List of Contributors xv
About the Editor xxi
Preface xxiii
1 Biomass Refining and Biofoundry: Key Products, Process Limitations, and Future Aspects 1
Lucas Ramos, Jesús Jiménez Ascencio, James Villar, Mónica Ma. Cruz- Santos, and Anuj Kumar Chandel
1.1 Introduction 1
1.1.1 Biomass Diversity and Major Principle Feedstock in the World 2
1.1.1.1 Major Feedstocks 3
1.1.2 Biomass Refining Methods 4
1.1.2.1 Sugars- First Approach 4
1.1.2.2 Lignin- First Approach 5
1.1.3 Key Products from Biorefinery Based from Listed Top 12 Biochemicals from U.S. Department of Energy 9
1.1.4 Process Limitations and Net- Zero Environment 13
1.1.5 Biofoundry and Advanced Bioeconomy 14
1.1.6 Conclusion and Future Directions 16
Acknowledgments 17
References 17
2 Structural Carbohydrates Conversion into Sugars, Fuels, Chemicals, and Sustainable Materials 27
Katarina Mihajlovski, Nevena Ili¿, Galina Jev¿enovi¿, and Marija Mili¿
2.1 Introduction 27
2.1.1 What are Structural Carbohydrates? 27
2.1.2 Cellulose 28
2.1.2.1 Cellulose Conversions to Sugars 29
2.1.2.2 Cellulose Conversions to Fuels 31
2.1.2.3 Cellulose Conversions to Sustainable Materials 32
2.1.3 Hemicellulose 33
2.1.3.1 Hemicellulose Conversion to Sugars 33
2.1.3.2 Hemicellulose Conversion to Chemicals 35
2.1.3.3 Hemicellulose Conversion to Fuels 37
2.1.3.4 Hemicellulose Conversion to Sustainable Materials 39
2.1.4 Pectin 39
2.1.4.1 Pectin Conversions to Sugars 41
2.1.4.2 Pectin Conversions to Fuels 42
2.1.4.3 Pectin Conversions to Chemicals 42
2.1.4.4 Pectin Conversions to Sustainable Materials 45
2.1.5 Oligosaccharides 46
2.1.5.1 Oligosaccharides Conversions to Sugars 46
2.1.5.2 Oligosaccharides Conversions to Fuels 48
2.1.5.3 Oligosaccharides Conversions to Chemicals 48
2.2 Conclusions 51
References 51
3 Integrating Lignocellulosic Biomass Processing, Biomanufacturing, and Biofoundries: Innovations and Challenges in the Bioeconomy 59
Yaimé Delgado- Arcaño, Alisson Dias da Silva Ruy, Leila Maria Aguilera Campos, and Oscar Daniel Valmaña- García
3.1 Introduction 59
3.2 Advances in Biomass Processing: Pretreatment and Purification Strategies 60
3.2.1 Pretreatment Methods of Lignocellulosic Biomass 60
3.2.2 Separation and Purification of the Interest Compounds 64
3.3 Bioeconomy and Biofoundries: How Automation and Synthetic Biology can Enhance Biorefineries 65
3.3.1 Bibliometric Analysis 66
3.3.2 Design- Build- Test- Learn (DBTL) in Biofabrication and Synthetic Biology 68
3.3.3 Biofoundry and Process Integration in Biorefinery 69
3.3.4 Global Expansion of Biofoundries: Innovation and Collaboration 71
3.4 Economic Competitiveness in the Production of Bioproducts of Commercial Interest 72
3.4.1 Techno- Economic Analysis and Life Cycle Assessments for Sustainable Bioproducts 72
3.4.2 Market of Bioproducts: Insights and Challenges 75
3.4.3 Market Growth, Cost Challenges, and Policy Drivers in Biorefineries 76
3.4.4 Biomanufacturing and Biofoundries: Addressing Technological and Operational Challenges 77
3.5 Conclusions 78
References 79
4 Lignin Valorization Is the Key for a Win-Win Situation in a Biomass Refinery 87
Lucas Ramos, Carina Prado, Maria Teresa Ferreira Ramos Raimundo, Uirajá C. M. Ruschoni, Vinícius Pereira Shibukawa, and Anuj Kumar Chandel
4.1 Introduction 87
4.2 Lignin: Dispensable Source of Renewable Carbon 88
4.3 Lignin Chemistry 90
4.4 Lignin Extraction Methods 92
4.5 Lignin Conversion Route 94
4.6 Biological Routes 94
4.6.1 Microbial Degradation 95
4.6.2 Enzymatic Conversion 95
4.6.3 Fermentation 96
4.7 Chemical Routes 96
4.7.1 Thermal Decomposition 96
4.7.2 Catalytic Depolymerization 96
4.7.3 Electrochemical Conversion 97
4.8 Lignin in the Pulp and Paper Industry 97
4.9 Conclusion and Future Directions 99
Acknowledgment 99
References 99
5 Sustainable Production of Advanced Alcohol- Based Biofuels in Biorefinery: From Alcohols to Sustainable Aviation Fuels 105
Danielle Matias Rodrigues, Paula Zaghetto de Almeida, Allan H. Félix de Mélo, Juliana Velasco de Castro Oliveira, Ana Paula Jacobus, and Henrique Macedo Baudel
5.1 Introduction 105
5.2 Bioethanol 106
5.3 Advanced Alcohol- Based Fuels 108
5.4 Biobutanol: The Biofoundry as a Tool to Optimize 109
5.4.1 Clostridium Pathway: Acetone- Butanol- Ethanol (ABE) Synthesis 110
5.4.2 S. cerevisiae 111
5.4.3 E. coli 112
5.5 Biofoundry Synthetic Biology Tools 113
5.5.1 2,3- Bdo 115
5.6 Sustainable Aviation Fuel (SAF) 117
5.7 Conclusion 118
References 119
6 Biomanufacturing of Smart Packaging Materials, Cosmetics, Therapeutics, and Nanomaterials Through Lignocellulosic Biorefinery Framework 127
Sounak Maitra, Muskaan Sethi, Prisha Inani, Palak Shrivastava, C. Shriya, and Samuel Jacob
6.1 Introduction 127
6.2 Lignocellulosic Raw Materials and Their Potential as Industrial Raw Materials 128
6.2.1 Corn Wastes 128
6.2.2 Sugarcane and Sugar Beet Residues 129
6.2.2.1 Bagasse 129
6.2.2.2 Molasses 130
6.2.2.3 Vinasse 130
6.2.2.4 Wastewater from the Sugar Industry 130
6.2.3 Paddy Processing Wastes 130
6.2.4 Potato Processing Wastes 131
6.2.4.1 Potato Peels 133
6.2.4.2 Potato Starch from Processing Wastes 133
6.2.4.3 Potato Protein 133
6.2.4.4 Potato Wastewater 133
6.2.5 Oil Processing Industry Residues 134
6.3 Smart Packaging Materials 135
6.3.1 Starch and Lignocellulose- Based Biopolymers 135
6.3.1.1 Starch- Based Biopolymer 135
6.3.1.2 Lignocellulosic- Based Biopolymer 136
6.3.2 PLA, PHA, and PHB 136
6.3.2.1 Polylactic Acid (PLA) 136
6.3.2.2 Polyhydroxyalkanoates (PHA) 137
6.3.2.3 Polyhydroxybutyrate (PHB) 137
6.4 Cosmetics and Therapeutics 138
6.4.1 Active Pharmaceutical Components from Bioresources 138
6.4.2 Bio- Oil as a Resource for the Cosmetics Industry 139
6.4.3 Application of Bio- Oils in the Cosmetics Industry 141
6.5 Bio- Nanotechnology Through Biomass 141
6.6 Conclusion 142
References 142
7 White Biotechnology for Skincare: Unveiling the Power of Bioactives for the Cosmetic Industry 151
Samatha Paladugu, Sarepalli Sai Sathwik, and Mamatha Potu
7.1 Introduction 151
7.2 Fermented Bioactives 153
7.3 Innovative Approaches in Green Bio- ferment Cosmetic Formulations 156
7.4 Green Bio Ferments 158
7.5 Active Compounds from Bioferments 160
7.5.1 Organic Acids 160
7.5.2 Amino Acids 161
7.5.2.1 The Function of Amino Acids in Skin and Hair Care 162
7.5.3 Gaba 164
7.5.3.1 Efficacy of Lactobacillus- Fermented GABA on Dermal Fibroblasts 165
7.5.4 Peptides 166
7.5.4.1 Types of Peptides 167
7.5.5 Antioxidant Substances 168
7.5.6 Short- Chain Fatty Acids 169
7.6 Application of Bioferments in Skincare 170
7.6.1 Reducing Wrinkles and Signs of Aging 170
7.6.2 Strengthening Skin Barrier 170
7.6.3 Reducing Inflammation 171
7.6.4 Helping Wound Healing 172
7.6.5 Fighting Acne 172
7.7 KINMATI: The Advanced Probiotic Biofermented Raw Material for Skincare 173
7.8 Future of Bio- ferments, Active Ingredients, and Green Formulations 173
7.8.1 Increasing Demand for Eco- Friendly Ingredients 174
7.8.2 Shift to Natural Emollients, Solvents, Surfactants, Thickeners, Exfoliators, Fragrances, Colourants, and Antioxidants 174
7.8.3 Safer Preservation Methods 175
7.8.4 Balancing Efficacy and Stability with NaDES 175
7.8.5 Sustainability Commitments of Industry Leaders 175
7.9 Conclusion 176
7.9.1 Regulatory Challenges 176
7.9.2 Challenges in Sustainable Packaging 177
7.9.3 Manufacturing Challenges 177
7.9.4 Challenges for Biotech Skincare Startups 177
7.9.5 From a Consumer Perspective 178
Acknowledgments 178
References 178
8 Biotechnological Advancements in Lactic Acid Bacteria Fermentation: Metabolic Pathways and Metabolite Profiles 189
Samatha Paladugu, Sarepalli Sai Sathwik, and Sreelatha Beemagani
8.1 Introduction 189
8.2 Metabolism of Carbohydrates (Mono, Di, Oligo, and Polysaccharides) 190
8.2.1 Homofermentation 190
8.2.2 Heterofermentation 191
8.3 Monosaccharides 191
8.4 Disaccharides 192
8.5 Oligosaccharides 193
8.6 Polysaccharides and Indigestible Carbohydrates 193
8.7 Indigestible Starch/Resistant Starch 193
8.8 Metabolism of Nitrogen Source (Proteins) 195
8.8.1 Metabolism of Amino Acids 197
8.8.2 Arginine Deiminase Pathway 197
8.8.3 Glutamate Decarboxylase Pathway 197
8.8.4 Metabolism of Branched- Chain and Aromatic Amino Acids 198
8.8.5 d- Amino Acid Production 198
8.9 Utilization and Metabolism of Malic Acid and Citric Acid 199
8.10 Metabolite Profiles of Lactobacillus Ferments 200
8.10.1 Organic Acids 200
8.10.2 Bacteriocins 200
8.11 Vitamins 201
8.12 Short- chain Fatty Acids 202
8.13 Exopolysaccharides 202
8.14 Antioxidant Substances 202
8.15 Production of Polyols 203
8.16 Metabolomic Profiles of Different Lactic Acid Bacteria in the Rice Fermentation 203
8.16.1 Nonvolatile Compounds 204
8.16.2 Volatile Compounds 204
8.16.3 Other Volatile Compounds 204
Acknowledgments 208
References 208
9 Biofoundry in Microbial Protein Production: Process Challenges and Future Scenario 219
Simab Kanwal, Sher Zaman Safi, Aphichart Karnchanatat, and Piroonporn Srimongkol
9.1 Introduction 219
9.2 Microorganisms and Protein Production 220
9.3 Strain Selection for Protein Production 221
9.4 Protein- Rich Biomass Production 222
9.5 Microbial Bioprocessing 223
9.6 Cultivation Systems 224
9.7 Bioreactors for Protein Production 224
9.8 Downstream Processing 225
9.9 Strategies in Synthetic Bioengineering 227
9.9.1 Microbial Engineering 227
9.9.2 Metabolic Pathway Optimization 228
9.9.3 High- Throughput Screening 228
9.10 Challenges and Future Prospects 229
9.11 Conclusions 231
References 231
10 Nanotechnological Interventions in the Advancement of Lignocellulose Bio- Foundry: Current Status and Future Prospects 237
Carlos Lopez- Ortiz, Alan Chavez- Hita Wong, Aldo Sosa, and Nagamani Balagurusamy
10.1 Introduction 237
10.2 Advancing Lignocellulose Bio- Foundries: Pretreatment Strategies and Nanotechnology Integration 238
10.3 Catalytic Nanomaterials and Enzyme Immobilization for Lignocellulose Biomass Conversion 239
10.4 Underlying the Interactions of Nanotechnology Mechanism in Lignocellulose Bio- Foundry 242
10.5 Factors Affecting Nanotechnology Use and Its Performance in Bio- Foundry Using Lignocellulosic Biomass 245
10.6 Challenges and Considerations Using Nanotechnology in Lignocellulose Bio- Foundry 246
10.7 Future Perspectives of Nanotechnology in Biofuel Production 248
10.8 Conclusion 248
References 249
11 Synthetic Biology in the Realm of Genome Engineering for Improved Biocatalysts and Production 257
José Daniel Cano Montoya, Diego Hernandez, and Josman Velasco
11.1 Introduction 257
11.2 The Design-Build-Test-Learn Cycle for Optimizing Biological Systems 258
11.3 The Synthetic Biology Toolkit for Genome Engineering 259
11.3.1 DNA Fragment Assembly Tools 259
11.3.1.1 Ligation- Independent Cloning 260
11.3.1.2 Gibson Assembly 260
11.3.1.3 Yeast- Assisted DNA Assembly 261
11.3.2 Genome- Editing Techniques 261
11.3.2.1 Clustered Regularly Interspaced Short Palindromic Repeats 261
11.3.2.2 Transcription Activator- Like Effector Nucleases 263
11.3.2.3 Zinc Finger Nucleases 264
11.4 Production and Improvement of Biocatalysts 264
11.4.1 Chassis Organisms for the Production of Biocatalysts 265
11.4.1.1 Escherichia coli 265
11.4.1.2 Bacillus subtilis 267
11.4.1.3 Pseudomonas putida 268
11.4.1.4 Filamentous Fungi 268
11.4.1.5 Pichia pastoris 269
11.4.1.6 Mammalian Cell Expression Systems 269
11.4.1.7 Plant Cells 270
11.4.2 Techniques for the Improvement of Biocatalysts 271
11.4.2.1 Directed Evolution 271
11.4.2.2 Rational Design 272
11.4.2.3 Chemical Modification of Enzymes 272
11.5 Conclusions and Final Remarks 273
Acknowledgment 273
Declaration 273
References 274
12 Multi- omics Technologies Paving the Way for the Success of Biorefinery 279
Shruti Ahlawat, Somya Gupta, Ritika Yadav, and Krishna Kant Sharma
12.1 Introduction 279
12.2 Lignocellulosic Biomass 280
12.3 Steps in Biorefinery 280
12.3.1 Step 1- Pretreatment of LC Biomass 281
12.3.1.1 Physical Pretreatment 281
12.3.1.2 Chemical Pretreatment 281
12.3.1.3 Physio- chemical Pretreatment Processes 282
12.3.1.4 Biological Pretreatment Method 283
12.3.2 Step 2- Saccharification 283
12.3.3 Step 3- Fermentation 284
12.4 Various Value- Added Products Generated from Lignocellulosic Biomass 284
12.5 Cellulose- Based Value- Added Products 285
12.5.1 Lactic Acid 285
12.5.2 Bioethanol 286
12.5.3 Biomethane 286
12.5.4 Biodiesel 286
12.5.5 Biobutanol 286
12.6 Hemicellulose- Based Value- Added Products 287
12.6.1 Xylitol 287
12.6.2 Xylooligosaccharides (XOS) 287
12.6.3 Furfural 288
12.7 Lignin- Based Value- Added Products 288
12.7.1 Biopolymers 288
12.7.2 Biochar 288
12.8 CRISPR/Cas9 and - Omics Technologies 289
12.9 Utilization of - Omics Technologies Toward Biorefinery Success 289
12.10 Role in Efficient Enzyme Production 293
12.11 Role in Microalgae- Based Biorefinery 296
12.12 Conclusion 297
Conflict of Interest 298
Author Contributions 298
Funding 298
References 298
13 Sustainability Assessment of Genetically Engineered Biocatalysts Producing Biofuels and Biochemicals 309
Andreza A. Longati, Christian de Oliveira Martins, Gabriel Baioni, Adilson José da Silva, Thais Suzane Milessi, and Felipe Fernando Furlan
13.1 Introduction 309
13.2 The Role of Genetically Modified Organisms in Biorefineries 310
13.3 Metabolic Modeling in the Development of Genetically Modified Organisms 312
13.3.1 Metabolic Modeling 313
13.3.2 Metabolic Modeling for Genetically Modified Organisms 315
13.4 Parameters to Evaluate the Sustainability of Genetically Modified Organisms 315
13.4.1 Environmental Perspective 316
13.4.2 Economic Perspective 321
13.4.3 Social Perspective 323
13.5 Case Studies of Genetically Modified Organisms 324
13.6 Conclusions 327
Acknowledgments 328
References 328
14 Lean Manufacturing Toward Minimum Waste Discharge and Potential Gains in the Biorefinery and Biotechnology Industries 337
Fabricio M. Gomes, Messias Borges Silva, Giovani Maltempi- Mendes, and Anuj Kumar Chandel
14.1 Introduction 337
14.2 The Fundamentals of Lean Manufacturing 337
14.3 The Five Principles of Lean 338
14.4 Waste Reduction in Biotechnology: Unique Challenges 338
14.5 Types of Waste in Biotechnology 338
14.6 Managing Biohazardous Waste 339
14.7 Lean Tools for Biotechnology 339
14.7.1 Kaizen 340
14.7.2 Value Stream Mapping (VSM) 340
14.7.3 5s 340
14.7.4 Kanban 341
14.8 Total Productive Maintenance 341
14.9 Lean Manufacturing and Digitalization in Biotechnology 341
14.10 Real- Time Data Analytics 341
14.11 Digital Twins 342
14.12 Potential Gains from Lean Implementation in Biotechnology 342
14.13 Cost Savings 342
14.13.1 Improved Process Efficiency 343
14.13.2 Environmental Sustainability 343
14.14 Lean Manufacturing's Role in Addressing Sustainability Goals 343
14.15 Regulatory Compliance and Lean in Biotechnology 344
14.16 Commercial Aspects of Lean Implementation in Biorefineries 344
14.17 Case Study: Lean Implementation at Pfizer 345
14.18 Case Study: Novartis and Lean Implementation in Biopharma 348
14.19 Conclusion 348
Acknowledgments 348
References 348
Index 351
