Biofoundry Techniques for Biotechnology Applications

Dr. Anuj Kumar Chandel, Renewable Carbon and Biology Systems Laboratory-ReCABS, Department of Biotechnology, Engineering School of Lorena, University of São Paulo (EEL-USP), Lorena, São Paulo, Brazil. Dr Chandel has over 23 years’ research experience working on various aspects of industrial biotechnology, including the production of industrial enzymes, biofuels, and bio-based products and membrane-based separation of fats, proteins, and viruses. He is currently coordinating research on lignin valorization into PHA, biolipids, biogas, and catalytic links.

• List of Contributors xvAbout the Editor xxiPreface xxiii1 Biomass Refining and Biofoundry: Key Products, Process Limitations, and Future Aspects 1Lucas Ramos, Jesús Jiménez Ascencio, James Villar, Mónica Ma. Cruz-Santos, and Anuj Kumar Chandel1.1 Introduction 12 Structural Carbohydrates Conversion into Sugars, Fuels, Chemicals, and Sustainable Materials 27Katarina Mihajlovski, Nevena Iliæ, Galina Jevðenoviæ, and Marija Miliæ2.1 Introduction 272.2 Conclusions 513 Integrating Lignocellulosic Biomass Processing, Biomanufacturing, and Biofoundries: Innovations and Challenges in the Bioeconomy 59Yaimé Delgado-Arcaño, Alisson Dias da Silva Ruy, Leila Maria Aguilera Campos, and Oscar Daniel Valmaña-García3.1 Introduction 593.2 Advances in Biomass Processing: Pretreatment and Purification Strategies 603.3 Bioeconomy and Biofoundries: How Automation and Synthetic Biology can Enhance Biorefineries 653.4 Economic Competitiveness in the Production of Bioproducts of Commercial Interest 723.5 Conclusions 784 Lignin Valorization Is the Key for a Win–Win Situation in a Biomass Refinery 87Lucas Ramos, Carina Prado, Maria Teresa Ferreira Ramos Raimundo, Uirajá C. M. Ruschoni, Vinícius Pereira Shibukawa, and Anuj Kumar Chandel4.1 Introduction 874.2 Lignin: Dispensable Source of Renewable Carbon 884.3 Lignin Chemistry 904.4 Lignin Extraction Methods 924.5 Lignin Conversion Route 944.6 Biological Routes 944.7 Chemical Routes 964.8 Lignin in the Pulp and Paper Industry 974.9 Conclusion and Future Directions 995 Sustainable Production of Advanced Alcohol-Based Biofuels in Biorefinery: From Alcohols to Sustainable Aviation Fuels 105Danielle Matias Rodrigues, Paula Zaghetto de Almeida, Allan H. Félix de Mélo, Juliana Velasco de Castro Oliveira, Ana Paula Jacobus, and Henrique Macedo Baudel5.1 Introduction 1055.2 Bioethanol 1065.3 Advanced Alcohol-Based Fuels 1085.4 Biobutanol: The Biofoundry as a Tool to Optimize 1095.5 Biofoundry Synthetic Biology Tools 1135.6 Sustainable Aviation Fuel (SAF) 1175.7 Conclusion 1186 Biomanufacturing of Smart Packaging Materials, Cosmetics, Therapeutics, and Nanomaterials Through Lignocellulosic Biorefinery Framework 127Sounak Maitra, Muskaan Sethi, Prisha Inani, Palak Shrivastava, C. Shriya, and Samuel Jacob6.1 Introduction 1276.2 Lignocellulosic Raw Materials and Their Potential as Industrial Raw Materials 1286.3 Smart Packaging Materials 1356.4 Cosmetics and Therapeutics 1386.5 Bio-Nanotechnology Through Biomass 1416.6 Conclusion 1427 White Biotechnology for Skincare: Unveiling the Power of Bioactives for the Cosmetic Industry 151Samatha Paladugu, Sarepalli Sai Sathwik, and Mamatha Potu7.1 Introduction 1517.2 Fermented Bioactives 1537.3 Innovative Approaches in Green Bio-ferment Cosmetic Formulations 1567.4 Green Bio Ferments 1587.5 Active Compounds from Bioferments 1607.6 Application of Bioferments in Skincare 1707.7 KINMATI: The Advanced Probiotic Biofermented Raw Material for Skincare 1737.8 Future of Bio-ferments, Active Ingredients, and Green Formulations 1737.9 Conclusion 1768 Biotechnological Advancements in Lactic Acid Bacteria Fermentation: Metabolic Pathways and Metabolite Profiles 189Samatha Paladugu, Sarepalli Sai Sathwik, and Sreelatha Beemagani8.1 Introduction 1898.2 Metabolism of Carbohydrates (Mono, Di, Oligo, and Polysaccharides) 1908.3 Monosaccharides 1918.4 Disaccharides 1928.5 Oligosaccharides 1938.6 Polysaccharides and Indigestible Carbohydrates 1938.7 Indigestible Starch/Resistant Starch 1938.8 Metabolism of Nitrogen Source (Proteins) 1958.9 Utilization and Metabolism of Malic Acid and Citric Acid 1998.10 Metabolite Profiles of Lactobacillus Ferments 2008.11 Vitamins 2018.12 Short-chain Fatty Acids 2028.13 Exopolysaccharides 2028.14 Antioxidant Substances 2028.15 Production of Polyols 2038.16 Metabolomic Profiles of Different Lactic Acid Bacteria in the Rice Fermentation 2039 Biofoundry in Microbial Protein Production: Process Challenges and Future Scenario 219Simab Kanwal, Sher Zaman Safi, Aphichart Karnchanatat, and Piroonporn Srimongkol9.1 Introduction 2199.2 Microorganisms and Protein Production 2209.3 Strain Selection for Protein Production 2219.4 Protein-Rich Biomass Production 2229.5 Microbial Bioprocessing 2239.6 Cultivation Systems 2249.7 Bioreactors for Protein Production 2249.8 Downstream Processing 2259.9 Strategies in Synthetic Bioengineering 2279.10 Challenges and Future Prospects 2299.11 Conclusions 23110 Nanotechnological Interventions in the Advancement of Lignocellulose Bio-Foundry: Current Status and Future Prospects 237Carlos Lopez-Ortiz, Alan Chavez-Hita Wong, Aldo Sosa, and Nagamani Balagurusamy10.1 Introduction 23710.2 Advancing Lignocellulose Bio-Foundries: Pretreatment Strategies and Nanotechnology Integration 23810.3 Catalytic Nanomaterials and Enzyme Immobilization for Lignocellulose Biomass Conversion 23910.4 Underlying the Interactions of Nanotechnology Mechanism in Lignocellulose Bio-Foundry 24210.5 Factors Affecting Nanotechnology Use and Its Performance in Bio-Foundry Using Lignocellulosic Biomass 24510.6 Challenges and Considerations Using Nanotechnology in Lignocellulose Bio-Foundry 24610.7 Future Perspectives of Nanotechnology in Biofuel Production 24810.8 Conclusion 24811 Synthetic Biology in the Realm of Genome Engineering for Improved Biocatalysts and Production 257José Daniel Cano Montoya, Diego Hernandez, and Josman Velasco11.1 Introduction 25711.2 The Design–Build–Test–Learn Cycle for Optimizing Biological Systems 25811.3 The Synthetic Biology Toolkit for Genome Engineering 25911.4 Production and Improvement of Biocatalysts 26411.5 Conclusions and Final Remarks 27312 Multi-omics Technologies Paving the Way for the Success of Biorefinery 279Shruti Ahlawat, Somya Gupta, Ritika Yadav, and Krishna Kant Sharma12.1 Introduction 27912.2 Lignocellulosic Biomass 28012.3 Steps in Biorefinery 28012.4 Various Value-Added Products Generated from Lignocellulosic Biomass 28412.5 Cellulose-Based Value-Added Products 28512.6 Hemicellulose-Based Value-Added Products 28712.7 Lignin-Based Value-Added Products 28812.8 CRISPR/Cas9 and -Omics Technologies 28912.9 Utilization of -Omics Technologies Toward Biorefinery Success 28912.10 Role in Efficient Enzyme Production 29312.11 Role in Microalgae-Based Biorefinery 296\12.12 Conclusion 29713 Sustainability Assessment of Genetically Engineered Biocatalysts Producing Biofuels and Biochemicals 309Andreza A. Longati, Christian de Oliveira Martins, Gabriel Baioni, Adilson José da Silva, Thais Suzane Milessi, and Felipe Fernando Furlan13.1 Introduction 30913.2 The Role of Genetically Modified Organisms in Biorefineries 31013.3 Metabolic Modeling in the Development of Genetically Modified Organisms 31213.4 Parameters to Evaluate the Sustainability of Genetically Modified Organisms 31513.5 Case Studies of Genetically Modified Organisms 32413.6 Conclusions 32714 Lean Manufacturing Toward Minimum Waste Discharge and Potential Gains in the Biorefinery and Biotechnology Industries 337Fabricio M. Gomes, Messias Borges Silva, Giovani Maltempi-Mendes, and Anuj Kumar Chandel14.1 Introduction 33714.2 The Fundamentals of Lean Manufacturing 33714.3 The Five Principles of Lean 33814.4 Waste Reduction in Biotechnology: Unique Challenges 33814.5 Types of Waste in Biotechnology 33814.6 Managing Biohazardous Waste 33914.7 Lean Tools for Biotechnology 33914.8 Total Productive Maintenance 34114.9 Lean Manufacturing and Digitalization in Biotechnology 34114.10 Real-Time Data Analytics 34114.11 Digital Twins 34214.12 Potential Gains from Lean Implementation in Biotechnology 34214.13 Cost Savings 34214.14 Lean Manufacturing's Role in Addressing Sustainability Goals 34314.15 Regulatory Compliance and Lean in Biotechnology 34414.16 Commercial Aspects of Lean Implementation in Biorefineries 34414.17 Case Study: Lean Implementation at Pfizer 34514.18 Case Study: Novartis and Lean Implementation in Biopharma 34814.19 Conclusion 348Acknowledgments 348References 348Index 351