and N sources), variations
in pH, temperature, aeration, etc.
The enrichment techniques are designed for selective multiplication of only some of the microorganisms present in a sample. These
approaches however take a long time (20-40 days), and require considerable labour and money.
The main isolation methods used routinely for isolation from soil samples are: sponging (soil directly), dilution, gradient plate, aerosol
dilution, flotation, and differential centrifugation. Often these methods are used in conjunction with an enrichment technique.

Screening of Microorganisms for New Products - The next step after isolation of microorganisms is their screening. A set of highly
selective procedures, which allows the detection and isolation of microorganisms producing the desired metabolite, constitutes primary
screening. Ideally, primary screening should be rapid, inexpensive, predictive, specific but effective for a broad range of compounds and
applicable on a large scale.
Primary screening is time consuming and labour intensive since a large number of isolates have to be screened to identify a few potential
ones. However this is possibly the most critical step since it eliminates the large bulk of unwanted useless isolates, which are either non
producers or producers of known compounds.
Computer based databases play an important role by instantaneously providing detailed information about the already known microbial
antibiotic compounds.
Rapid and effective screening techniques have been devised for a variety of microbial products, which utilize either a property of the
product or that of its biosynthetic pathway for detection of desirable isolates. Some of the screening techniques are relatively simple, e.g.,
for extracellular enzymes and enzyme inhibitors.
However for most microbial products of high value, the screening is usually complex and tedious, and often may involve two or more
steps, e.g., for antimicrobials. In some cases, it may be desirable to concentrate on a group of organisms expected to yield new products.
For example, the search for new antibiotics now focusses on rare Actinomycetes, i.e., Actinomycetes other than those belonging to the
genus Streptomyces. Suitably designed specialized screening techniques may be used to detect compounds having various
pharmacological activities other than antibiotics.
Inoculum Development - The preparation of a population of microorganisms from a dormant stock culture to an active state of growth
that is suitable for inoculation in the final production stage is called inoculum development. As a first step in inoculum development,
inoculum is taken from a working stock culture to initiate growth in a suitable liquid medium.
Bacterial vegetative cells and spores are suspended, usually, in sterile tap water, which is then added to the broth. In case of nonsporulating
fungi and actinomycetes the hyphae are fragmented and then transferred to the broth.
Inoculum development is generally done using flask cultures; flasks of 50 ml to 12 litres may be used and their number can be increased as
per need. Where needed, small fermenters may be used.
Inoculum development is usually done in a stepwise sequence to increase the volume to the desired level. At each step, inoculum is used at
0.5-5% of the medium volume; this allows a 20-200-fold increase in inoculum volume at each step. Typically, the inoculum used for
production stage is about 5% of the medium volume.

Culture Media - Inoculum preparation media are quite different from production media. These media are designed for rapid microbial
growth, and little or no product accumulation will normally occur. Many production processes depend on inducible enzymes.
In all such cases, the appropriate inducers must be included either in all the stages or at least in the final stages of inoculum development.
This will ensure the presence of the concerned inducible enzymes at high levels for the production to start immediately after inoculation.

Contamination - The inoculum used for production tanks must be contamination free. But the risk of contamination is always present
during inoculum development. Therefore, every effort must be made to detect as well as prevent contamination.

Sterilization - Sterilization is the process of inactivating or removing all living organisms from a substance or surface. In concept, it is
regarded as absolute in that all living cells must be inactivated / removed, usually in a single step at the given time. But in practice, the
success of sterilization procedures is only a probability.Therefore, the probability of a cell escaping inactivation/filtration does exist
although it is usually very small.
When a closed system is sterilized once, it remains so indefinitely since it has no openings for the entry of microorganisms. But most
fermentation vessels are open systems; such systems are initially sterilized and must be kept sterilized by ensuring the removal of living
cells at their entry points, e.g., the cotton plug of a culture flask.

Common Contaminants - The most common contaminants of different industrial processes are considerably different. Some examples
are given below.

1. In canning industry, Clostridium butylicum is the chief concern. This obligate anaerobe can grow in sealed cans, and produce heat
resistant spores and a deadly toxin. However, it is not a problem for catsup (too acidic), jam and jellies (too high sugar concentration) and
milk (stored at low temperature).
2. Organisms like lactobacillus are a problem in production of wine.
3. In antibiotic industry, potential contaminants are many, e.g., molds, yeast, and many bacteria, including Bacillus.
4.The most dreaded contaminants of fermentation industry are phages. The only effective protection against phages is to develop resistant
strains.

Sterilization Procedures - Sterilization involves either inactivation or removal of living organisms. This may be achieved by
(i) heating,
(ii) irradiation.
(iii) Chemicals or
(iv) filtration; these are briefly discussed below.

Heating. It is the most commonly used and the least expensive sterilizing agent. Dry heat is used in ovens and is suitable for sterilization
of solids, which can withstand the high temperatures needed for sterilization, e.g., laboratory glassware, talc, etc. Steam, i.e., moist or wet
heat, is used for sterilization of media and fermenter vessels.
An autoclave uses steam for sterilization (at 121°C and 15p.s.i.). the period of time at this temperature pressure depending on medium
volume, e.g., 12-15 min for 200 mi. 17-22 min for 500 ml, 20-25 min for 1 I and 30-35 min for 2 l. But sterilization of oils will require a
few hours, and concentrated media (10-20% solid) must be agitated for effective sterilization.
Autoclaves can also be used to sterilize laboratory vessels, small volumes of media and even small fermenters.Large fermenters are
sterilized by either a direct injection of steam or by indirect heating by passing steam through heat exchange coils or a jacket. The steam
should always be saturated.
Media sterilization may be achieved in a continuous flow sterilization system either by direct steam injection or by indirect steam heating,
and then filled in a sterile fermenter. Alternatively, the medium may be filled in the fermenter and steam-sterilized with the latter.
Heat killing in most part is due to protein inactivation. In general, moist heat is far superior to dry heat. Bacterial spores are the most heat
resistant, e.g., spores of thermophilic bacteria can survive steam at 30p.s.i. at 134°C for 1-10 min and dry heat at 180°C for up to 15 min.

Radiation. High energy X-rays are used for sterilization of a variety of labware and of food. In general, vegetative cells are much more
susceptible than bacterial spores (Clostridium spores can resist nearly 0.5 M rad). But Deinococcus radiodurans vegetative cells can
survive 6 M rad.
Viruses are usually similar to bacterial spores but some viruses, e.g., encephalitis virus require up to 4.5 M rad. In practice, 2.5 M rad is
used for sterilizing pharmaceutical and medical products. X-rays cause inactivation by inducing single and doublestrand DNA breaks, and
by producing free radicals and peroxides, to which -SH enzymes are particularly susceptible.

Chemicals. The chemicals used for sterilization cause inactivation by oxidation or alkylation; these are formaldehyde, H2O2, ethylene
oxide, propylene oxide etc. H2O2 (10-25% w/v) is being increasingly used in the sterilization of milk and of containers for food products.
It is a powerful oxidizing agent, kills both vegetative cells and spores and is very safe. Ethylene oxide is used for sterilizing equipments,
which are likely to be damaged by heat, and is very effective, but highly toxic and violently explosive if mixed with air.

Filtration. Aerobic fermentation requires a very high rate of air supply often equaling 1 vol of air (equal to medium volume) every minute.
Air contains both fungal spores and bacteria, which are ordinarily removed by filtration using either a depth filter or a screen filter.
Depth filters are made from fibrous or powdered materials pressed or bonded together in a relatively thick layer; the materials used are
fiberglass, cotton, mineral wool, cellulose fibers, etc. in form of mats, wads or cylinders.
Modem depth filters are cylinders of bonded borosilicate microfibers. Depth filters allow higher filtration rates and efficiencies than screen
filters, but are not suitable for filtration of moist air.
Screen filters are membranes of cellulose esters or other polymers with pores of 0.45 µm or smaller (bacterial contaminants are 0.5 µm or
larger). Usually, a microfibers profiler is used with such filters to remove gross contamination.
All filters themselves must be sterilized before they can be used to sterilize the air. Filters are also used to sterilize the effluent gases from
fermenters, especially in case of pathogenic microorganisms.

Strain Improvement - After an organism producing a valuable product is identified, it becomes necessary to increase the product yield
from fermentation to minimise production costs. Product yields can be increased by
(i) developing a suitable medium for fermentation,
(ii) refining the fermentation process and
(iii) improving the productivity of the strain.

Generally, major improvements arise from the last approach; therefore, all fermentation enterprises place a considerable emphasis on this
activity. The techniques and approaches used to genetically modify strains, to increase the production of the desired product are called
strain improvement or strain development.
Strain improvement is based on the following three approaches:
(i) mutant selection,
(ii) recombination, and
(iii) recombinant DNA technology.

Mutant Selection - Large scale mutant selection programmes begin when favourable reports of clinical trials are obtained. In the early
stages, selection of spontaneous mutants may be helpful, but induced mutations are the most common sources of improvements.
Many mutations bring about marked changes in a biochemical character of practical interest; these are called major mutations. Some major
mutations can be useful in strain improvement.
For example, a mutant strain (S-604) of Streptomyces aureofaciens produces 6-demethyl tetracycline in place of tetracycline; this
demethylated form of tetracycline is the major commercial form of tetracycline.
In contrast, most improvements in biochemical production have been due to the stepwise accumulation of so called minor genes. These
genes lead to small increases (or decreases) in the antibiotic or other biochemical production, and selection may be expected to result in a
10-15% increase in yield.
The selected strains are usually subjected to successive cycles of mutagenesis and selection; after several cycles, a large increase is yield is
likely to be obtained. Mutants of Penicillium chrysogenum were selected for increased penicillin production; each cycle of selection was
preceded by Mutagen (chemical) treatment and resulted in only small changes in penicillin yield.
The two types are associated with different strains of A. tumefaciens. There is also a related disease ("hairy root disease") in which
infected tissues proliferate in root tissue and produce an opine. This disease is associated with the bacterium A. rhizogenes.
Formation of opines explains the ecological significance of tumor formation. Each strain of Agrobacterium synthesizes enzymes
(permease, dehydrogenase) that allow it to metabolize the specific type of opine formed by the tumor it induces. Thus by stimulating the
plant to form opines, the bacteria insure themselves a supply of nutrients specifically designed for them.
After several (about dozen) cycles of selection, a strain (E 15-1) was obtained that yielded 55% more penicillin than the original strain
(Fleming strain).

Selective Isolation of Mutants - A majority of desirable mutants, especially the 'minor gene' mutants, showing increased production are
isolated by screening a large number of clones surviving the mutagen treatment; this is called secondary screening. But this approach
requires a large amount of work.
Therefore, efforts have increasingly focussed on developing techniques for the isolation of particular classes of mutants, which are likely to
be overproducers.
1. Isolation of auxotrophic mutants is the basis for commercial amino acid production in Japan from the bacterium Corynebacterium
glutamicus. For example, phe- mutants of C glutamicus accumulate tyrosine.
2. Many analogue-resistant mutants have feed-back insensitive enzymes of the biosynthetic pathway the analogue of whose product was
used for selection of such cells. Such mutants tend to overproduce the end product of the concerned pathway.
3. Sometimes revertants from nonproducing mutants of a strain are high producers, e.g., one such reversion mutant of Streptomyces
viridifaciens showed over 6-fold increase in chlortetracycline production over the original strain from which the nonproducing mutant was
obtained.
4. Reversion mutants of appropriate auxotrophs may often be high producers.
5. In some cases, selection for resistance to the antibiotic produced by the organism itself may lead to increased yields.
6. Sometimes, mutants with altered cell membrane permeability show high production of some metabolites.
7. Mutants have been selected to produce altered metabolites, especially in case of aminogycoside antibiotics. For example, Pseudomonas
aureofaciens produces the antibiotic pyrrolnitrin; a mutant of this fungus yields 4'- fluoropyrrolnitrin.

Mutant selection has been the most successful approach for strain improvement, but major advances are being made in the exploitation of
other strategies, i.e., recombination and recombinant DNA technology.

Different Approaches in Utilization of Mutation and Genetic Recombination for Strain Improvement -

Approach Chief feature Example/Remark

The main approach to strain improvement; produces new
A. Mutant Selection : Types
alleles of existing genes
Used in, the initial stages of strain improvement; also for
1. Spontaneous Mutations Occur without any treatment with a mutagen
maintenance of improved strains
Induced by chemical (mainly) or physical Mutagenesis followed by selection; several cycles
2. Induced Mutations
mutagens employed
Production of 6-demethyl tetracycline in place of
3. Major Mutations Affect the pattern of metabolite production
tetracycline by S. aureofaciens
Small gains in each cycle of selection; substantial
4. Minor Mutations Affect the rate metabolite production
improvement after several cycles
B. Mutant Selection :Strategies
Enhanced production of an amino acid, e.g., phe mutants
1. Auxotrophic mutants Defective biosynthesis of a biochemical
accumulate tyrosine
Overproduction of metabolites, e.g., amino acids by C.
2. Analogue resistant mutants Feedback insensitive enzymes
glutamicus
Some mutants are high producers, e.g., chlortetracycline
3. Revertants of nonproducing mutants
by S. viridifaciens
Some are high produces, e.g. chlortetracycline by S.
4. Revertants of auxotrophic mutants
viridifaciens
5. Resistance to the antibiotic produced Increased production, e.g., chlortetracycline by S.
by the organism itself aureofaciens
C. Recombination Produces new combinations of existing alleles
1. Sexual reproduction Conjugation; fusion of gametes Some bacteria and Actinomycetes; fungi and yeast
Nuclear fusion followed, by mitotic
2. Heterokaryosis Fungi
recombination and mitotic reduction
Protoplasts produced by lytic enzymes fusion
3. Protoplast fusion Bacteria, Actinomycetes, fungi; quite; successful
by PEG, recombinant recovery

Bioreactors - A bioreactor is a device in which a substrate of low value is utilized by living cells or enzymes to generate a product of
higher value. Bioreactors are extensively used for food processing, fermentation, waste treatment, etc. On the basis of the agent used,
bioreactors are grouped into two broad classes:
(i) those based on living cells and,
(ii) those employing enzymes.

But in terms of process requirements, they are of the following types:

(i) aerobic,
(ii) anaerobic,
(iii) solid state, and
(iv) immobilized cell bioreactors.

All bioreactors deal with heterogeneous systems having two or more phases, e.g., liquid, gas, solid. Therefore, optimal conditions for
fermentation necessitate efficient transfer of mass, heat and momentum from one phase to the other.
A bioreactor should provide for the following:
(i) agitation (for mixing of cells and medium),
(ii) aeration (aerobic fermenters; for O2 supply),
(iii) regulation of factors like temperature, pH, pressure, aeration, nutrient feeding, liquid level, etc.,
(iv) sterilization and maintenance of sterility, and
(v) withdrawal of cells/medium (for continuous fermenters). Modem fermenters are usually integrated with computers for efficient process
monitoring, data acquisition, etc.
The size of fermenters ranges from 1-21 laboratory fermenters to 500,000 1 or, occasionally, even more; fermenters of upto 1.2 million
litres have been used. Generally, 20-25% of fermenter volume is left unfilled with medium as "head space" to allow for splashing, foaming
and aeration. The fermenter design varies greatly depending on the type of fermentation for which it is used.

Immobilized Cell Bioreactors - Bioreactors of this type are based on immobilized cells. Cell immobilization is advantageous when

(i) the enzymes of interest are intracellular,

(ii) extracted enzymes are unstable,
(iii) the cells do not have interfering enzymes or such enzymes are easily inactivated/removed and
(iv) the products are low molecular weight compounds released into the medium.

Under these conditions, immobilized cells offer the following advantages over enzyme immobilization:

(i) enzyme purification is not needed,

(ii) high activity of even unstable enzymes,
(iii) high operational stability,
(iv) lower cost and
(v) possibility of application in multistep enzyme reactions. In addition, immobilization permits continuous operation of bioreactor, which
reduces the reactor volume and, consequently, pollution problems. Obviously, immobilized cells are used for such biotransformations of
compounds, which require action of a single enzyme.
Cell immobilization may be achieved in one of the following ways.
(1) Cells may be directly bound to water insoluble carriers, e.g., cellulose, dextran, ion exchange resins, porous glass, brick, sand, etc., by
adsorption, ionic bonds or covalent bonds.
(2) They can be cross linked to bi- or multifunctional reagents, e.g., glutaraldehyde, etc.
(3) Polymer matrices may be used for entrapping cells; such matrices are polyacrylamide cell, ҝ-carrageenan (a polysaccharide isolated
from a seaweed), calcium alginate (alginate is extracted from seaweed), poly glycol oligomers, etc.
Out of these approaches, calcium alginate immobilization is the most commonly used since it can be used for even very sensitive cells.
Cell immobilization has been used for commercial production of amino acids, organic acids, etc.

Bioreactor Media - The medium composition is as critical to product yields as high producing strains of microorganisms. The medium not
only provides the nutrients needed for microbial growth but also for the metabolite production.
The organisms vary greatly in their nutrient requirements from autotrophs, which produce all the biochemicals required from simple
inorganic nutrients deriving their energy from oxidation of some inorganic component of the medium to the difficult organisms like lactic
acid bacteria, which require many organic compounds for their growth.
The various media may be grouped into two broad categories:
(i) synthetic and
(ii) complex.

A synthetic or chemically defined medium is desirable for various studies, but product yields from such media are generally low. Foaming
is not a problem with such media. The complex media contain undefined constituents like soybean meal, molasses, corn steep liquor, etc.,
and give much higher yields of metabolites.
Carbon source can be simple, e.g., sugar, alcohol, etc., or complex carbohydrates, proteins, molasses, potatoes, sweet potatoes, etc. In
many processes, precursors need to be provided, e.g., phenylacetic acid for penicillin G, inorganic cobalt for vit. B12.
Buffers are also added to prevent drastic changes in pH, and anti foam would often be needed when complex media are used. For much
fermentation, e.g., antibiotic production, medium suited for rapid cell growth is unsuitable for product formation. In such cases, specialized
media for production have to be devised.

Downstream Processing - The various processes used for the actual recovery of useful products from a fermentation or any other
industrial process is called downstream processing. The cost of downstream processing (DSP) is often more than 50% of the
manufacturing cost, and there is product loss at each step of DSP.

Therefore, the DSP should be efficient, involve as few steps as possible (to avoid product loss), and be cost-effective. The various steps in
DSP are as follows:
(i) separation of particles,
(ii) disintegration of cells,
(iii) extraction,
(iv) concentration,
(v) purification and
(vi) drying.
Separation of Particles - The first step in DSP is the separation of solids, usually cells, from the liquid medium. This is generally
achieved as follows.
Filtration. It is used for the separation of filamentous fungi and filamentous bacteria, e.g., streptomycetes, and often for yeast flocks. The
various techniques of filtration employed are, surface filtration, depth filtration, centrifugal filtration, cross flow filtration, and rotary drum
vacuum filtration.
Centrifugation. It may be used to separate bacteria and usually protein precipitates. But difficulties arise due to small differences in the
densities of the particles and the medium. In addition, equipment cost, power consumption, temperature, etc. are the other disadvantages.
Flocculation and Floatation. Flocculation, i.e., sticking together of cells, can be induced by inorganic salts, mineral hydrocolloids are
organic polyelectrolytes. Since sedimentation rate of a particle increases with size, flocculated cells can be recovered by centrifugation.
In cases, where flocculation is not effective, very fine gas bubbles can be created by sparging, release of overpressure or electrolysis. The
gas bubbles adsorb to and surround the cells, raising them to the surface of medium in form of foam (floatation); long chain fatty acids or
amines promote stable foam formation.
The cells collected in the foam are readily recovered. Flocculation and floatation are used for the most efficient recovery of microbial
biomass in some single cell protein production systems.

Antibiotic Preparation - Antibiotics are metabolites having preferential antimicrobial activity. Therefore, they are widely used for curing
of human ailments caused by microorganisms. But some of the antibiotics have antitumour activity as well.
The antibiotic penicillin was discovered by Fleming in 1929, but its commercial production could commence only during early 1940s.
Although more than 7000 antibiotic compounds have been isolated, only 100 or so are being used to treat human, animal and plant
diseases.
Antibiotic compounds are used either in their natural form or as semisynthetic derivatives the latter are usually produced by isolating the
antibiotic nucleus and its chemical modification. Antibiotics are produced by both fungi and bacteria but over 50% of them are obtained
from Streptomyces alone.
Inoculum. A high yielding strain is a prerequisite for antibiotic production. Therefore, constant strain improvement is an integral part of
commercial production activities. Inoculum development begins on specific solid media, and subsequently specific liquid media are used.
The inoculum is prepared usually in the form of a spore suspension, which is transferred into the fermenters. As a rule, the number of
stages between the preserved material and the final inoculum stage is kept to the minimum to minimise the risk of the organism losing its
high yield potential.
Fermenter. Antibiotics are generally produced in stainless steel fermenters (30,000-200,000 1 medium volume) used in the batch or fed
batch mode. Agitation is mostly by impellers, but air-lift system is also used. Water cooling is often used to maintain the temperature
between 24-26°C for most antibiotic producers.
Generally, the fermenter is maintained at above atmospheric pressure; this reduces contamination risk and enhances O2 supply in the
medium. Sterile air is supplied as per need, and for some processes, e.g., penicillin production, materials need to be added throughout the
process. In most cases, it is critical to prevent contamination, and suitable cleaning procedures between fermenter runs must be adhered to.
The final stage fermenter is preferably used for antibiotic production for the longest possible period. But the initial stages of fermentation
are designed for considerable microbial growth; typically, these are carried out in seed stage fermenters of smaller size.
One or more seed-stages may be used, depending on the process and the strain, to produce the maximum amount of biomass in the correct
physiological state for high antibiotic production when introduced in the final stage fermenter.
Production Medium. Antibiotic production employs a variety of media, a different one for each stage of operation. A considerable
research effort is directed at the developing seed-stage and production media to reduce costs and to enhance yields. A typical production
medium has about 10% (w/v) solids.
Generally, yields are much higher on complex media. In some cases, a suitable precursor for the antibiotic is also provided, e.g., for
penicillin G production phenylacetic acid or phenoxyacetic acid is used as precursor.
Since the antibiotics are secondary metabolites, the production medium is so designed that a key nutrient becomes limiting at a critical
stage to initiate the secondary metabolism in the organism. The nutrient to be made limiting depends on the process, e.g., glucose for
penicillin production and phosphate for several antibiotics produced by Streptomyces.
In most production processes, the production fermenter is run in a fed batch mode in which a nutrient, e.g., glucose, is added continuously
throughout the fermentation to enhance the duration of antibiotic production. In such a case, small volumes of broth are usually withdrawn
to check increase in volume of the broth in the fermenter.
Antifoaming agents are added at the appropriate stage of fermentation to minimise foaming; silicones, vegetable oils, etc. are used for this
purpose. Selected microbiological, physical and chemical features are monitored during the fermentation in order to achieve a proper
control on the process.
The nutritional status of broth is monitored regularly to adjust nutrient and precursor (if any) feeding in fed-batch systems.
Microprocessors and computers are commonly used to record all the parameters and process changes, and to control various operations
like sterilization, etc.
At the end of final production stage incubation, the broth contains only a low concentration (3-35% of the total solutes in the broth) of the
antibiotic. The initial step in antibiotic recovery is separation of cells from the broth; this is usually achieved by filtration or centrifugation.
But in some cases, the whole broth is used for extraction. Antibiotic isolation and purification employs solvent extraction, ion exchange,
ultrafiltration, reverse osmosis, precipitation and crystallization.

List of Antibiotics Produced Commercially -

Antibiotic Produced by Activity Chemical Nature
Cephalosporin C Cephalosporium acremonium Gram+ and - bacteria Peptide
Gentamycin Micromonospora purpurea Gram+ bacteria Aminoglycoside
Griseofulvin Penicillium griseofulvum Gram+ and - bacteria Spirolactone
Kanamycin S. kanamyceticus Gram+ and - bacteria, and mycobacteria Aminoglycoside
Neomycins S. fradiae Gram+ and - bacteria Aminoglycoside
Pimaricin S. natalensis Antitumour Polyene
Penicillin G P. chrysogenum Gram+ bacteria Peptide
Polymixin B Bacillus polymyxa Antifungal Peptide
Streptomycin S. griceus Gram+ and - bacteria, and mycobacteria Aminoglycoside
Tetracyclines Streptomyces spp Gram+ and - bacteria Tetracycline

Media Used in the Different Stages of Antibiotic Production -

Stage Medium Constituents

Storage of spores Buffered salt, or glucose (10-20%), or glycerol (10-20%) solution

Growth and sporulation Carbohydrate (0.5-2%), N-source (0.2-1 %), chalk (0-1 %), NaCi (0-0.5%), phosphate (0-1 %), various salts, solid
support (e.g., rice, perlite, agar, etc.)
Spore recovery from solid Water/buffer solution; usually a surfactant is used
surface
Shaker-flask testing Lactose (5-8%), csL* (5-8%), chalk (0-1.6%), ammonium sulphate (0-0.5%), phenylacetic acid (added daily)
Seed-stage fermenter (growth Sugar (glucose, sucrose or lactose; 3-5%), Pharmamedia (2-5%), and/or CSL (3-5%), chalk (0-1 %), phosphate (0-
medium) 1 %), ammonium sulphate (0-0.5%), edible oil (0-0.5%)
Final stage fermenter Sugar (5-10%), CSL (5-9%) and/or Pharmamedia (35%), chalk (0-1 %), ammonium sulphate (0-1 %), phosphate
(production medium)** (0-0.5%), edible oil (0.3-0.8%), phenylacetic acid/ phenoxyacetic acid (0.3-0.6%)

Biotransformation of Antibiotics - Biotransformation is routinely used for commercial production of several useful antibiotics.
Semisynthetic antibiotics, e.g., semisynthetic penicillin and cephalosporins, are produced by chemical modification of the penicillin
nucleus, e.g., 6-aminopenicillanic acid. The penicillin nucleus is produced by microbial deacylation of naturally produced penicillin G and
penicillin V
Enzymes - Enzymes are proteins, which catalyse specific biochemical reactions in a very efficient manner. Enzymes have been used for
thousands of years as crude animal and plant preparations or as whole microorganisms, which were allowed to grow on substrates.
The industrial production of enzymes dates back to 1894 when 'fungal taka diastase was marketed for pharmaceutical use. Initially,
enzymes were produced by solid state fermentation, which is still used in Japan. But most current production processes are based on
submerged cultures, which are effectively aerated; the O2 requirement is generally as high as that for antibiotics.
Most industrially important enzymes are extracellular, which makes their recovery from the broth relatively easier. A number of enzymes
are produced on large scale and used in commercial operations.

List of Some Enzymes Used for Commercial Activities -

Enzyme Source Application Use in the Form

α - Amylase 1. Bacillius licheniformis Hydrolysis of starch to dextrans Extracellular, soluble
2. B.amylolique faciens
Glucoamylase Aspergillus niger Dextran hydrolysis to glucose Extracellular, soluble
Xylose (Glucose) isomerase Bacillus coagulans* Pure glucose to equilibrium mixture of glucose + fructose Immobilized whole cells
Alkaline Protease B. licheniformis, Detergents (protein digestion) Extracellular, soluble
B.subtilis
Neutral Protease B.amylolique faciens, Protein digestion in brewing substances Extracellular, soluble
B.subtilis
Acid Protease, e.g., rennet A. niger** Milk coagulation and cheese flavour enhancement Extracellular, soluble
Pectinase A. niger, Pectin hydrolysis in fruit juices Extracellular, soluble
B.subtilis
Glucanase A. niger, In fruit juices Extracellular, soluble
B.subtilis
Cellulase A.niger, Trichoderma reesei Cellulose hydrolysis in fruit juices Extracellular, soluble
Lipase Rhizopus Species Detergents, lipid hydrolysis Extracellular, soluble
Lactase A.niger Milk lactose hydrolysis to glucose Immobilized on glass beads

Fermentation - Inoculum is developed in several stages as is the case with other fermentations. The organism may then be multiplied in
one or more seed tank stages. The medium used for these stages is rather rich to support good growth.
The seed tank culture is finally inoculated into the production stage fermenter (25,000-100,000 1).The production medium is almost
always complex and is devised to maximise yields of the enzyme. Appropriate measures must be employed to ensure contamination
control.
Biomass of the organism begins to increase early during fermentation, while enzyme activity shows significant increases about midway
through the fermentation; the end of fermentation is signaled by cessation of enzyme synthesis.
Isolation and Purification - Isolation and purification is done immediately after termination of fermentation in a manner that retains the
enzyme activity. If the cells are to be used for immobilization, the biomass is isolated and treated to make it ready for use.
The extracellular enzymes are recovered directly from broth, while enzymes localized within cells are isolated by rupturing the cells.
Enzyme purification is based on various techniques whose efficacy and cost differ widely; the process used will mainly depend on the
purity needed and the cost, which is acceptable.

Types of Fermentation Process - The fermentation unit in industrial microbiology is analogous to a chemical plant in the chemical
industry. A fermentation process is a biological process and, therefore, has requirements of sterility and use of cellular enzymic reactions
instead of chemical reactions aided by inanimate catalysts, sometimes operating at elevated temperature and pressure.
Industrial fermentation processes may be divided into two main types, with various combinations and modifications. These are batch
fermentations and continuous fermentations

Batch Fermentation Process

A tank of fermenter is filled with the prepared mash of raw materials to be fermented. The temperature and pH for microbial fermentation
is properly adjusted, and occasionally nutritive supplements are added to the prepared mash. The mash is steam sterilized in a pure culture
process. The inoculum of a pure culture is added to the fermenter, from a separate pure culture vessel.
Fermentation proceeds, and after the proper time the contents of the fermenter, are taken out for further processing. The fermenter is
cleaned and the process is repeated. Thus each fermentation is a discontinuous process divided into batches

Continous Fermentation Process - Growth of microorganisms during batch fermentation confirms to the characteristic growth curve,
with a lag phase followed by a logarithmic phase. This, in turn, is terminated by progressive decrements I in the rate of growth until the
stationary phase is reached. This is because of limitation of one or more of the essential nutrients.
In continuous fermentation, the substrate is added to the fermenter contillously at a fixed rate. This maintains the organisms in the
logarithmic growth phase. The fermentation products are taken out continuously. The design and arrangements for continuous
fermentation, are some what complex.

Solid State Fermentation –Semi Solid OR Solid State Methods - In this the culture medium is impregnated in a carrier such as bagasse,
wheat bran, potato pulp, etc. and the organism is allowed to grow on this. This method allows greater surface area for growth. The
production of the desirable substance and the recovery is generally easier and satisfactory.
In the development of a fermentation process, the composition of the culture medium plays a major role and will determine to a very great
extent the level of end product. For example, a culture medium containing sucrose enables better production of citric acid by A. niger than
any other carbohydrate. The pH, temperature of incubation, aeration etc., are all important factors in fermentations and these have to be
optimized for each type of fermentation. Emphasis is generally placed on the use of cheap raw materials so that the cost of production is
low.
In such fermentations, microbial growth and product formation occur at the surface of solid substrates. Examples of such fermentations
are mushroom cultivation, mold ripened cheeses, starter cultures, etc. More recently, this approach has been used for the production of
extracellular enzymes, certain valuable chemicals, fungal toxins, and fungal spores (used for biotransformation).
Traditional substrates are several agricultural products, rice, wheat, maize, soybean, etc. The substrate provides a rich and complex source
of nutrients, which mayor may not need to be supplemented.
Such substrates selectively support mycelial organisms, which can grow at high nutrient concentrations and produce a variety of
extracellular enzymes, e.g., a large number of filamentous fungi, and a few bacteria (Actinomycetes and one strain of Bacillus).
According to the physical state, solid state fermentations are divided into two groups:
(i) low moisture solids fermented without or with occasional/continuous agitation, and
(ii) suspended solids fermented in packed columns, through which liquid is circulated. The fungi used for solid state fermentations are
usually obligate aerobes.
Solid state fermentations on large scale use stationary or rotary trays. Temperature and humidity controlled air is circulated through the
stacked solids. Less frequently, rotory drum type fermenters have been used.
Solid state fermentations offer certain unique advantages, but suffer from some important disadvantages. However, commercial application
of this process for biochemical production is chiefly confined to Japan.

Anaerobic Fermentation –Basically a fermenter designed to operate under micro acrophilic or anaerobic conditions will be the same as
that designed to operate under aerobic conditions, except that arrangements for intense agitation and aeration are unnecessary
Many anaerobic fermentations do, how ever, require mild aeration for the initial growth phase, and sufficient agitation for mixing and
maintenance of temperature.
In anaerobic fermentation, a provision for aeration is usually not needed. But in some cases, aeration may be needed initially for
inoculum build up. In most cases, a mixing device is also unnecessary; while in some cases initial mixing of the inoculum is necessary.
Once the fermentation begins, the gas produced in the process generates sufficient mixing.
The air present in the headspace of the fermentor should be replaced by CO2, H2, N2 or a suitable mixture of these; this is particularly
important for obligate anaerobes like Clostridium.
The fermentation usually liberates CO2 and H2, which are collected and used, e.g., CO2 for making dry ice and methanol, and for
bubbling into freshly inoculated fermenters.
In case of acetogens and other gas utilizing bacteria, O2free sterile CO2 or other gases are bubbled through the medium. Acetogens have
been cultured in 400 I fermenters by bubbling sterile CO2 and 3, kg cells could be harvested in each run.
Recovery of products from anaerobic fermenters does not require anaerobic conditions. But many enzymes of such organisms are highly
O2, sensitive. Therefore, when recovery of such enzymes is the objective, cells must be harvested under strictly anaerobic conditions.

Aerobic Fermentation –A number of industrial processes, although called 'fermentations', are carried on by microorganisms under
aerobic conditions. In older aerobic processes it was necessary to furnish a large surface area by exposing fermentation media to air.
In modern fermentation processes aerobic conditions are maintained in a closed fermenter with submerged cultures. The contents of the
fermenter are agitated with an impeller and aerated by forcing sterilized air
The main feature of aerobic fermentation is the provision for adequate aeration; in some cases, the amount of air needed per hour
is about 60-times the medium volume. Therefore, bioreactors used for aerobic fermentation have a provision for adequate supply of sterile
air, which is generally sparged into the medium.
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.
Generally, these bioreactors are of closed or batch type, but continuous flow reactors are also used such reactors provide a continuous
source of cells and are also suitable for product generation when the product is released into the medium

Surface Culture Method - In this method the organism is allowed to grow on the surface of a liquid medium without agitation. After an
appropriate incubation period the culture filtrate is separated from the cell mass and is processed to recover the desirable product.
Sometimes the biomass may be reused. Examples of such fermentations are the alcohol production, the beer production and citric acid
production. This method is generally time consuming and needs large, area or space.

Submerged Culture Method - In this process, the organism is grown in a liquid medium which is vigorously aerated and agitated in large
tanks called fermentors. The fermentor could be either an open tank or a closed tank and may be a batch type or a continuous type and are
generally made of non-corrosive type of metal or glass lined or of wood.
In batch fermentation, the organism is grown in a known amount of culture medium for a defined period of time and then the cell mass is
separated from the liquid before further processing while in the continuous culture, the culture medium is withdrawn depending on the rate
of product formation and the inflow of fresh medium. Most fermentation industries today use the submerged process for the production of
microbial products.

Important uses of industrial micro-organisms

Product Micro-organism Use

Vitamin B12 Streptomyces vitamin supplements
Lactic Acid Lactobacillius delbrueckii chemical reagents
Citric Acid Aspergillus niger food preservative
Ethanoic Acid Acetobacter sp. vinegar, solvent
Pectinases Micriorganism Aspergillus sp. degrading pectin
Ethanol Saccharomyces chemical reagents, drinks

Penicillin Penicillin chrysogenum antibiotic