Industrial Microbiology

Cover
Title Page
Copyright
Contents
Preface
Chapter 1 Historical Overview and Future Perspective
	1.1 Use of Fermentation Procedures Before the Discovery of Microorganisms (Neolithic Era = New Stone Age Until 1850)
	1.2 Investigation of Microorganisms and Beginning of Industrial Microbiology (1850 Until 1940)
	1.3 Development of New Products and Procedures: Antibiotics and Other Biomolecules (From 1940)
	1.4 Genetic Engineering Is Introduced into Industrial Microbiology (From Roughly 1980)
	1.5 Future Perspectives: Synthetic Microbiology
	References
	Further Reading
Chapter 2 Bioprocess Engineering
	2.1 Introduction
		2.1.1 Role of Bioreactors
		2.1.2 Basic Bioreactor Configurations
		2.1.3 Types of Growth Media
	2.2 Nonstructured Models
		2.2.1 Nonstructured Growth Models
			2.2.1.1 Unstructured Models
			2.2.1.2 Biotechnical Processes
		2.2.2 Modeling Fermentations
		2.2.3 Metabolic Pathways
		2.2.4 Manipulation of Metabolic Pathways
		2.2.5 Future of Pathway Design
	2.3 Oxygen Transport
		2.3.1 Aerobic versus Anaerobic Conditions
		2.3.2 kLa – Volumetric Mass Transfer Coefficient
	2.4 Heat Generating Aerobic Processes
	2.5 Product Recovery
		2.5.1 Basics
		2.5.2 In Situ Product Recovery (ISPR)
	2.6 Modeling and Simulation of Reactor Behavior
		2.6.1 Basic Approaches and Software
		2.6.2 Numerical Simulation of Bioreactor Function
		2.6.3 Contamination of Bioreactors
	2.7 Scale‐up
	References
	Further Reading
Chapter 3 Food
	3.1 Fermented Foods
		3.1.1 Food Preservation
		3.1.2 Flavor and Texture
		3.1.3 Health Benefits
		3.1.4 Economic Impact
	3.2 Microorganisms and Metabolism
		3.2.1 Fermentation Processes
		3.2.2 Starter Cultures
	3.3 Yeast Fermentations – Industrial Application of Saccharomyces Species
		3.3.1 Grain Fermentation for Ethanol Production – Beer
		3.3.2 Grain Fermentation for CO2 Production – Bread
			3.3.2.1 Yeast Preparation
		3.3.3 Fruit Fermentation – Wines and Ciders
	3.4 Vinegar – Incomplete Ethanol Oxidation by Acetic Acid Bacteria Such as Gluconobacter oxydans
		3.4.1 Substrates: Wine, Cider, and Malt
		3.4.2 Distilled (White) Vinegar
		3.4.3 Balsamic and Other Specialty Vinegars
	3.5 Bacterial and Mixed Fermentations – Industrial Application of Lactic Acid Bacteria, With or Without Yeast or Molds
		3.5.1 Milk – Cultured Milks – Buttermilk, Yogurt, Kefir, and Cheese
			3.5.1.1 Bacteriophage Contamination – Death of a Culture
		3.5.2 Meats – Sausages, Fish Sauces, and Pastes
		3.5.3 Vegetables – Sauerkrauts and Pickles, Olives
		3.5.4 Grains and Legumes – Soy Sauce, Miso, Natto, and Tempeh
		3.5.5 Cocoa and Coffee
	3.6 Fungi as Food
		3.6.1 Mushrooms
		3.6.2 Single‐Cell Protein – Fusarium venenatum
	3.7 Conclusions and Outlook
	References
	Further Reading
Chapter 4 Technical Alcohols and Ketones
	4.1 Introduction
	4.2 Ethanol Synthesis by Saccharomyces cerevisiae and Clostridium autoethanogenum
		4.2.1 Application
		4.2.2 Metabolic Pathways and Regulation
		4.2.3 Production Strains
		4.2.4 Production Processes
		4.2.5 Ethanol – Fuel of the Future?
		4.2.6 Alternative Substrates for Ethanol Fermentation by Cellulolytic Bacteria and Clostridium autoethanogenum
	4.3 1,3‐Propanediol Synthesis by Escherichia coli
		4.3.1 Application
		4.3.2 Metabolic Pathways and Regulation
		4.3.3 Production Strains
		4.3.4 Production Processes
	4.4 Butanol and Isobutanol Synthesis by Clostridia and Yeast
		4.4.1 History of Acetone–Butanol–Ethanol (ABE) Fermentation by Clostridium acetobutylicum and C. beijerinckii
		4.4.2 Application
		4.4.3 Metabolic Pathways and Regulation
		4.4.4 Production Strains
		4.4.5 Production Processes
		4.4.6 Product Toxicity
	4.5 Acetone Synthesis by Solventogenic Clostridia
		4.5.1 Application
		4.5.2 Metabolic Pathways and Regulation
		4.5.3 Production Strains
		4.5.4 Production Processes
	4.6 Outlook
	Further Reading
Chapter 5 Organic Acids
	5.1 Introduction
	5.2 Citric Acid
		5.2.1 Economic Impact and Applications
		5.2.2 Biochemistry of Citric Acid Accumulation
		5.2.3 Industrial Production by the Filamentous Fungus Aspergillus niger
		5.2.4 Yarrowia lipolytica: A Yeast as an Alternative Production Platform
	5.3 Lactic Acid
		5.3.1 Economic Impact and Applications
		5.3.2 Anaerobic Bacterial Metabolism Generating Lactic Acid
		5.3.3 Lactic Acid Production by Bacteria
		5.3.4 Lactic Acid Production by Yeasts
	5.4 Gluconic Acid
		5.4.1 Economic Impact and Applications
		5.4.2 Extracellular Biotransformation of Glucose to Gluconic Acid by Aspergillus niger
		5.4.3 Production of Gluconic Acid by Bacteria
	5.5 Succinic Acid
		5.5.1 Economic Impact and Applications
		5.5.2 Pilot Plants for Anaerobic or Aerobic Microbes
	5.6 Itaconic Acid
		5.6.1 Economic Impact and Applications
		5.6.2 Decarboxylation as a Driver in Itaconic Acid Accumulation
		5.6.3 Production Process by Aspergillus terreus
		5.6.4 Metabolic Engineering for Itaconic Acid Production
	5.7 Downstream Options for Organic Acids
	5.8 Perspectives
		5.8.1 Targeting Acrylic Acid – Microbes Can Replace Chemical Process Engineering
		5.8.2 Lignocellulose‐Based Biorefineries
	Further Reading
Chapter 6 Amino Acids
	6.1 Introduction
		6.1.1 Importance and Areas of Application
		6.1.2 Amino Acids in the Feed Industry
		6.1.3 Economic Significance
	6.2 Production of Amino Acids
		6.2.1 Conventional Development of Production Strains
		6.2.2 Advanced Development of Production Strains
	6.3 l‐Glutamate Synthesis by Corynebacterium glutamicum
		6.3.1 Synthesis Pathway and Regulation
		6.3.2 Production Process
	6.4 l‐Lysine
		6.4.1 Synthesis Pathway and Regulation
		6.4.2 Production Strains
		6.4.3 Production Process
	6.5 l‐Threonine Synthesis by Escherichia coli
		6.5.1 Synthesis Pathway and Regulation
		6.5.2 Production Strains
		6.5.3 Production Process
	6.6 l‐Phenylalanine
		6.6.1 Synthesis Pathway and Regulation
		6.6.2 Production Strains
		6.6.3 Production Process
	6.7 Outlook
	Further Reading
Chapter 7 Vitamins, Nucleotides, and Carotenoids
	7.1 Application and Economic Impact
	7.2 l‐Ascorbic Acid (Vitamin C)
		7.2.1 Biochemical Significance, Application, and Biosynthesis
		7.2.2 Regioselective Oxidation with Bacteria in the Production Process
	7.3 Riboflavin (Vitamin B2)
		7.3.1 Significance as a Precursor for Coenzymes and as a Pigment
		7.3.2 Biosynthesis by Fungi and Bacteria
		7.3.3 Production by Ashbya gossypii
		7.3.4 Production by Bacillus subtilis
		7.3.5 Downstream Processing and Environmental Compatibility
	7.4 Cobalamin (Vitamin B12)
		7.4.1 Physiological Relevance
		7.4.2 Biosynthesis
		7.4.3 Production with Pseudomonas denitrificans
	7.5 Purine Nucleotides
		7.5.1 Impact as Flavor Enhancer
		7.5.2 Development of Production Strains
		7.5.3 Production of Inosine or Guanosine with Subsequent Phosphorylation
	7.6 ?‐Carotene
		7.6.1 Physiological Impact and Application
		7.6.2 Production with Blakeslea trispora
	7.7 Perspectives
	Further Reading
Chapter 8 Antibiotics and Pharmacologically Active Compounds
	8.1 Microbial Substances Active Against Infectious Disease Agents or Affecting Human Cells
		8.1.1 Distribution and Impacts
		8.1.2 Diversity of Antibiotics Produced by Bacteria and Fungi
	8.2 ?‐Lactams
		8.2.1 History, Effect, and Application
		8.2.2 ?‐Lactam Biosynthesis
		8.2.3 Penicillin Production by Penicillium chrysogenum
		8.2.4 Cephalosporin Production by Acremonium chrysogenum
	8.3 Lipopeptides
		8.3.1 History, Effect, and Application
		8.3.2 Lipopeptide Biosynthesis
		8.3.3 Daptomycin Production by Streptomyces roseosporus
		8.3.4 Cyclosporine Production by Tolypocladium inflatum
	8.4 Macrolides
		8.4.1 History, Effect, and Application
		8.4.2 Macrolide Biosynthesis
		8.4.3 Erythromycin Production by Saccharopolyspora erythraea
	8.5 Tetracyclines
		8.5.1 History, Effect, and Application
		8.5.2 Tetracycline Biosynthesis
		8.5.3 Tetracycline Production by Streptomyces rimosus
	8.6 Aminoglycosides
		8.6.1 History, Effect, and Application
		8.6.2 Aminoglycoside Biosynthesis
		8.6.3 Tobramycin Production by Streptomyces tenebrarius
	8.7 Claviceps Alkaloids
		8.7.1 History, Effect, and Application
		8.7.2 Alkaloid Biosynthesis
		8.7.3 Ergotamine Production by Claviceps purpurea
	8.8 Perspectives
		8.8.1 Antibiotic Resistance
		8.8.2 New Research Model for Compound Identification
		8.8.3 Future Opportunities
	Further Reading
Chapter 9 Pharmaceutical Proteins
	9.1 History, Main Areas of Application, and Economic Importance
	9.2 Industrial Expression Systems, Cultivation and Protein Isolation, and Legal Framework
		9.2.1 Development of Production Strains
		9.2.2 Isolation of Pharmaceutical Proteins
		9.2.3 Regulatory Requirements for the Production of Pharmaceutical Proteins
	9.3 Insulins
		9.3.1 Application and Structures
		9.3.2 Manufacturing Processes by Escherichia coli and Saccharomyces cerevisiae
			9.3.2.1 Production of a Fusion Protein in E. coli
			9.3.2.2 Production of a Precursor Protein, the So‐Called Mini Proinsulin with the Host Strain S. cerevisiae
	9.4 Somatropin
		9.4.1 Application
		9.4.2 Manufacturing Process
	9.5 Interferons – Application and Manufacturing
	9.6 Human Granulocyte Colony‐Stimulating Factor
		9.6.1 Application
		9.6.2 Manufacturing Process
	9.7 Vaccines
		9.7.1 Application
		9.7.2 Manufacturing Procedure Using the Example of Gardasil™
		9.7.3 Manufacturing Process Based on the Example of a Hepatitis B Vaccine
	9.8 Antibody Fragments
	9.9 Enzymes
	9.10 Peptides
	9.11 View – Future Economic Importance
	Further Reading
Chapter 10 Enzymes
	10.1 Fields of Application and Economic Impacts
		10.1.1 Enzymes are Biocatalysts
		10.1.2 Advantages and Limitations of Using Enzymatic Versus Chemical Methods
		10.1.3 Brief History of Enzyme Used for the Industrial Production of Valuable Products
		10.1.4 Diverse Ways That Enzymes Are Used in Industry
	10.2 Enzyme Discovery and Improvement
		10.2.1 Screening for New Enzymes and Optimization of Enzymes by Protein Engineering
		10.2.2 Classical Development of Production Strains
		10.2.3 Genetic Engineering of Producer Strains
	10.3 Production Process for Bacterial or Fungal Enzymes
	10.4 Polysaccharide‐Hydrolyzing Enzymes
		10.4.1 Starch‐Cleaving Enzymes Produced by Bacillus and Aspergillus Species
		10.4.2 Cellulose‐Cleaving Enzymes: A Domain of Trichoderma reesei
		10.4.3 Production Strains
	10.5 Enzymes Used as Cleaning Agents
		10.5.1 Subtilisin‐Like Protease
		10.5.2 Bacillus sp. Production Strains and Production Process
	10.6 Feed Supplements – Phytases
		10.6.1 Fields of Applications of Phytase
		10.6.2 Phytase in the Animals Intestine
		10.6.3 Production of a Bacterial Phytase in Aspergillus niger
	10.7 Enzymes for Chemical and Pharmaceutical Industry
		10.7.1 Examples for Enzymatic Chemical Production
		10.7.2 Production of (S)‐Profens by Fungal Lipase
	10.8 Enzymes as Highly Selective Tools for Research and Diagnostics
		10.8.1 Microbial Enzymes for Analysis and Engineering of Nucleic Acids
		10.8.2 Specific Enzymes for Quantitative Metabolite Assays
	10.9 Perspectives
		10.9.1 l‐DOPA by Tyrosine Phenol Lyase
		10.9.2 Activation of Alkanes
		10.9.3 Enzyme Cascades
	References
	Further Reading
Chapter 11 Microbial Polysaccharides
	11.1 Introduction
	11.2 Heteropolysaccharides
		11.2.1 Xanthan: A Product of the Bacterium Xanthomonas campestris
			11.2.1.1 Introduction
			11.2.1.2 Regulatory Status
			11.2.1.3 Structure
			11.2.1.4 Biosynthesis
			11.2.1.5 Industrial Production of Xanthan
			11.2.1.6 Physicochemical Properties
			11.2.1.7 Applications
		11.2.2 Sphingans: Polysaccharides from Sphingomonas sp.
		11.2.3 Hyaluronic Acid: A High‐Value Polysaccharide for Cosmetic Applications
		11.2.4 Alginate: Alternatives to Plant‐Based Products by Pseudomonas and Azotobacter sp.
		11.2.5 Succinoglycan: Acidic Polysaccharide from Rhizobium sp.
	11.3 Homopolysaccharides
		11.3.1 ?‐Glucans
			11.3.1.1 Pullulan
			11.3.1.2 Dextran
		11.3.2 ?‐Glucans
			11.3.2.1 Linear ?‐glucans like cellulose and curdlan
			11.3.2.2 Branched ?‐Glucans Like Scleroglucan and Schizophyllan
		11.3.3 Fructosylpolymers like Levan
	11.4 Perspectives
	Further Reading
Chapter 12 Steroids
	12.1 Fields of Applications and Economic Importance
	12.2 Advantages of Biotransformations During Production of Steroids
	12.3 Development of Production Strains and Production Processes
	12.4 Applied Types of Biotransformation
	12.5 Synthesis of Steroids in Organic – Aqueous Biphasic System
	12.6 Side‐chain Degradation of Phytosterols by Mycobacterium to Gain Steroid Intermediates
	12.7 Biotransformation of Cholesterol to Gain Key Steroid Intermediates
	12.8 11‐Hydroxylation by Fungi During Synthesis of Corticosteroids
	12.9 Δ1‐Dehydrogenation by Arthrobacter for the Production of Prednisolone
	12.10 17‐Keto Reduction by Saccharomyces in Testosterone Production
	12.11 Double‐Bond Isomerization of Steroids
	12.12 Perspectives
	References
	Further Reading
Chapter 13 Bioleaching
	13.1 Acidophilic Microorganisms Dissolve Metals from Sulfide Ores
		13.1.1 Brief Overview on the Diversity of Acidophilic Mineral‐Oxidizing Microorganisms
		13.1.2 Natural and Man‐Made Habitats of Mineral‐oxidizing Microorganisms
		13.1.3 Biological Catalysis of Metal Sulfide Oxidation
		13.1.4 Importance of Biofilm Formation and Extracellular Polymeric Substances for Bioleaching by Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans
	13.2 Bioleaching of Copper, Nickel, Zinc, and Cobalt
		13.2.1 Economic Impact
		13.2.2 Heap, Dump, or Stirred‐tank Bioleaching of Copper, Nickel, Zinc, and Cobalt
	13.3 Gold
		13.3.1 Economic Impact
		13.3.2 Unlocking Gold by Biooxidation of the Mineral Matrix
	13.4 Uranium
		13.4.1 Economic Impact
		13.4.2 In Situ Biomining of Uranium
	13.5 Perspectives
		13.5.1 Urban Mining – Processing of Electronic Waste and Industrial Residues
		13.5.2 Microbial Iron Reduction for Dissolution of Mineral Oxides
		13.5.3 Biomining Goes Underground – In Situ Leaching as a Green Mining Technology?
	References
	Further Reading
Chapter 14 Wastewater Treatment Processes
	14.1 Introduction
		14.1.1 Historical Development of Sewage Treatment
		14.1.2 Resources from Wastewater Treatment
		14.1.3 Wastewater and Storm Water Drainage
		14.1.4 Wastewater Characterization and Processes for Effective Wastewater Treatment
		14.1.5 Suspended or Immobilized Bacteria as Biocatalysts for Effective Sewage Treatment
	14.2 Biological Basics of Carbon, Nitrogen, and Phosphorus Removal from Sewage
		14.2.1 Aerobic and Anaerobic Degradation of Carbon Compounds
			14.2.1.1 Mass and Energy Balance
		14.2.2 Fundamentals of Nitrification
		14.2.3 Elimination of Nitrate by Denitrification
		14.2.4 New Nitrogen Elimination Processes
		14.2.5 Microbial Phosphate Elimination
	14.3 Wastewater Treatment Processes
		14.3.1 Typical Process Sequence in Municipal Sewage Treatment Plants
		14.3.2 Activated Sludge Process
		14.3.3 Trickling Filters
		14.3.4 Technical Options for Denitrification
		14.3.5 Biological Phosphate Elimination
		14.3.6 Sewage Sludge Treatment
			14.3.6.1 Aerobic and Anaerobic Sewage Sludge Treatment
			14.3.6.2 Sanitation and Quality Assurance of Sewage Sludge
	14.4 Advanced Wastewater Treatment
		14.4.1 Elimination of Micropollutants
		14.4.2 Wastewater Disinfection
	14.5 Future Perspectives
	References
	Further Reading
Index
EULA