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Biofoundry Techniques for Biotechnology Applications
Anuj Kumar Chandel (Edited by), Chandel (Author)
9781394309924, Wiley
Hardback, published 27 February 2026
384 pages
24.4 x 17 x 2.2 cm, 0.85 kg
Extensive reference on the integration of biofoundry techniques with lignocellulose biorefinery processes Biofoundry Techniques for Biotechnology Applications presents concepts, perspectives, and technical advancements on thermochemical and biochemical pathways in biochemical conversion of lignocellulosic feedstock into platform chemicals, specialty chemicals/fuels, and materials. It covers a broad range of topics from biomass refining to synthetic biology and process automation, integrating recent advancements in biotechnology, process engineering, and sustainability assessment. This book helps readers solve several critical problems related to the development and implementation of lignocellulosic biorefineries and biofoundries, such as the costs, time, and labor associated with generating and testing experimental designs, through practical solutions and insights that are directly applicable to professional practice. The book also reviews the shift towards process automation and modeling, integration, process scaling, and machine learning which is revitalizing the traditional laboratory setting and powering a paradigm change in the field of biomanufacturing. Contributed to by a diverse range of international experts in biorefinery research, synthetic biology, bioprocess engineering, and lean manufacturing, Biofoundry Techniques for Biotechnology Applications includes information on: Biofoundry Techniques for Biotechnology Applications serves as an invaluable source of up-to-date information for researchers, academics, and graduate and postgraduate students in the fields of microbial biotechnology, applied microbiology, biochemical engineering, and environmental science and engineering.
List of Contributors xv About the Editor xxi Preface xxiii 1 Biomass Refining and Biofoundry: Key Products, Process Limitations, and Future Aspects 1 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 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 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 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 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 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 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 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 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 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 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 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 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 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
Lucas Ramos, Jesús Jiménez Ascencio, James Villar, Mónica Ma. Cruz- Santos, and Anuj Kumar Chandel
Katarina Mihajlovski, Nevena Ilić, Galina Jevđenović, and Marija Milić
Yaimé Delgado- Arcaño, Alisson Dias da Silva Ruy, Leila Maria Aguilera Campos, and Oscar Daniel Valmaña- García
Lucas Ramos, Carina Prado, Maria Teresa Ferreira Ramos Raimundo, Uirajá C. M. Ruschoni, Vinícius Pereira Shibukawa, and Anuj Kumar Chandel
Danielle Matias Rodrigues, Paula Zaghetto de Almeida, Allan H. Félix de Mélo, Juliana Velasco de Castro Oliveira, Ana Paula Jacobus, and Henrique Macedo Baudel
Sounak Maitra, Muskaan Sethi, Prisha Inani, Palak Shrivastava, C. Shriya, and Samuel Jacob
Samatha Paladugu, Sarepalli Sai Sathwik, and Mamatha Potu
Samatha Paladugu, Sarepalli Sai Sathwik, and Sreelatha Beemagani
Simab Kanwal, Sher Zaman Safi, Aphichart Karnchanatat, and Piroonporn Srimongkol
Carlos Lopez- Ortiz, Alan Chavez- Hita Wong, Aldo Sosa, and Nagamani Balagurusamy
José Daniel Cano Montoya, Diego Hernandez, and Josman Velasco
Shruti Ahlawat, Somya Gupta, Ritika Yadav, and Krishna Kant Sharma
Andreza A. Longati, Christian de Oliveira Martins, Gabriel Baioni, Adilson José da Silva, Thais Suzane Milessi, and Felipe Fernando Furlan
Fabricio M. Gomes, Messias Borges Silva, Giovani Maltempi- Mendes, and Anuj Kumar Chandel
Subject Areas: Biology, life sciences [PS]
