Preface xvii
List of Contributors xix
1 Engineered Microorganisms for Production of Biocommodities 1
Akhil Rautela and Sanjay Kumar
1.1 Introduction 1
1.2 Fundamentals of Genetic Engineering 2
1.2.1 DNA-altering Enzymes 2
1.2.1.1 DNA Polymerases 4
1.2.1.2 Nucleases 4
1.2.1.3 Ligases 5
1.2.1.4 DNA-modifying Enzymes 6
1.2.2 Vectors 7
1.2.3 Incorporation of Modified DNA into Host 8
1.2.3.1 Introducing Recombinants into Prokaryotes 8
1.2.3.2 Introducing Recombinants into Eukaryotic Hosts 9
1.2.4 Selection of Transformants 10
1.2.4.1 Direct Selection 10
1.2.4.2 Identification of the Clone from a Gene Library 11
1.3 Beneficial Biocommodities Produced Through Engineered Microbial Factories 12
1.3.1 Biopolymers 13
1.3.1.1 Cellulose 14
1.3.1.2 Poly-¿- glutamic Acid 15
1.3.1.3 Hyaluronic Acid 16
1.3.1.4 Polyhydroxyalkoate 18
1.3.2 Organic Acids 20
1.3.2.1 Citric Acid 21
1.3.2.2 Lactic Acid 23
1.3.2.3 Succinic Acid 24
1.3.2.4 Fumaric Acid 26
1.3.3 Therapeutic Proteins 27
1.4 Photosynthetic Production of Biofuels 28
1.4.1 Biohydrogen 29
1.4.2 Biodiesel 30
1.4.3 Bioethanol 31
1.4.4 Terpenoids 32
1.5 Conclusion 34
References 34
2 Microbial Cell Factories for the Biosynthesis of Vanillin and Its Applications 49
Sukumaran Karthika, Manoj Kumar, Santhalingam Gayathri, Perumal Varalakshmi, and Balasubramaniem Ashokkumar
2.1 Introduction 49
2.2 Natural Sources of Vanilla and Its Production 51
2.3 Biotechnological Production of Vanillin 52
2.3.1 Enzymatic Synthesis of Vanillin 52
2.3.2 Microbial Biotransformation of Ferulic Acid to Vanillin 54
2.3.3 Agro-wastes as a Source for Biovanillin Production 58
2.4 Strain Development for Improved Production of Vanillin 60
2.4.1 Metabolic and Genetic Engineering 60
2.5 Bioactive Properties of Vanillin 63
2.5.1 Antimicrobial Activity 63
2.5.2 Antioxidant Activity 63
2.5.3 Anticancer Activity 64
2.5.3.1 Apoptosis Pathway 64
2.5.3.2 Tumor Necrosis Factor-induced Apoptosis 64
2.5.3.3 Cell Cycle Arrest 65
2.5.3.4 Nuclear Factor ¿B (NF-¿B) Pathway 65
2.5.4 Anti-sickling Activity 65
2.5.5 Hypolipidemic Activity 66
2.6 Conclusion 66
Acknowledgments 66
References 67
3 Antimicrobials: Targets, Functions, and Resistance 77
Madhuri Dutta, Sinjini Patra, Shivam Saxena, and Anasuya Roychowdhury
3.1 Introduction 77
3.2 Classification of Antibiotics 77
3.2.1 Classification of Antibiotics Based on Mode of Action: Bactericidal and Bacteriostatic 78
3.2.2 Classification of Antibiotics Based on the Spectrum of Action: Broad-and Narrow-spectrum Antibiotics 79
3.3 Antibacterial Agents 79
3.3.1 Penicillins 79
3.3.1.1 Mechanism of Action 82
3.3.1.2 Clinical Implications 83
3.3.2 Cephalosporins 83
3.3.2.1 Mechanism of Action 83
3.3.2.2 Clinical Indications 85
3.3.3 Macrolides 85
3.3.3.1 Mechanism of Action 85
3.3.3.2 Clinical Indications 85
3.3.4 Fluoroquinolones 86
3.3.4.1 Mechanism of Action 86
3.3.4.2 Clinical Indication 86
3.3.5 Sulfonamides 87
3.3.5.1 Mechanism of Action 87
3.3.5.2 Clinical Indication 88
3.3.6 Tetracyclines 88
3.3.6.1 Mechanism of Action 88
3.3.6.2 Clinical Indication 88
3.3.7 Aminoglycosides 89
3.3.7.1 Mechanism of Action 89
3.3.7.2 Clinical Indication 89
3.4 Antifungal Agents 89
3.4.1 Polyenes 90
3.4.1.1 Mechanism of Action 90
3.4.1.2 Clinical Indication 90
3.4.2 Azoles 90
3.4.2.1 Mechanism of Action 90
3.4.2.2 Clinical Indication 93
3.4.3 Echinocandins 93
3.4.3.1 Mechanism of Action 94
3.4.3.2 Clinical Indication 94
3.4.4 Flucytosine 95
3.4.4.1 Mechanism of Action 95
3.4.4.2 Clinical Implication 95
3.5 Antiviral agents 95
3.6 Antiparasitic Agents 98
3.6.1 Antiprotozoan Agents 98
3.6.2 Antihelminthic Agents 101
3.6.3 Ectoparasiticides 101
3.7 Antimicrobial Resistance 101
3.7.1 Genetic Basis of AMR 102
3.7.2 Mechanistic Basis of Antimicrobial Resistance 102
3.8 Conclusion 103
Acknowledgment 104
References 104
4 Trends in Antimicrobial Therapy: Current Approaches and Future Prospects 111
Mohan Kumar Verma, Santhalingam Gayathri, BalasubramaniemAshokkumar, and Perumal Varalakshmi
4.1 Introduction 111
4.2 Antibiotics: A Brief History 112
4.2.1 Classification of Antibiotics 113
4.2.2 Evolution of Antibiotics 113
4.2.3 Mechanism of Action of Antibiotics 113
4.3 AMR: A Global Burden 113
4.3.1 Global Scenario 114
4.3.2 Origin of SUPERBUGS and the "END of Antibiotics" 116
4.4 Antimicrobial Resistance and Virulence 117
4.4.1 Molecular Insights and Mechanism of AMR 117
4.4.2 Antibiotic Resistance in Bacteria 118
4.4.2.1 Horizontal Gene Transfer 118
4.4.2.2 Increased Mutation Rate 118
4.4.2.3 Antibiotic Inactivation 118
4.4.2.4 Alteration of the Antibiotic Targets 119
4.4.2.5 Changes in Cell Permeability and Efflux 119
4.4.2.6 The Major Facilitator Superfamily 119
4.4.2.7 The ATP-Binding Cassette Superfamily 119
4.4.2.8 The Multidrug and Toxic Compound Extrusion Family 120
4.4.2.9 The Resistance-Nodulation-Division (RND) Superfamily 120
4.4.2.10 The Small Multidrug-Resistance Family 120
4.4.3 Development of Antibiotic Resistance 120
4.4.4 Prioritization of Antibiotic Resistant Bacteria 120
4.4.5 Understanding Biofilm Resistance 122
4.5 Alternatives to Antibiotics 122
4.5.1 Peptide Antibiotics 122
4.5.1.1 Cationic Antimicrobial Peptides (CAMPs) 122
4.5.1.2 Marine Antimicrobial Peptides 123
4.5.2 Nano Drugs 124
4.5.3 Probiotics 125
4.5.4 Bacteriocins 126
4.5.5 Bdellovibrio 127
4.5.6 Bdellovibrio as Live Antimicrobial Agent 128
4.6 Antibiotics: Global Action Plan on Antimicrobial Resistance 129
4.7 Conclusion 130
Acknowledgment 130
References 131
5 Fermentation Strategies in the Food and Beverage Industry 141
Mohit Bibra, R. Navanietha Krishnaraj, and Rajesh K. Sani
5.1 Introduction 141
5.2 Current Trends in Food Fermentation 143
5.2.1 Fermentation Types 144
5.2.1.1 Spontaneous Fermentation 144
5.2.1.2 Back-Slopping Fermentation 144
5.2.1.3 Starter-Culture Fermentation 144
5.2.2 Microbial Cultures 145
5.2.2.1 Starter Cultures 145
5.2.2.2 Adjunct Cultures 155
5.2.2.3 Bio-protective Cultures 155
5.2.2.4 Probiotic Cultures 155
5.3 Future Directions 156
5.3.1 Use of Defined Mixed Cultures 156
5.3.2 Nanotechnology 157
5.3.2.1 Nanosensors 157
5.3.2.2 Nanoparticles 157
5.3.2.3 Nanocomposites 157
5.3.3 Meat Analogues 158
5.4 Conclusions 158
5.5 Questions for Thought 159
References 160
6 Bioactive Oligosaccharides: Production, Characterization, and Applications 165
R. Aanandhalakshmi, K. Sundar, and B. Vanavil
6.1 Introduction 165
6.2 Sources, Types, Structure of Oligosaccharides 166
6.2.1 Plant Source 166
6.2.2 Animal Source 167
6.2.3 Insect Source 167
6.2.4 Marine Source 167
6.2.5 Microbial Source 168
6.2.6 Synthetic Oligosaccharides 168
6.2.7 Pseudo-oligosaccharides 168
6.3 Production Methods of Oligosaccharides 169
6.3.1 Chemical Methods 169
6.3.2 Physical Methods 169
6.3.3 Enzymatic Hydrolysis 171
6.3.4 Microbial Production of Oligosaccharides 171
6.4 Extraction, Separation, and Purification of Oligosaccharides 172
6.5 Characterization of Oligosaccharides 174
6.6 Functional Properties of Oligosaccharides 174
6.7 Applications of Oligosaccharides 175
6.7.1 Functional Foods, Nutraceuticals, and Prebiotics 176
6.7.2 Pharmaceutical and Medical Applications 176
6.7.2.1 Effects on Intestinal Microflora 176
6.7.2.2 Effects on Urogenital Infections 177
6.7.2.3 Type II Diabetes and Obesity 177
6.7.2.4 Immunomodulatory and Antitumor Activities 178
6.7.2.5 Effect on Cardiovascular Risk 178
6.7.2.6 Lowering of Cholesterol 178
6.7.2.7 Role in Osteoporosis 178
6.7.2.8 Antihypertensive Effects 179
6.7.2.9 Hepatic Protection 179
6.7.2.10 Antioxidant and Neuroprotective Agent 179
6.7.2.11 Antimicrobial Activity 180
6.7.2.12 Antibiotics 180
6.7.2.13 Oligosaccharides as Vaccine Components 181
6.7.3 Environmental Fortification 181
6.7.4 Cosmetics 182
6.7.5 Elicitors and Agriculture 182
6.7.6 Novel Biomaterials 183
6.8 Market Potential of Oligosaccharides 183
6.9 Future Prospects 184
References 184
7 Biopolymers: A Retrospective Analysis in the Facet of Biomedical Engineering 201
Gayathri Ravichandran and Aravind Kumar Rengan
7.1 Introduction 201
7.2 Natures' Advanced Materials: A Glance at Its Structure and Properties 202
7.2.1 Polypeptides 202
7.2.1.1 Collagen 202
7.2.1.2 Elastin 202
7.2.1.3 Silk Fibroin 204
7.2.1.4 Gelatin 204
7.2.1.5 Albumin 205
7.2.1.6 Casein 205
7.2.2 Polysaccharides 205
7.2.2.1 Cellulose 205
7.2.2.2 Starch 206
7.2.2.3 Cyclodextrin 207
7.2.2.4 Hyaluronic Acid 207
7.2.2.5 Chitosan 208
7.2.2.6 K-carrageenan 208
7.2.2.7 Agarose 209
7.2.2.8 Alginate 209
7.2.3 Polynucleotides-based Biopolymers 210
7.3 Smart Biopolymers 211
7.3.1 Chemical-Responsive Biopolymers 211
7.3.1.1 pH-Sensitive Smart Biopolymers 211
7.3.1.2 Glucose-Responsive Biopolymers 212
7.3.2 Physically Responsive Biopolymers 212
7.3.2.1 Temperature-Sensitive Smart Biopolymers 212
7.3.2.2 Light-Responsive Smart Polymers 213
7.3.2.3 Electric-Responsive Smart Polymers 213
7.3.2.4 Magnetic-Responsive Smart Polymers 214
7.3.2.5 Redox-Responsive Biopolymer 215
7.3.3 Biochemical Stimuli-Responsive Biopolymers 215
7.3.3.1 Enzyme-Responsive Biopolymer 215
7.4 Fundamental Applications of Biopolymers in Biomedical Engineering 216
7.4.1 Biopolymers in Cancer Theranostics 216
7.4.1.1 Drug Delivery 217
7.4.1.2 Cancer Diagnosis and Molecular Imaging 218
7.4.2 Biopolymeric-based Biosensor 219
7.4.3 Wound Healing 222
7.4.4 Tissue Engineering and Regenerative Medicine 223
7.4.4.1 Biopolymers as Bioink for 3D Scaffolds 225
7.4.4.2 Corneal Regeneration 225
7.4.4.3 Neural Tissue Engineering 226
7.4.4.4 Bone Tissue Engineering 227
7.4.4.5 Cartilage Tissue Regeneration 227
7.4.5 Biopolymers for Biological Implants 229
7.4.6 Biopolymers in Other Applications 230
7.5 Processing Techniques for the Contrivance of Biopolymers 230
7.5.1 3D Bioprinting 230
7.5.2 4D Bioprinting 232
7.5.3 Electrospinning 233
7.6 Conclusion 234
Acknowledgments 234
References 234
8 Metabolic Engineering Strategies to Enhance Microbial Production of Biopolymers 247
Shailendra Singh Shera and Rathindra Mohan Banik
8.1 Introduction 247
8.2 Microbes as Cell Factories for the Production of Speciality Biochemicals 248
8.2.1 Bacteria as Cell Factories for the Production of Biopolymers 249
8.2.1.1 Polysaccharides 249
8.2.1.2 Polyesters 250
8.2.1.3 Polyamides 251
8.2.2 Fungus as Cell Factories for the Production of Biopolymers 252
8.2.2.1 Polysaccharides 253
8.2.2.2 Polyester 253
8.2.2.3 Polyamides 254
8.2.3 Microalgae as Cell Factories for the Production of Biopolymers 254
8.2.3.1 Polysaccharides from Microalgae 255
8.2.3.2 Polyester 255
8.2.3.3 Polyamides 256
8.3 Microbial Production Pathways for Various Types of Biopolymers 256
8.3.1 Polysaccharide Production Pathways in Bacteria 256
8.3.2 Mechanism of Fungal Polysaccharides Synthesis 260
8.3.3 Mechanism of Synthesis of Polyester in Bacteria 260
8.3.4 Mechanism of Synthesis of Polyamide in Bacteria 262
8.4 Tools and Technologies Available for Metabolic Engineering 262
8.4.1 Metabolic Pathway Reconstruction 263
8.4.2 Metabolic Flux Analysis 264
8.4.3 Metabolic Control Analysis 266
8.4.4 Omics Analysis 266
8.5 Dynamic Metabolic Flux Analysis and its Role in Metabolic Engineering 268
8.6 Production of Biopolymers from Metabolically Engineered Microbes 269
8.6.1 Metabolic Modification of Pathway for Synthesis of Polysaccharides 269
8.6.2 Levan 271
8.6.3 Metabolic Modification of Pathway for Synthesis of Polyester 271
8.6.4 Metabolic Modification of Pathway for Synthesis of Polyamides 272
8.6.5 Culture of Metabolically Engineered Microbes in Fermentation or Bioreactor for Production of Biopolymer 273
8.7 Recovery and Purification of Biopolymers from Fermentation Broth 275
8.7.1 Separation and Purification of Xanthan 275
8.7.2 Separation of Poly-L- lysine 277
8.8 Conclusion and Future Challenges 278
Acknowledgments 278
References 279
Web References 285
9 Bioplastics Production: What Have We Achieved? 287
Tanvi Govil, David R. Salem, and Rajesh K. Sani
9.1 Introduction 287
9.2 Current Trends 289
9.3 Different Types of Bioplastics 291
9.3.1 Bio-based Polyethylene (Bio-PE) 291
9.3.2 Bio-based PET 292
9.3.3 Polylactic Acid 293
9.3.4 Starch Blends 294
9.3.5 Polyhydroxyalkanoate 295
9.3.6 Polybutylene Succinate 298
9.3.7 Polybutylene Adipate Terephthalate 299
9.3.8 Polycaprolactone 299
9.3.9 Epoxies 300
9.3.10 Cellulose Acetate 300
9.4 Challenges Facing the Bioplastics Industry 301
9.5 Misconceptions and Negative Impacts 301
9.6 Take Home Message and Future Directions 302
9.7 Questions for Thought 303
Acknowledgments 304
Conflict of Interest 304
References 304
10 Conversion of Lignocellulosic Biomass to Ethanol: Recent Advances 311
Ramiya Baskaran, Vignesh Natarajan, Shereena Joy, and Chandraraj Krishnan
10.1 Introduction 311
10.2 LCB: Structure, Composition, and Recalcitrance 312
10.3 LCB to Ethanol: Bioprocess Strategies 313
10.4 Pretreatment of LCB 313
10.4.1 Physical Pretreatment 316
10.4.2 Physicochemical Pretreatment 319
10.4.2.1 Steam Explosion 320
10.4.2.2 Liquid Hot Water 320
10.4.2.3 Ammonia Fiber Explosion 321
10.4.3 Chemical Pretreatment 321
10.4.3.1 Dilute Acid Pretreatment (DAP) 322
10.4.3.2 Alkali Pretreatment 322
10.4.3.3 Organosolv 323
10.4.3.4 Ionic Liquid (IL) and Deep Eutectic Solvent (DES) 323
10.4.3.5 Supercritical Fluid Pretreatment 324
10.4.4 Biological Pretreatment 325
10.4.4.1 Bacterial Pretreatment 325
10.4.4.2 Fungal Pretreatment 325
10.4.4.3 Enzymatic Pretreatment 326
10.4.5 Optimization of Pretreatment Process 326
10.5 Enzymatic Hydrolysis 327
10.5.1 Cellulose Hydrolysis 327
10.5.2 Xylan Hydrolysis 328
10.5.3 Accessory Enzymes 328
10.5.4 Auxiliary Activity and Non-Hydrolytic Enzymes 330
10.5.5 Enzyme Cocktail for Biomass Hydrolysis 331
10.5.5.1 Cocktail Development 331
10.6 High Solids Loading Enzymatic Hydrolysis (HSLEH) 335
10.6.1 Enzyme Inhibitors and Detoxification 335
10.6.2 Cellulase Feedback Inhibition 336
10.6.3 Rheology 337
10.6.4 Reactors and Impellers 337
10.7 Fermentation 338
10.8 Genetic Engineering in LCB Bioconversion 343
10.9 Conclusions 344
Acknowledgments 344
References 344
11 Advancement in Biogas Technology for Sustainable Energy Production 359
Rouf Ahmad Dar, Saroj Bala, and Urmila Gupta Phutela
11.1 Introduction 359
11.2 Biogas Developments Worldwide 360
11.3 Biogas Development in India 363
11.4 Recent Issues in Biogas Production 365
11.5 Current Trends in Biogas Production 365
11.6 Advanced Anaerobic Digestion Methodologies 367
11.6.1 Anaerobic Membrane Reactor (AnMBRs) 368
11.6.2 Dry Anaerobic Digestion Technology (DADT) 368
11.6.3 Anaerobic Co-digestion Technology (AcoD) 369
11.7 Role of Biotechnology in Enhancing Biogas Production 370
11.8 Application of Nanotechnology in Biogas and Methane Production 371
11.9 Biogas Upgrading Technologies 372
11.10 Conclusion 372
References 378
12 Biofertilizers: A Sustainable Approach Towards Enhancing the Agricultural Productivity 387
Satya Sundar Mohanty
12.1 Introduction 387
12.2 Types of Biofertilizers 388
12.2.1 Nitrogen-Fixing Biofertilizer 389
12.2.1.1 Free-Living Nitrogen-Fixing Microorganisms 390
12.2.1.2 Photosynthetic Nitrogen-Fixing Microorganisms 390
12.2.2 Phosphorus Biofertilizer 391
12.2.2.1 Phosphate-solubilizing Bacteria (PSB) 392
12.2.2.2 Phosphate-mobilizing Microorganisms 394
12.2.3 Plant-Growth- promoting Biofertilizers 394
12.3 Effect on Bioremediation of Environmental Pollutants 396
12.4 Bioformulations and Its Types 398
12.5 Preparation of Biofertilizers 401
12.6 Various Modes of Biofertilizer Application 402
12.7 Challenges to Commercialization of Biofertilizers 403
12.8 Future Perspective 403
References 404
13 Biofertilizers from Food and Agricultural By-Products and Wastes 419
Veknesh Arumugam, Muhammad Heikal Ismail, and Winny Routray
13.1 Introduction 419
13.2 Biofertilizer 420
13.2.1 N2-fixing Biofertilizer 422
13.2.1.1 Free-living N2-fixing Biofertilizer 422
13.2.1.2 Symbiotic N2-Fixing Biofertilizer 424
13.2.2 Phosphate-solubilizing Biofertilizers 425
13.2.3 Phosphate-mobilizing Biofertilizer 425
13.2.4 Plant-Growth- promoting Biofertilizers 426
13.3 Agricultural Waste 426
13.3.1 Agro-industrial Wastes 428
13.4 Food Waste 430
13.5 Biofertilizer Production Using Fermentation Technology 432
13.5.1 Solid-State Fermentation (SSF) 433
13.5.2 Submerged Fermentation (SmF) 435
13.5.3 Production of N2-fixing Biofertilizer 438
13.5.3.1 Production of Rhizobium Biofertilizer 438
13.5.3.2 Production of Azotobacter Biofertilizer 438
13.5.3.3 Production of Azospirillum Biofertilizer 439
13.5.4 Production of Phosphate-solubilizing Biofertilizer 439
13.5.5 Production of Phosphate-mobilizing Biofertilizer 439
13.6 Biofertilizer for Organic Farming 440
13.7 Conclusion 441
Conflict of Interest 441
References 442
Index 449
