Modern Industrial Microbiology and Biotechnology

Preface
SECTION A INTRODUCTION
1. Introduction: Scope of Biotechnology and
Industrial Microbiology
1.1 Nature of Biotechnology and Industrial Microbiology
1.2 Characteristics of Industrial Microbiology
1.2.1 Industrial vs medical microbiology
1.2.2 Multi-disciplinary or Team-work nature of
industrial microbiology
1.2.3 Obsolescence in industrial microbiology
1.2.4 Free communication of procedures in industrial microbiology
1.3 Patents and Intellectual Property Rights in
Industrial Microbiology and Biotechnology
1.4 The Use of the Word `Fermentation’ in Industrial Microbiology
1.5 Organizational Set-up in an Industrial Microbiology Establishment
Suggested Readings
SECTION B BIOLOGICAL BASIS OF PRODUCTIVITY IN
INDUSTRIAL MICROBIOLOGY AND BIOTECHNOLOGY
2. Some Microorganisms Commonly Used in
Industrial Microbiology and Biotechnology
2.1 Basic Nature of Cells of Living Things
2.2 Classification of Living Things: Three Domains of Living Things
2.3 Taxonomic Grouping of Micro-organisms Important in
Industrial Microbiology and Biotechnology
2.3.1 Bacteria
2.3.2 Eucarya: Fungi
2.4 Characteristics Important in Microbes Used in
Industrial Microbiology and Biotechnolgy
Suggested Readings
3. Aspects of Molecular Biology and Bioinformatics of
Relevance in Industrial Microbiology and Biotechnology
3.1 Protein Synthesis
3.2 The Polymerase Chain Reaction
3.2.1 Some applications of PCR in industrial microbiology and
biotechnology
3.3 Microarrays
3.3.1 Applications of microarray technology
3.4 Sequencing of DNA
3.4.1 Sequencing of short DNA fragments
3.4.2 Sequencing of genomes or large DNA fragments
3.5 The Open Reading Frame and the Identification of Genes
3.6 Metagenomics
3.7 Nature of Bioinformatics
3.7.1 Some contributions of bioinformatics to biotechnology
Suggested Readings
4. Industrial Media and the Nutrition of Industrial Organisms
4.1 The Basic Nutrient Requirements of Industrial Media
4.2 Criteria for the Choice of Raw Materials Used in Industrial Media
4.3 Some Raw Materials Used in Compounding Industrial Media
4.4 Growth Factors
4.5 Water
4.6 Some Potential Sources of Components of Industrial Media
4.6.1 Carbohydrate sources
4.6.2 Protein sources
4.7 The Use of Plant Waste Materials in Industrial Microbiology Media:
Saccharification of Polysaccharides
4.7.1 Starch
4.7.2 Cellulose, hemi-celluloses and lignin in plant materials
Suggested Readings
5. Metabolic Pathways for the Biosynthesis of
Industrial Microbiology Products
5.1 The Nature of Metabolic Pathways
5.2 Industrial Microbiological Products as Primary and Secondary Metabolites
5.2.1 Products of primary metabolism
5.2.2 Products of secondary metabolism
5.3 Trophophase-idiophase Relationships in the Production of
Secondary Products
5.4 Role of Secondary Metabolites in the Physiology of
Organisms Producing Them
5.5 Pathways for the Synthesis of Primary and Secondary Metabolites of
Industrial Importance
5.5.1 Catabolism of carbohydrates
5.5.2 The Catabolism of hydrocarbons
5.6 Carbon Pathways for the Formation of Some
Industrial Products Derived from Primary Metabolism
5.6.1 Catabolic products
5.6.2 Anabolic products
5.7 Carbon Pathways for the Formation of Some Products of
Microbial Secondary Metabolism of Industrial Importance
Suggested Readings
6. Overproduction of Metabolites of Industrial Microorganisms
6.1 Mechanisms Enabling Microorganisms to Avoid Overproduction of
Primary Metabolic Products Through Enzyme Regulation
6.1.1 Substrate induction
6.1.2 Catabolite regulation
6.1.3 Feedback regulation
6.1.4 Amino acid regulation of RNA synthesis
6.1.5 Energy charge regulation
6.1.6 Permeability control
6.2 Derangement or Bypassing of Regulatory Mechanisms for
the Over-production of Primary Metabolites
6.2.1 Metabolic control
6.2.2 Permeability
6.3 Regulation of Overproduction in Secondary Metabolites
6.3.1 Induction
6.3.2 Catabolite regulation
6.3.3 Feedback regulation
6.3.4 ATP or energy charge regulation of secondary metabolites
6.4 Empirical Methods Employed to Disorganize Regulatory
Mechanisms in Secondary Metabolite Production
Suggested Readings
7. Screening for Productive Strains and Strain
Improvement in Biotechnological Organisms
7.1 Sources of Microorganisms Used in Biotechnology
7.1.1 Literature search and culture collection supply
7.1.2 Isolation de novo of organisms producing
metabolites of economic importance
7.2 Strain Improvement
7.2.1 Selection from naturally occurring variants
7.2.2 Manipulation of the genome of
industrial organisms in strain improvement
Suggested Readings
8. The Preservation of the Gene Pool in
Industrial Organisms: Culture Collections
8.1 The Place of Culture Collections in
Industrial Microbiology and Biotechnology
8.2 Types of Culture Collections
8.3 Handling Culture Collections
8.4 Methods of Preserving Microorganisms
8.4.1 Microbial preservation methods based on the
reduction of the temperature of growth
8.4.2 Microbial preservation methods based on dehydration
8.4.3 Microbial preservation methods based on the
reduction of nutrients
8.4.4 The need for experimentation to determine the
most appropriate method of preserving an organism
Suggested Redings
SECTION C BASIC OPERATIONS IN INDUSTRIAL FERMENTATIONS
9. Fermentors and Fermentor Operation
9.1 Definition of a Fermentor
9.2 The Aerated Stirred Tank Batch Fermentor
9.2.1 Construction materials for fermentors
9.2.2 Aeration and agitation in a fermentor
9.2.3 Temperature control in a fermentor
9.2.4 Foam production and control
9.2.5 Process control in a fermentor
9.3 Anerobic Batch Fermentors
9.4 Fermentor Configurations
9.4.1 Continuous fermentations
9.5 Fed-batch Cultivation
9.6 Design of New Fermentors on the
Basis of Physiology of the Organisms: Air Lift Fermentors
9.7 Microbial Experimentation in the Fermentation Industry:
The Place of the Pilot Plant
9.8 Inoculum Preparation
9.9 Surface or Solid State Fermentors
Suggested Readings
10. Extraction of Fermentation Products
10.1 Solids (Insolubles) Removal
10.1.1 Filtration
10.1.2 Centrifugation
10.1.3 Coagulation and flocculation
10.1.4 Foam fractionation
10.1.5 Whole-broth treatment
10.2 Primary Product Isolation
10.2.1 Cell disruption
10.2.2 Liquid extraction
10.2.3 Dissociation extraction
10.2.4 Ion-exchange adsorption
10.2.5 Precipitation
10.3 Purification
10.3.1 Chromatography
10.3.2 Carbon decolorization
10.3.3 Crystallization
10.4 Product Isolation
10.4.1 Crystalline processing
10.4.2 Drying
Suggested Readings
11. Sterility in Industrial Microbiology
11.1 The Basis of Loss by Contaminants
11.2 Methods of Achieving Sterility
11.2.1 Physical methods
11.2.2 Chemical methods
11.3 Aspects of Sterilization in Industry
11.3.1 The sterilization of the fermentor and its accessories
11.3.2 Media sterilization
11.4 Viruses (Phages) in Industrial Microbiology
11.4.1 Morphological grouping of bacteriophages
11.4.2 Lysis of hosts by phages
11.4.3 Prevention of phage contamination
11.4.4 Use of phage resistant mutants
11.4.5 Inhibition of phage multiplication with chemicals
11.4.6 Use of adequate media conditions and other practices
Suggested Readings
SECTION D ALCOHOL-BASED FERMENTATION INDUSTRIES
12. Production of Beer
12.1 Barley Beers
12.1.1 Types of barley beers
12.1.2 Raw materials for brewing
12.1.3 Brewery processes
12.1.4 Beer defects
12.1.5 Some developments in beer brewing
12.2 Sorghum Beers
12.2.1 Kaffir beer and other traditional sorghum beers
Suggested Readings
13. Production of Wines and Spirits
13.1 Grape Wines
13.1.1 Processes in wine making
13.1.2 Fermentation
13.1.3 Ageing and storage
13.1.4 Clarification
13.1.5 Packaging
13.1.6 Wine defects
13.1.7 Wine preservation
13.1.8 Classification of wines
13.2 Palm Wine
13.3 The Distilled Alcoholic (or Spirit) Beverages
13.3.1 Measurement of the alcoholic strength of distilled beverages
13.3.2 General principles in the production of spirit beverages
13.3.3 The spirit beverages
Suggested Readings
14. Production of Vinegar
14.1 Uses
14.2 Measurement of Acetic Acid in Vinegar
14.3 Types of Vinegar
14.4 Organisms Involved
14.5 Manufacture of Vinegar
14.5.1 The Orleans (or slow) method
14.5.2 The trickling generators (quick) method
14.5.3 Submerged generators
14.6 Processing of Vinegar
Suggested Readings
SECTION E USE OF WHOLE CELLS FOR FOOD RELATED PURPOSES
15. Single Cell Protein (SCP)
15.1 Substrates for Single Cell Protein Production
15.1.1 Hydrocarbons
15.1.2 Alcohols
15.1.3 Waste products
15.2 Microorganisms Used in SCP Production
15.3 Use of Autotrophic Microorganisms in SCP Production
15.4 Safety of Single Cell Protein
15.4.1 Nucleic acids and their removal from SCP
15.5 Nutritional Value of Single Cell Protein
Suggested Readings
16. Yeast Production
16.1 Production of Baker’s Yeast
16.1.1 Yeast strain used
16.1.2 Culture maintenance
16.1.3 Factory production
16.2 Food Yeasts
16.2.1 Production of food yeast
16.3 Feed Yeasts
16.4 Alcohol Yeasts
16.5 Yeast Products
Suggested Readings
17. Production of Microbial Insecticides
17.1 Alternatives to Chemical Insecticides
17.2 Biological Control of Insects
17.2.1 Desirable properties in organisms to be used for
biological control
17.2.2 Candidates which have been considered as
biological control agents
17.2.3 Bacillus thuringiensis Insecticidal toxin
17.3 Production of Biological Insecticides
17.3.1 Submerged fermentations
17.3.2 Surface culture
17.3.3 In vivo culture
17.4 Bioassay of Biological Insecticides
17.5 Formulation and Use of Bioinsecticides
17.5.1 Dusts
17.5.2 Liquid formulation
17.6 Safety Testing of Bioinsecticides
17.7 Search and Development of New Bioinsecticides
Suggested Readings
18. The Manufacture of Rhizobium Inoculants
18.1 Biology of Rhizobium
18.1.1 General properties
18.1.2 Cross-inoculation groups of rhizobium
18.1.3 Properties desirable in strains to be selected for
use as rhizobium inoculants
18.1.4 Selection of strains for use as rhizobial inoculants
18.2 Fermentation of Rhizobia
18.3 Inoculant Packaging for Use
18.3.1 Seed inoculants
18.3.2 Soil inoculants
18.4 Quality Control
Suggested Readings
19. Production of Fermented Foods
19.1 Introduction
19.2 Fermented Food from Wheat: Bread
19.2.1 Ingredients for modern bread-making
19.2.2 Systems of bread-making
19.2.3 Role of yeasts in bread-making
19.3 Fermented Foods Made from Milk
19.3.1 Composition of milk
19.3.2 Cheese
19.3.3 Yoghurt and fermented milk foods
19.4 Fermented Foods from Corn
19.4.1 Ogi, koko, mahewu
19.5 Fermented Foods from Cassava: Garri, Foo-Foo, Chikwuange,
Kokonte, Bikedi, and Cinguada
19.5.1 Garri
19.5.2 Foo-foo, chikwuangue, lafun, kokonte,
bikedi, and cinguada
19.6 Fermented Vegetables
19.6.1 Sauerkraut
19.6.2 Cucumbers (pickling)
19.7 Fermentations for the Production of the
Stimulant Beverages: Tea, Coffee, and Cocoa
19.7.1 Tea production
19.7.2 Coffee fermentation
19.7.3 Cocoa fermentation
19.8 Fermented Foods Derived from Legumes and Oil Seeds
19.8.1 Fermented foods from Soybeans
19.8.2 Fermented foods from beans: Idli
19.8.3 Fermented foods from Protein-rich Oil-seeds
19.8.4 Food condiments made from fish
Suggested Readings
SECTION F PRODUCTION OF METABOLITES AS BULK CHEMICALS OR
AS INPUTS IN OTHER PROCESSES
20. Production of Organic Acids and Industrial Alcohol
20.1 Organic Acids
20.1.1 Production of citric acid
20.1.2 Uses of citric acid
20.1.3 Biochemical basis of the production of citric acid
20.1.4 Fermentation for citric acid production
20.1.5 Extraction
20.1.6 Lactic acid
20.2 Industrial Alcohol Production
20.2.1 Properties of ethanol
20.2.2 Uses of ethanol
20.2.3 Denatured alcohol
20.2.4 Manufacture of ethanol
20.2.5 Some developments in alcohol production
Suggested Readings
21. Production of Amino Acids by Fermentation
21.1 Uses of Amino Acids
21.2 Methods for the Manufacture of Amino Acids
21.2.1 Semi-fermentation
21.2.2 Enzymatic process
21.2.3 Production of amino acids by the direct fermentation
21.3 Production of Glutamic Acid by Wild Type Bacteria
21.4 Production of Amino Acids by Mutants
21.4.1 Production of amino acids by auxotrophic mutants
21.4.2 Production of amino acids by regulatory mutants
21.5 Improvements in the Production of Amino Acids Using
Metabolically Engineered Organisms
21.5.1 Strategies to modify the terminal pathways
21.5.2 Strategies for increasing precursor availability
21.5.3 Metabolic engineering to improve transport of
amino acids outside the cell
21.6 Fermentor Production of Amino Acid
21.6.1 Fermentor procedure
21.6.2 Raw materials
21.6.3 Production strains
21.6.4 Down stream processing
Suggested Readings
22. Biocatalysts: Immobilized Enzymes and Immobilized Cells
22.1 Rationale for Use of Enzymes from Microorganisms
22.2 Classification of Enzymes
22.3 Uses of Enzymes in Industry
22.4 Production of Enzymes
22.4.1 Fermentation for enzyme production
22.4.2 Enzyme extraction
22.4.3 Packaging and finishing
22.4.4 Toxicity testing and standardization
22.5 Immobilized Biocatalysts: Enzymes and Cells
22.5.1 Advantages of immobilized biocatalysts in general
22.5.2 Methods of immobilizing enzymes
22.5.3 Methods for the immobilization of cells
22.6 Bioreactors Designs for Usage in Biocatalysis
22.7 Practical Application of Immobilized Biological Catalyst Systems
22.8 Manipulation of Microorganisms for Higher Yield of Enzymes
22.8.1 Some aspects of the biology of extracellular enzyme production
Suggested Readings
23. Mining Microbiology: Ore Leaching (Bioleaching) by
Microorganisms
23.1 Bioleaching
23.2 Commercial Leaching Methods
23.2.1 Irrigation-type processes
23.2.2 Stirred tank processes
23.3 Microbiology of the Leaching Process
23.4 Leaching of Some Metal Sulfides
23.5 Environmental Conditions Affecting Bacterial Leaching
Suggested Readings
SECTION G PRODUCTION OF COMMODITIES OF MEDICAL IMPORTANCE
24. Production of Antibiotics and Anti-Tumor Agents
24.1 Classification and Nomenclature of Antibiotics
24.2 Beta-Lactam Antibiotics
24.2.1 Penicillins
24.2.2 Cephalosporins
24.2.3 Other beta-lactam antibiotics
24.3 The Search for New Antibiotics
24.3.1 The need for new antibiotics
24.3.2 The classical method for searching for antibiotics:
random search in the soil
24.4 Combating Resistance and Expanding the Effectiveness of
Existing Antibiotics
24.4.1 Refinements in the procedures for
the random search for new antibiotics in the soil
24.4.2 Newer approaches to searching for antibiotics
24.5 Anti-Tumor Antibiotics
24.5.1 Nature of tumors
24.5.2 Mode of action of anti-tumor antibiotics
24.5.3 Search for new anti-tumor antibiotics
24.6 Newer Methods for Searching for Antibiotic and Anti-tumor Drugs
Suggested Readings
25. Production of Ergot Alkaloids
25.1 Nature of Ergot Alkaloids
25.2 Uses of Ergot Alkaloids and their Derivates
25.3 Production of Ergot Alkaloids
25.4 Physiology of Alkaloid Production
Suggested Readings
26. Microbial Transformation and Steroids and Sterols
26.1 Nature and Use of Steroids and Sterols
26.2 Uses of Steroids and Sterols
26.2.1 Sex hormones
26.2.2 Corticosteroids
26.2.3 Saponins
26.2.4 Heterocyclic steroids
26.3 Manufacture of Steroids
26.3.1 Types of microbial transformations in steroids and sterols
26.3.2 Fermentation conditions used in steroid transformation
26.4 Screening for Microorganisms
Suggested Readings
27. Vaccines
27.1 Nature and Importance of Vaccines
27.2 Body Defenses against Communicable Diseases
27.2.1 Innate or non-specific immunity
27.3 Traditional and Modern Methods of Vaccine Production
27.3.1 Traditional vaccines
27.3.2 Newer approaches in vaccinology
27.4 Production of Vaccines
27.4.1 Production of virus vaccines
27.4.2 Production of bacterial toxoids
27.4.3 Production of killed bacterial vaccines
27.5 Control of Vaccines
27.6 Vaccine Production versus Other Aspects of Industrial Microbiology
Suggested Readings
28. Drug Discovery in Microbial Metabolites: The Search for
Microbial Products with Bioactive Properties
28.1 Conventional Processes of Drug Discovery
28.1.1 Cell-based assays
28.1.2 Receptor binding assays
28.1.3 Enzyme assays
28.2 Newer Methods of Drug Discovery
28.2.1 Computer aided drug design
28.2.2 Combinatorial chemistry
28.2.3 Genomic methods in the search for new drugs,
including antibiotics
28.2.4 Search for drugs among unculturable microorganisms
28.4 Approval of New Antibiotic and other Drugs by the Regulating Agency
28.4.1 Pre-submission work by the pharmaceutical firm
28.4.2 Submission of the new drug to the FDA
28.4.3 Approval
28.4.4 Post approval research
Suggested Readings
SECTION H WASTE DISPOSAL
29. Treatment of Wastes in Industry
29.1 Methods for the Determination of Organic Matter Content in Waste Waters
29.1.1 Dissolved oxygen
29.1.2 The biological or biochemical oxygen demand (BOD) tests
29.1.3 Permanganate value (PV) test
29.1.4 Chemical oxygen demand (COD)
29.1.5 Total organic carbon (TOC)
29.1.6 Total suspended solids (TSS)
29.1.7 Volatile suspended solids (VSS)
29.2 Wastes from Major Industries
29.3 Systems for the Treatment of Wastes
29.3.1 Aerobic breakdown of raw waste waters
29.4 Treatment of the Sludge: Anaerobic Breakdown of Sludge
29.5 Waste Water Disposal in the Pharmaceutical Industry
Suggested Readings
Glossary
Index