Biomanufacturing: history and perspective

Machine learning: an advancement in biochemical engineering

One of the most remarkable techniques recently introduced into the field of bioprocess engineering is machine learning. Bioprocess engineering has drawn much attention due to its vast application in different domains like biopharmaceuticals, fossil fuel alternatives, environmental remediation, and food and beverage industry, etc. However, due to their unpredictable mechanisms, they are very often challenging to optimize. Furthermore, biological systems are extremely complicated; hence, machine learning algorithms could potentially be utilized to improve and build new biotechnological processes. Gaining insight into the fundamental mathematical understanding of commonly used machine learning algorithms, including Support Vector Machine, Principal Component Analysis, Partial Least Squares and Reinforcement Learning, the present study aims to discuss various case studies related to the application of machine learning in bioprocess engineering. Recent advancements as well as challenges posed in this area along with their potential solutions are also presented.

Diverting organic waste from landfills via insect biomanufacturing using engineered black soldier flies (Hermetia illucens)

A major roadblock towards the realisation of a circular economy are the lack of high-value products that can be generated from waste. Black soldier flies (BSF; Hermetia illucens) are gaining traction for their ability to rapidly consume large quantities of organic wastes. However, these are primarily used to produce a small variety of products, such as animal feed ingredients and fertiliser. Using synthetic biology, BSF could be developed into a novel sustainable biomanufacturing platform to valorise a broader variety of organic waste feedstocks into enhanced animal feeds, a large variety of high-value biomolecules including industrial enzymes and lipids, and improved fertiliser.

Innovation in precision fermentation for food ingredients

A transformation in our food production system is being enabled by the convergence of advances in genome-based technologies and traditional fermentation. Science at the intersection of synthetic biology, fermentation, downstream processing for product recovery, and food science is needed to support technology development for the production of fermentation-derived food ingredients. The business and markets for fermentation-derived ingredients, including policy and regulations are discussed. A patent landscape of fermentation for the production of alternative proteins, lipids and carbohydrates for the food industry is provided. The science relating to strain engineering, fermentation, downstream processing, and food ingredient functionality that underpins developments in precision fermentation for the production of proteins, fats and oligosaccharides is examined. The production of sustainably-produced precision fermentation-derived ingredients and their introduction into the market require a transdisciplinary approach with multistakeholder engagement. Successful innovation in fermentation-derived ingredients will help feed the world more sustainably.

Noninvasive and Continuous Monitoring of On-Chip Stem Cell Osteogenesis Using a Reusable Electrochemical Immunobiosensor

Noninvasive monitoring of biofabricated tissues during the biomanufacturing process is needed to obtain reproducible, healthy, and functional tissues. Measuring the levels of biomarkers secreted from tissues is a promising strategy to understand the status of tissues during biofabrication. Continuous and real-time information from cultivated tissues enables users to achieve scalable manufacturing. Label-free biosensors are promising candidates for detecting cell secretomes since they can be noninvasive and do not require labor-intensive processes such as cell lysing. Moreover, most conventional monitoring techniques are single-use, conducted at the end of the fabrication process, and, challengingly, are not permissive to in-line and continual detection. To address these challenges, we developed a noninvasive and continual monitoring platform to evaluate the status of cells during the biofabrication process, with a particular focus on monitoring the transient processes that stem cells go through during in vitro differentiation over extended periods. We designed and evaluated a reusable electrochemical immunosensor with the capacity for detecting trace amounts of secreted osteogenic markers, such as osteopontin (OPN). The sensor has a low limit of detection (LOD), high sensitivity, and outstanding selectivity in complex biological media. We used this OPN immunosensor to continuously monitor on-chip osteogenesis of human mesenchymal stem cells (hMSCs) cultured 2D and 3D hydrogel constructs inside a microfluidic bioreactor for more than a month and were able to observe changing levels of OPN secretion during culture. The proposed platform can potentially be adopted for monitoring a variety of biological applications and further developed into a fully automated system for applications in advanced cellular biomanufacturing.

Genome-scale metabolic network models for industrial microorganisms metabolic engineering: Current advances and future prospects

The construction of high-performance microbial cell factories (MCFs) is the centerpiece of biomanufacturing. However, the complex metabolic regulatory network of microorganisms poses great challenges for the efficient design and construction of MCFs. The genome-scale metabolic network models (GSMs) can systematically simulate the metabolic regulation process of microorganisms in silico, providing effective guidance for the rapid design and construction of MCFs. In this review, we summarized the development status of 16 important industrial microbial GSMs, and further outline the technologies or methods that continuously promote high-quality GSMs construction from five aspects: I) Databases and modeling tools facilitate GSMs reconstruction; II) evolving gap-filling technologies; III) constraint-based model reconstruction; IV) advances in algorithms; and V) developed visualization tools. In addition, we also summarized the applications of GSMs in guiding metabolic engineering from four aspects: I) exploring and explaining metabolic features; II) predicting the effects of genetic perturbations on metabolism; III) predicting the optimal phenotype; IV) guiding cell factories construction in practical experiment. Finally, we discussed the development of GSMs, aiming to provide a reference for efficiently reconstructing GSMs and guiding metabolic engineering.

Development, characterization and application of 3D printed adsorbents for in situ recovery of taxadiene from microbial cultivations

Microbial cell factories are an attractive alternative to produce high-value natural products using sustainable processes. However, product recovery is one of the main challenges to reduce production cost and make these technologies economically interesting. In this work, new resins were formulated to 3D print hydrophobic adsorbents for the recovery of biologics from microbial cultivations. Benzyl methacrylate (BEMA) and butyl methacrylate (BUMA) were selected as functional monomers suitable for the adsorption of hydrophobic compounds. Pore morphology was tailored through the inclusion of pore forming agents (porogens) in the resin. Different porogens and porogen concentrations were evaluated resulting in materials with different porous networks. Sudan 1 and the anticancer drug paclitaxel were employed as model compounds to test the adsorption performance of hydrophobic and terpene molecules onto the developed 3D printed materials. The material with greatest adsorption capacity was obtained using BEMA monomer with 40 % (v/v) porogen (BEMA40). The performance of BEMA40 to recover taxadiene from small-scale (5 mL) Saccharomyces cerevisiae cultivations was tested and compared with commercial Diaion HP-20 beads. Taxadiene titres on BEMA40 (46 ± 2 mg/L) and Diaion HP-20 (54 ± 4 mg/L) were comparable, with no taxadiene detected in the cells and cell-free media, suggesting near 100 % taxadiene partition on the adsorbents. Compared to commercial beads, 3D printed adsorbents can be customized with adjustments in the resin formulation, are well adaptable to diverse bioreactor types, do not clog sampling ports and columns and are easier to handle during post processing. The results of this work demonstrate the potential of 3D printing to fabricate hydrophobic interaction adsorbent materials and their application in the recovery of biological products.

Automated in vivo enzyme engineering accelerates biocatalyst optimization

Achieving cost-competitive bio-based processes requires development of stable and selective biocatalysts. Their realization through in vitro enzyme characterization and engineering is mostly low throughput and labor-intensive. Therefore, strategies for increasing throughput while diminishing manual labor are gaining momentum, such as in vivo screening and evolution campaigns. Computational tools like machine learning further support enzyme engineering efforts by widening the explorable design space. Here, we propose an integrated solution to enzyme engineering challenges whereby ML-guided, automated workflows (including library generation, implementation of hypermutation systems, adapted laboratory evolution, and in vivo growth-coupled selection) could be realized to accelerate pipelines towards superior biocatalysts.

ATP-free in vitro biotransformation of starch-derived maltodextrin into poly-3-hydroxybutyrate via acetyl-CoA

In vitro biotransformation (ivBT) facilitated by in vitro synthetic enzymatic biosystems (ivSEBs) has emerged as a highly promising biosynthetic platform. Several ivSEBs have been constructed to produce poly-3-hydroxybutyrate (PHB) via acetyl-coenzyme A (acetyl-CoA). However, some systems are hindered by their reliance on costly ATP, limiting their practicality. This study presents the design of an ATP-free ivSEB for one-pot PHB biosynthesis via acetyl-CoA utilizing starch-derived maltodextrin as the sole substrate. Stoichiometric analysis indicates this ivSEB can self-maintain NADP+/NADPH balance and achieve a theoretical molar yield of 133.3%. Leveraging simple one-pot reactions, our ivSEBs achieved a near-theoretical molar yield of 125.5%, the highest PHB titer (208.3 mM, approximately 17.9 g/L) and the fastest PHB production rate (9.4 mM/h, approximately 0.8 g/L/h) among all the reported ivSEBs to date, and demonstrated easy scalability. This study unveils the promising potential of ivBT for the industrial-scale production of PHB and other acetyl-CoA-derived chemicals from starch.

Pseudomonas putida as a platform for medium-chain length α,ω-diol production: Opportunities and challenges

Medium-chain-length α,ω-diols (mcl-diols) play an important role in polymer production, traditionally depending on energy-intensive chemical processes. Microbial cell factories offer an alternative, but conventional strains like Escherichia coli and Saccharomyces cerevisiae face challenges in mcl-diol production due to the toxicity of intermediates such as alcohols and acids. Metabolic engineering and synthetic biology enable the engineering of non-model strains for such purposes with P. putida emerging as a promising microbial platform. This study reviews the advancement in diol production using P. putida and proposes a four-module approach for the sustainable production of diols. Despite progress, challenges persist, and this study discusses current obstacles and future opportunities for leveraging P. putida as a microbial cell factory for mcl-diol production. Furthermore, this study highlights the potential of using P. putida as an efficient chassis for diol synthesis.

Exploring engineering strategies that enhance de novo production of exotic cyclopropane fatty acids in Saccharomyces cerevisiae

Cycloalkanes have broad applications as specialty fuels, lubricants, and pharmaceuticals but are not currently available from renewable sources, whereas, production of microbial cycloalkanes such as cyclopropane fatty acids (CFA) has bottlenecks. Here, a systematic investigation was undertaken into the biosynthesis of CFA in Saccharomyces cerevisiae heterologously expressing bacterial CFA synthase. The enzyme catalyzes formation of a 3-membered ring in unsaturated fatty acids. Monounsaturated fatty acids in phospholipids (PL) are the site of CFA synthesis; precursor cis-Δ9 C16 and C18 fatty acids were enhanced through OLE1 and SAM2 overexpression which enhanced CFA in PL. CFA turnover from PL to storage in triacylglycerols (TAG) was achieved by phospholipase PBL2 overexpression and acyl-CoA synthase to increase flux to TAG. Consequently, CFA storage as TAG reached 12 mg g-1 DCW, improved 3-fold over the base strain and >22% of TAG was CFA. Our research improves understanding of cycloalkane biosynthesis in yeast and offers insights into processing of other exotic fatty acids.

Improving microbial production of value-added products through the intervention of magnetic fields

The magnetic field application is emerging as an auxiliary physical strategy to facilitate rapid biomass accumulation and intracellular production of compounds. However, the underlying mechanisms and principles governing the application of magnetic fields for microbial growth and biotransformation are not yet fully understood. Therefore, a better understanding of interdisciplinary technologies integration, expanded magnetic field application, and scaled-up industrial implementation is crucial. In this review, the magnetic field characteristics, magnetic field-assisted fermentation devices, and the working mechanism of magnetic field have been reviewed comprehensively from both physical and microbiological perspectives. The review suggests that magnetic fields affect the biochemical processes in microorganisms by mediating nutrient transport across membranes, electron transfer during photosynthesis and respiration, enzyme activity and gene expression. Moreover, the recent advances in magnetic field application for microbial fermentation and conversion in biochemical, food and agricultural fields have been summarized.

Harnessing genetic engineering to drive economic bioproduct production in algae

Our reliance on agriculture for sustenance, healthcare, and resources has been essential since the dawn of civilization. However, traditional agricultural practices are no longer adequate to meet the demands of a burgeoning population amidst climate-driven agricultural challenges. Microalgae emerge as a beacon of hope, offering a sustainable and renewable source of food, animal feed, and energy. Their rapid growth rates, adaptability to non-arable land and non-potable water, and diverse bioproduct range, encompassing biofuels and nutraceuticals, position them as a cornerstone of future resource management. Furthermore, microalgae's ability to capture carbon aligns with environmental conservation goals. While microalgae offers significant benefits, obstacles in cost-effective biomass production persist, which curtails broader application. This review examines microalgae compared to other host platforms, highlighting current innovative approaches aimed at overcoming existing barriers. These approaches include a range of techniques, from gene editing, synthetic promoters, and mutagenesis to selective breeding and metabolic engineering through transcription factors.

Engineering of increased L-Threonine production in bacteria by combinatorial cloning and machine learning

The goal of this study is to develop a general strategy for bacterial engineering using an integrated synthetic biology and machine learning (ML) approach. This strategy was developed in the context of increasing L-threonine production in Escherichia coli ATCC 21277. A set of 16 genes was initially selected based on metabolic pathway relevance to threonine biosynthesis and used for combinatorial cloning to construct a set of 385 strains to generate training data (i.e., a range of L-threonine titers linked to each of the specific gene combinations). Hybrid (regression/classification) deep learning (DL) models were developed and used to predict additional gene combinations in subsequent rounds of combinatorial cloning for increased L-threonine production based on the training data. As a result, E. coli strains built after just three rounds of iterative combinatorial cloning and model prediction generated higher L-threonine titers (from 2.7 g/L to 8.4 g/L) than those of patented L-threonine strains being used as controls (4-5 g/L). Interesting combinations of genes in L-threonine production included deletions of the tdh, metL, dapA, and dhaM genes as well as overexpression of the pntAB, ppc, and aspC genes. Mechanistic analysis of the metabolic system constraints for the best performing constructs offers ways to improve the models by adjusting weights for specific gene combinations. Graph theory analysis of pairwise gene modifications and corresponding levels of L-threonine production also suggests additional rules that can be incorporated into future ML models.

Status and developmental trends in recombinant collagen preparation technology

Recombinant collagen is a pivotal topic in foundational biological research and epitomizes the application of critical bioengineering technologies. These technological advancements have profound implications across diverse areas such as regenerative medicine, organ replacement, tissue engineering, cosmetics and more. Thus, recombinant collagen and its preparation methodologies rooted in genetically engineered cells mark pivotal milestones in medical product research. This article provides a comprehensive overview of the current genetic engineering technologies and methods used in the production of recombinant collagen, as well as the conventional production process and quality control detection methods for this material. Furthermore, the discussion extends to foresee the strides in physical transfection and magnetic control sorting studies, envisioning an enhanced preparation of recombinant collagen-seeded cells to further fuel recombinant collagen production.

Humans and robots: Friends of the future? A bird's eye view of biomanufacturing industry 5.0

The evolution of industries have introduced versatile technologies, motivating limitless possibilities of tackling pivotal global predicaments in the arenas of medicine, environment, defence, and national security. In this direction, ardently emerges the new era of Industry 5.0 through the eyes of biomanufacturing, which integrates the most advanced systems 21st century has to offer by means of integrating artificial systems to mimic and nativize the natural milieu to substitute the deficits of nature, thence leading to a new meta world. Albeit, it questions the natural order of the living world, which necessitates certain paramount stipulations to be addressed for a successful expansion of biomanufacturing Industry 5.0. Can humans live in synergism with artificial beings? How can humans establish dominance of hierarchy with artificial counterparts? This perspective provides a bird's eye view on the plausible direction of a new meta world inquisitively. For this purpose, we propose the influence of internet of things (IoT) via new generation interfacial systems, such as, human-machine interface (HMI) and brain-computer interface (BCI) in the domain of tissue engineering and regenerative medicine, which can be extended to target modern warfare and smart healthcare.

Synergistic investigation of natural and synthetic C1-trophic microorganisms to foster a circular carbon economy

A true circular carbon economy must upgrade waste greenhouse gases. C1-based biomanufacturing is an attractive solution, in which one carbon (C1) molecules (e.g. CO2, formate, methanol, etc.) are converted by microbial cell factories into value-added goods (i.e. food, feed, and chemicals). To render C1-based biomanufacturing cost-competitive, we must adapt microbial metabolism to perform chemical conversions at high rates and yields. To this end, the biotechnology community has undertaken two (seemingly opposing) paths: optimizing natural C1-trophic microorganisms versus engineering synthetic C1-assimilation de novo in model microorganisms. Here, we pose how these approaches can instead create synergies for strengthening the competitiveness of C1-based biomanufacturing as a whole.

From observational to actionable: rethinking omics in biologics production

As the era of omics continues to expand with increasing ubiquity and success in both academia and industry, omics-based experiments are becoming commonplace in industrial biotechnology, including efforts to develop novel solutions in bioprocess optimization and cell line development. Omic technologies provide particularly valuable 'observational' insights for discovery science, especially in academic research and industrial R&D; however, biomanufacturing requires a different paradigm to unlock 'actionable' insights from omics. Here, we argue the value of omic experiments in biotechnology can be maximized with deliberate selection of omic approaches and forethought about analysis techniques. We describe important considerations when designing and implementing omic-based experiments and discuss how systems biology analysis strategies can enhance efforts to obtain actionable insights in mammalian-based biologics production.

Biosynthesis of Lacto-N-biose I from starch and N-acetylglucosamine via an in vitro synthetic enzymatic biosystem

Human milk oligosaccharides (HMOs) are very distinctive components in human milk and are beneficial for infant health. Lacto-N-biose I (LNB) is the core structural unit of HMOs, which could be used for the synthesis of other HMOs. In this study, an ATP-free in vitro synthetic enzymatic biosystem contained four thermostable enzymes (alpha-glucan phosphorylase from Thermococcus kodakarensis, UDP-glucose-hexose-1-phosphate uridylyltransferase from Thermotoga maritima, UDP-glucose 4-epimerase from T. maritima, lacto-N-biose phosphorylase from Clostridium thermobutyricum) were constructed for the biosynthesis of LNB from starch and N-acetylglucosamine (GlcNAc). Under the optimal conditions, 0.75 g/L and 2.23 g/L LNB was produced from 1.1 g/L and 4.4 g/L GlcNAc and excess starch, with the molar yield of 39% and 29% based on the GlcNAc concentration, respectively, confirming the feasibility of this in vitro synthetic enzymatic biosystem for LNB synthesis and shedding light on the biosynthesis of other HMOs using LNB as the core structural unit from low cost polysaccharides.

Atmospheric and Room Temperature Plasma (ARTP) Mutagenesis Improved the Anti-MRSA Activity of Brevibacillus sp. SPR20

Brevibacillus sp. SPR20 produced potentially antibacterial substances against methicillin-resistant Staphylococcus aureus (MRSA). The synthesis of these substances is controlled by their biosynthetic gene clusters. Several mutagenesis methods are used to overcome the restriction of gene regulations when genetic information is absent. Atmospheric and room temperature plasma (ARTP) is a powerful technique to initiate random mutagenesis for microbial strain improvement. This study utilized an argon-based ARTP to conduct the mutations on SPR20. The positive mutants of 40% occurred. The M27 mutant exhibited an increase in anti-MRSA activity when compared to the wild-type strain, with the MIC values of 250-500 and 500 μg/mL, respectively. M27 had genetic stability because it exhibited constant activity throughout fifteen generations. This mutant had similar morphology and antibiotic susceptibility to the wild type. Comparative proteomic analysis identified some specific proteins that were upregulated in M27. These proteins were involved in the metabolism of amino acids, cell structure and movement, and catalytic enzymes. These might result in the enhancement of the anti-MRSA activity of the ARTP-treated SPR20 mutant. This study supports the ARTP technology designed to increase the production of valuable antibacterial agents.

Efficient Autotransporter-Mediated Extracellular Secretion of a Heterologous Recombinant Protein by Escherichia coli

The autotransporter protein secretion system has been used previously to target the secretion of heterologous proteins to the bacterial cell surface and the extracellular milieu at the laboratory scale. The platform is of particular interest for the production of "difficult" recombinant proteins that might cause toxic effects when produced intracellularly. One such protein is IrmA. IrmA is a vaccine candidate that is produced in inclusion bodies requiring refolding. Here, we describe the use and scale-up of the autotransporter system for the secretion of an industrially relevant protein (IrmA). A plasmid expressing IrmA was constructed such that the autotransporter platform could secrete IrmA into the culture supernatant fraction. The autotransporter platform was suitable for the production and purification of IrmA with comparable physical properties to the protein produced in the cytoplasm. The production of IrmA was translated to scale-up protein production conditions resulting in a yield of 29.3 mg/L of IrmA from the culture supernatant, which is consistent with yields of current industrial processes. IMPORTANCE Recombinant protein production is an essential component of the biotechnology sector. Here, we show that the autotransporter platform is a viable method for the recombinant production, secretion, and purification of a "difficult" to produce protein on an industrially relevant scale. Use of the autotransporter platform could reduce the number of downstream processing operations required, thus accelerating the development time and reducing costs for recombinant protein production.

Current advances for omics-guided process optimization of microbial manufacturing

Currently, microbial manufacturing is widely used in various fields, such as food, medicine and energy, for its advantages of greenness and sustainable development. Process optimization is the committed step enabling the commercialization of microbial manufacturing products. However, the present optimization processes mainly rely on experience or trial-and-error method ignoring the intrinsic connection between cellular physiological requirement and production performance, so in many cases the productivity of microbial manufacturing could not been fully exploited at economically feasible cost. Recently, the rapid development of omics technologies facilitates the comprehensive analysis of microbial metabolism and fermentation performance from multi-levels of molecules, cells and microenvironment. The use of omics technologies makes the process optimization more explicit, boosting microbial manufacturing performance and bringing significant economic benefits and social value. In this paper, the traditional and omics technologies-guided process optimization of microbial manufacturing are systematically reviewed, and the future trend of process optimization is prospected.

Carrier-Free Immobilization of Multi-Enzyme Complex Facilitates In Vitro Synthetic Enzymatic Biosystem for Biomanufacturing

A method is developed for carrier-free immobilization of multi-enzyme complexes with more than four enzymes by utilization of polypeptide interactions (SpyCatcher-SpyTag and dockerin-cohesin) and enzyme component self-oligomerization. Two pairs of scaffoldins with different arrangements of SpyCatcher-SpyTag and cohesins are prepared to recruit the four dockerin-containing cascade enzymes (i. e., alpha-glucan phosphorylase, phosphoglucomutase, inositol 1-phosphate synthase, and inositol 1-phosphatase) that can convert starch into inositol, forming multi-enzyme complexes. These self-assembled enzyme complexes show higher initial reaction rates than the four-enzyme cocktail. Moreover, water-insoluble self-assembled multi-enzyme complexes are observed, being the carrier-free immobilized multi-enzyme complex aggregates. These immobilized enzyme complexes can be recycled easily by simple centrifuging followed by resuspension for another round of reaction. Not only can these immobilized enzyme complexes be obtained by mixing the purified enzyme components, but also by the mixing of crude cell extracts. Therefore, the strategy for the carrier-free immobilization of enzyme complex sheds light on improving the catalytic capability of in vitro synthetic enzymatic biosystems.

Biotechnological and food synthetic biology potential of platform strain: Bacillus licheniformis

Bacillus licheniformis is one of the most characteristic Gram-positive bacteria. Its unique genetic background and safety characteristics make it have important biologic applications in the food industry, including, the biosynthesis of high value-added bioproducts, probiotic functions, biological treatment of wastes derived from food production, etc. In this review, these recent advances are summarized and presented systematically for the first time. In addition, we highlight synthetic biology strategies as a potential driver of developing this strain for wider and more efficient application in the food industry. Finally, we present the current challenges faced and provide our unique perspective on relevant future research directions. In summary, this review will provide an illuminating and comprehensive perspective that will allow an in-depth understanding of B. licheniformis and promote its more effective development in the food industry.

Transcription factor-based biosensors for screening and dynamic regulation

Advances in synthetic biology and genetic engineering are bringing into the spotlight a wide range of bio-based applications that demand better sensing and control of biological behaviours. Transcription factor (TF)-based biosensors are promising tools that can be used to detect several types of chemical compounds and elicit a response according to the desired application. However, the wider use of this type of device is still hindered by several challenges, which can be addressed by increasing the current metabolite-activated transcription factor knowledge base, developing better methods to identify new transcription factors, and improving the overall workflow for the design of novel biosensor circuits. These improvements are particularly important in the bioproduction field, where researchers need better biosensor-based approaches for screening production-strains and precise dynamic regulation strategies. In this work, we summarize what is currently known about transcription factor-based biosensors, discuss recent experimental and computational approaches targeted at their modification and improvement, and suggest possible future research directions based on two applications: bioproduction screening and dynamic regulation of genetic circuits.

High value valorization of lignin as environmental benign antimicrobial

Lignin is a natural aromatic polymer of p-hydroxyphenylpropanoids with various biological activities. Noticeably, plants have made use of lignin as biocides to defend themselves from pathogen microbial invasions. Thus, the use of isolated lignin as environmentally benign antimicrobial is believed to be a promising high value approach for lignin valorization. On the other hand, as green and sustainable product of plant photosynthesis, lignin should be beneficial to reduce the carbon footprint of antimicrobial industry. There have been many reports that make use of lignin to prepare antimicrobials for different applications. However, lignin is highly heterogeneous polymers different in their monomers, linkages, molecular weight, and functional groups. The structure and property relationship, and the mechanism of action of lignin as antimicrobial remains ambiguous. To show light on these issues, we reviewed the publications on lignin chemistry, antimicrobial activity of lignin models and isolated lignin and associated mechanism of actions, approaches in synthesis of lignin with improved antimicrobial activity, and the applications of lignin as antimicrobial in different fields. Hopefully, this review will help and inspire researchers in the preparation of lignin antimicrobial for their applications.

Biosynthesis of artificial starch and microbial protein from agricultural residue

Growing populations and climate change pose great challenges to food security. Humankind is confronting a serious question: how will we feed the world in the near future? This study presents an out-of-the-box solution involving the highly efficient biosynthesis of artificial starch and microbial proteins from available and abundant agricultural residue as new feed and food sources. A one-pot biotransformation using an in vitro coenzyme-free synthetic enzymatic pathway and baker's yeast can simultaneously convert dilute sulfuric acid-pretreated corn stover to artificial starch and microbial protein under aerobic conditions. The β-glucosidase-free commercial cellulase mixture plus an ex vivo two-enzyme complex containing cellobiose phosphorylase and potato α-glucan phosphorylase displayed on the surface of Saccharomyces cerevisiae, showed better cellulose hydrolysis rates than a commercial β-glucosidase-rich cellulase mixture. This is because the channeling of the hydrolytic product from the solid cellulosic feedstock to the yeast mitigated the inhibition of the cellulase cocktail. Animal tests have shown that the digestion of artificial amylose results in slow and relatively small changes in blood sugar levels, suggesting that it could be a new health food component that prevents obesity and diabetes. A combination of the utilization of available agricultural residue and the biosynthesis of starch and microbial protein from non-food biomass could address the looming food crisis in the food-energy-water nexus.

Biomanufacturing by In Vitro Biotransformation (ivBT) Using Purified Cascade Multi-enzymes

In vitro biotransformation (ivBT) refers to the use of an artificial biological reaction system that employs purified enzymes for the one-pot conversion of low-cost materials into biocommodities such as ethanol, organic acids, and amino acids. Unshackled from cell growth and metabolism, ivBT exhibits distinct advantages compared with metabolic engineering, including but not limited to high engineering flexibility, ease of operation, fast reaction rate, high product yields, and good scalability. These characteristics position ivBT as a promising next-generation biomanufacturing platform. Nevertheless, challenges persist in the enhancement of bulk enzyme preparation methods, the acquisition of enzymes with superior catalytic properties, and the development of sophisticated approaches for pathway design and system optimization. In alignment with the workflow of ivBT development, this chapter presents a systematic introduction to pathway design, enzyme mining and engineering, system construction, and system optimization. The chapter also proffers perspectives on ivBT development.

Continuous biomanufacturing with microbes - upstream progresses and challenges

Current biomanufacturing facilities are mainly built for batch or fed-batch operations, which are subject to low productivities and do not achieve the great bioconversion potential of the rewired cells generated via modern biotechnology. Continuous biomanufacturing should be the future directions for high-yield and low-cost manufacturing of various fermentation products. This review discusses the major challenges and the strategies for continuous biomanufacturing with microbes, which include minimizing contamination risk, enhancing genetic stability over a long-term continuous operation, achieving high product titer, rate, and yield simultaneously by decoupling cell growth from product formation, and using modeling approach to accelerate research and development of continuous biomanufacturing. New strain designs and process engineering strategies, including integration with artificial intelligence, are also discussed for intelligent and the next generation of continuous biomanufacturing.

Prospects for carbon-negative biomanufacturing

Biomanufacturing has the potential to reduce demand for petrochemicals and mitigate climate change. Recent studies have also suggested that some of these products can be net carbon negative, effectively removing CO₂ from the atmosphere and locking it up in products. This review explores the magnitude of carbon removal achievable through biomanufacturing and discusses the likely fate of carbon in a range of target molecules. Solvents, cleaning agents, or food and pharmaceutical additives will likely re-release their carbon as CO₂ at the end of their functional lives, while carbon incorporated into non-compostable polymers can result in long-term sequestration. Future research can maximize its impact by focusing on reducing emissions, achieving performance advantages, and enabling a more circular carbon economy.

Efficient Bioproduction of Human Milk Alpha-Lactalbumin in Komagataella phaffii

Alpha-lactalbumin (α-LA; the most abundant whey protein in human milk) contributes to infant development, providing bioactive peptides and essential amino acids. Here, Komagataella phaffii (K. phaffii) was selected as the production host. We found that the K. phaffii host X33 was suitable for expressing the target protein, yielding 5.2 mg·L^-1 α-LA. Thereafter, several secretory signal peptides were applied to obtain a higher titer of α-LA. The strain with α-factor secretory signal peptide secreted the highest extracellular titer. Additionally, promoters AOX1, GAP, and GAP(m) were compared and applied. The strain with the promoter AOX1 produced the highest extracellular titer. In addition, coexpressing human protein disulfide isomerase A3 (hPDIA3) increased the titer by 27%. Human α-LA production by the strain X33-pPICZαA-hLALBA-hPDIA3 reached 56.3 mg·L^-1 in a 3 L bioreactor. This is the first report of successful secretory human α-LA expression in K. phaffii and lays foundations for the simulation of human milk for infant formulas and further development of bioengineered milk.

Uses of knockout, knockdown, and transgenic models in the studies of glucose transporter 4

Currently, glucose transporter 4 (GLUT4) has been considered as the key player for the insulin-stimulated glucose transport in the muscle and adipose tissues. The development of recombinant DNA techniques allows the creations of genetically knockout, knockdown and transgenic animals and cells for the study of GLUT4’s physiological functions. Here, we have used key words to search the PubMed and summarized the methods used in Slc2a4 gene knockout, GLUT4 knockdown and overexpression in the whole body and tissue specific manner. The whole body GLUT4-null mice have growth retardation, but normal glucose tolerance and basal glucose turnover rates. Compared with whole body Slc2a4 knockout mice, adipose and muscle double knockout mice have impaired insulin tolerance and glucose intolerance. The results of GLUT4 knockdown in 3T3-L1 adipocytes have shown that its expression is needed for lipogenesis after, but not during, differentiation. Transgenic mice with the whole body GLUT4 overexpression have normal body weight and lowered blood glucose level. The adipose tissue specific overexpression of GLUT4 leads to increases in mouse body weight and adipose tissue weight. The insulin-stimulated GLUT4 translocation in the skeletal muscle contributes to the regulation of glucose homeostasis. Data from both transgenic overexpression and tissue specific Slc2a4 knockout indicate that GLUT4 probably plays a role in the glucose uptake in the fasting state. More studies are warranted to use advanced molecular biology tools to decipher the roles of GLUT4 in the control of glucose homeostasis.

Biotechnology Applications of Cell-Free Expression Systems

Cell-free systems are a rapidly expanding platform technology with an important role in the engineering of biological systems. The key advantages that drive their broad adoption are increased efficiency, versatility, and low cost compared to in vivo systems. Traditionally, in vivo platforms have been used to synthesize novel and industrially relevant proteins and serve as a testbed for prototyping numerous biotechnologies such as genetic circuits and biosensors. Although in vivo platforms currently have many applications within biotechnology, they are hindered by time-constraining growth cycles, homeostatic considerations, and limited adaptability in production. Conversely, cell-free platforms are not hindered by constraints for supporting life and are therefore highly adaptable to a broad range of production and testing schemes. The advantages of cell-free platforms are being leveraged more commonly by the biotechnology community, and cell-free applications are expected to grow exponentially in the next decade. In this study, new and emerging applications of cell-free platforms, with a specific focus on cell-free protein synthesis (CFPS), will be examined. The current and near-future role of CFPS within metabolic engineering, prototyping, and biomanufacturing will be investigated as well as how the integration of machine learning is beneficial to these applications.

Single in-line biomass probe detects CHO cell growth by capacitance and bacterial contamination by conductivity in bioreactor

BACKGROUND

Real time process data facilitates timely decisions, enables better process control, and can increase quality assurance. Biological drugs (mol. Wt. ≥ 40 kDa) are manufactured using mammalian cells such as Chinese hamster ovary (CHO) cells in bioreactors and have significant risks of contamination during processing. In such processes, in-line monitoring of biomass can provide real-time cell growth profiles and indications of bioreactor health.

METHODS

An in-line conductivity/capacitance probe (Aber Instruments, Aberystwyth, UK) for monitoring CHO cell growth during fed batch cultures for producing an IgG1 monoclonal antibody was employed. Cell growth was measured in real-time using the capacitance probe (pF cm^-1 ) while being compared with off-line measurements using a metabolic analyzer (Nova Biomedical, Waltham, MA, USA). Conductivity measurements (mS cm^-1 ) detected variations in the solute concentrations in the bioreactor due to nutrient feed, bicarbonate buffer, and cellular metabolism by-products.

RESULTS AND CONCLUSION

Abnormal increases in conductivity were found to consistently correspond to bacterial contamination, which was confirmed by orthogonal methods. The contaminated bioreactor runs exhibited sharp increases in conductivity rates hours before dissolved oxygen levels precipitously decreased due to bacterial growth. It is proposed that in-line measurement of conductivity could be employed for early detection of bacterial contaminations. The probe may be adopted in pharmaceutical aseptic aqueous liquid handling processes.

Prototyping of microbial chassis for the biomanufacturing of high-value chemical targets

Metabolic engineering technologies have been employed with increasing success over the last three decades for the engineering and optimization of industrial host strains to competitively produce high-value chemical targets. To this end, continued reductions in the time taken from concept, to development, to scale-up are essential. Design-Build-Test-Learn pipelines that are able to rapidly deliver diverse chemical targets through iterative optimization of microbial production strains have been established. Biofoundries are employing in silico tools for the design of genetic parts, alongside combinatorial design of experiments approaches to optimize selection from within the potential design space of biological circuits based on multi-criteria objectives. These genetic constructs can then be built and tested through automated laboratory workflows, with performance data analysed in the learn phase to inform further design. Successful examples of rapid prototyping processes for microbially produced compounds reveal the potential role of biofoundries in leading the sustainable production of next-generation bio-based chemicals.

Production of myo-inositol: Recent advance and prospective

Myo-inositol and its derivatives have been extensively used in the pharmaceutics, cosmetics, and food and feed industries. In recent years, compared with traditional chemical acid hydrolysis, biological methods have been taken as viable and cost-effective ways to myo-inositol production from cheap raw materials. In this review, we provide a thorough overview of the development, progress, current status, and future direction of myo-inositol production (e.g., chemical acid hydrolysis, microbial fermentation, and in vitro enzymatic biocatalysis). The chemical acid hydrolysis of phytate suffers from serious phosphorous pollution and intricate product separation, resulting in myo-inositol production at a high cost. For microbial fermentation, creative strategies have been provided for the efficient myo-inositol biosynthesis by synergetic utilization of glucose and glycerol in Escherichia coli. In vitro cascade enzymatic biocatalysis is a multienzymatic transformation of various substrates to myo-inositol. Here, the different in vitro pathways design, the source of selected enzymes, and the catalytic condition optimization have been summarized and analyzed. Also, we discuss some important existing challenges and suggest several viewpoints. The development of in vitro enzymatic biosystems featuring low cost, high volumetric productivity, flexible compatibility, and great robustness could be one of the promising strategies for future myo-inositol industrial biomanufacturing.

Applications, challenges, and needs for employing synthetic biology beyond the lab

Synthetic biology holds great promise for addressing global needs. However, most current developments are not immediately translatable to 'outside-the-lab' scenarios that differ from controlled laboratory settings. Challenges include enabling long-term storage stability as well as operating in resource-limited and off-the-grid scenarios using autonomous function. Here we analyze recent advances in developing synthetic biological platforms for outside-the-lab scenarios with a focus on three major application spaces: bioproduction, biosensing, and closed-loop therapeutic and probiotic delivery. Across the Perspective, we highlight recent advances, areas for further development, possibilities for future applications, and the needs for innovation at the interface of other disciplines.

Omics-Driven Biotechnology for Industrial Applications

Biomanufacturing is a key component of biotechnology that uses biological systems to produce bioproducts of commercial relevance, which are of great interest to the energy, material, pharmaceutical, food, and agriculture industries. Biotechnology-based approaches, such as synthetic biology and metabolic engineering are heavily reliant on "omics" driven systems biology to characterize and understand metabolic networks. Knowledge gained from systems biology experiments aid the development of synthetic biology tools and the advancement of metabolic engineering studies toward establishing robust industrial biomanufacturing platforms. In this review, we discuss recent advances in "omics" technologies, compare the pros and cons of the different "omics" technologies, and discuss the necessary requirements for carrying out multi-omics experiments. We highlight the influence of "omics" technologies on the production of biofuels and bioproducts by metabolic engineering. Finally, we discuss the application of "omics" technologies to agricultural and food biotechnology, and review the impact of "omics" on current COVID-19 research.

Complex natural product production methods and options

Natural products have had a major impact upon quality of life, with antibiotics as a classic example of having a transformative impact upon human health. In this contribution, we will highlight both historic and emerging methods of natural product bio-manufacturing. Traditional methods of natural product production relied upon native cellular host systems. In this context, pragmatic and effective methodologies were established to enable widespread access to natural products. In reviewing such strategies, we will also highlight the development of heterologous natural product biosynthesis, which relies instead on a surrogate host system theoretically capable of advanced production potential. In comparing native and heterologous systems, we will comment on the base organisms used for natural product biosynthesis and how the properties of such cellular hosts dictate scaled engineering practices to facilitate compound distribution. In concluding the article, we will examine novel efforts in production practices that entirely eliminate the constraints of cellular production hosts. That is, cell free production efforts will be introduced and reviewed for the purpose of complex natural product biosynthesis. Included in this final analysis will be research efforts made on our part to test the cell free biosynthesis of the complex polyketide antibiotic natural product erythromycin.

Efficient production of myo-inositol in Escherichia coli through metabolic engineering

BACKGROUND

The biosynthesis of high value-added compounds using metabolically engineered strains has received wide attention in recent years. Myo-inositol (inositol), an important compound in the pharmaceutics, cosmetics and food industries, is usually produced from phytate via a harsh set of chemical reactions. Recombinant Escherichia coli strains have been constructed by metabolic engineering strategies to produce inositol, but with a low yield. The proper distribution of carbon flux between cell growth and inositol production is a major challenge for constructing an efficient inositol-synthesis pathway in bacteria. Construction of metabolically engineered E. coli strains with high stoichiometric yield of inositol is desirable.

RESULTS

In the present study, we designed an inositol-synthesis pathway from glucose with a theoretical stoichiometric yield of 1 mol inositol/mol glucose. Recombinant E. coli strains with high stoichiometric yield (> 0.7 mol inositol/mol glucose) were obtained. Inositol was successfully biosynthesized after introducing two crucial enzymes: inositol-3-phosphate synthase (IPS) from Trypanosoma brucei, and inositol monophosphatase (IMP) from E. coli. Based on starting strains E. coli BW25113 (wild-type) and SG104 (ΔptsG::glk, ΔgalR::zglf, ΔpoxB::acs), a series of engineered strains for inositol production was constructed by deleting the key genes pgi, pfkA and pykF. Plasmid-based expression systems for IPS and IMP were optimized, and expression of the gene zwf was regulated to enhance the stoichiometric yield of inositol. The highest stoichiometric yield (0.96 mol inositol/mol glucose) was achieved from recombinant strain R15 (SG104, Δpgi, Δpgm, and RBSL5-zwf). Strain R04 (SG104 and Δpgi) reached high-density in a 1-L fermenter when using glucose and glycerol as a mixed carbon source. In scaled-up fed-batch bioconversion in situ using strain R04, 0.82 mol inositol/mol glucose was produced within 23 h, corresponding to a titer of 106.3 g/L (590.5 mM) inositol.

CONCLUSIONS

The biosynthesis of inositol from glucose in recombinant E. coli was optimized by metabolic engineering strategies. The metabolically engineered E. coli strains represent a promising method for future inositol production. This study provides an essential reference to obtain a suitable distribution of carbon flux between glycolysis and inositol synthesis.

Efficient Multi-Enzymes Immobilized on Porous Microspheres for Producing Inositol From Starch

In vitro synthetic enzymatic biosystem is considered to be the next generation of biomanufacturing platform. This biosystem contains multiple enzymes for the implementation of complicated biotransformatiom. However, the hard-to-reuse and instability of multiple enzymes limit the utilization of this biosystem in industrial process. Multi-enzyme immobilization might be a feasible alternative to address these problems. Herein, porous microspheres are used as carriers to co-immobilize multiple enzymes for producing inositol from starch. At first, all the enzymes (i.e., α-glucan phosphorylase aGP, phosphoglucose mutase PGM, inositol 1-phosphate synthase IPS, and inositol monophosphatase IMP) for converting starch to inositol were immobilized on porous microspheres individually to check the effect of immobilization, then all the enzymes are co-immobilized on porous microspheres. Compared to reaction system containing all the individual immobilized enzymes, the reaction system containing the co-immobilized enzymes exhibit ∼3.5 fold of reaction rate on producing inositol from starch. This reaction rate is comparable to that by free enzyme mixture. And the co-immobilized multi-enzyme system show higher thermal stability and recovery stability than free enzyme mixture. After 7 batches, the immobilized enzymes retain 45.6% relative yield, while the free enzyme mixture only retain 13.3% relative yield after 3 batches. Co-immobilization of multiple enzymes on porous microspheres for biomanufacturing would shed light on the application of in vitro synthetic enzymatic biosystem in industrial scale.

GEMs: genetically engineered microorganisms and the regulatory oversight of their uses in modern food production

Over the past several decades, the use of genetically engineered microorganisms (GEMs, often referred to as Genetically Modified Microorganisms or GMMs) has become widespread in the production of food processing aids and other food ingredients. GEMs are advancing food production by increasing efficiency, reducing waste and resource requirements, and ultimately enabling beneficial innovations such as the cost-effective fortification of food with essential nutrients, vitamins, and amino acids, and delivery of tailored enzymes to achieve unique food processing capabilities. Regulatory agencies, including those in the European Union, United States, and Canada review the safety of GEMs when evaluating food substances produced using GEMs to ensure that both the microorganism and the resulting food substance are safe. This paper provides a summary of historical and current use of GEMs in food manufacture, an overview of frameworks that regulate their use, and a description of the safety assessment of both GEMs and food substances produced with GEMs. The paper encourages regulatory agencies around the globe to take a more aligned approach to the safety evaluation and regulatory oversight of GEM-produced food ingredients and enzymes, a category of food substances that enables more sustainable consumer food choices.

Biomaterials for stem cell engineering and biomanufacturing

Recent years have witnessed the expansion of tissue failures and diseases. The uprising of regenerative medicine converges the sight onto stem cell-biomaterial based therapy. Tissue engineering and regenerative medicine proposes the strategy of constructing spatially, mechanically, chemically and biologically designed biomaterials for stem cells to grow and differentiate. Therefore, this paper summarized the basic properties of embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs) and adult stem cells. The properties of frequently used biomaterials were also described in terms of natural and synthetic origins. Particularly, the combination of stem cells and biomaterials for tissue repair applications was reviewed in terms of nervous, cardiovascular, pancreatic, hematopoietic and musculoskeletal system. Finally, stem-cell-related biomanufacturing was envisioned and the novel biofabrication technologies were discussed, enlightening a promising route for the future advancement of large-scale stem cell-biomaterial based therapeutic manufacturing.

Glycosylation influences activity, stability and immobilization of the feruloyl esterase 1a from Myceliophthora thermophila

Heterologous protein production is widely used in industrial biotechnology. However, using non-native production hosts can lead to enzymes with altered post-translational modifications, such as glycosylation. We have investigated how production in a non-native host affects the physicochemical properties and enzymatic activity of a feruloyl esterase from Myceliophthora thermophila, MtFae1a. The enzyme was produced in two microorganisms that introduce glycosylation (M. thermophila and Pichia pastoris) and in Escherichia coli (non-glycosylated). Mass spectrometric analysis confirmed the presence of glycosylation and revealed differences in the lengths of glycan chains between the enzymes produced in M. thermophila and P. pastoris. The melting temperature and the optimal temperature for activity of the non-glycosylated enzyme were considerably lower than those of the glycosylated enzymes. The three MtFae1a versions also exhibited differences in specific activity and specificity. The catalytic efficiency of the glycosylated enzymes were more than 10 times higher than that of the non-glycosylated one. In biotechnology, immobilization is often used to allow reusing enzyme and was investigated on mesoporous silica particles. We found the binding kinetics and immobilization yield differed between the enzyme versions. The largest differences were observed when comparing enzymes with and without glycosylation, but significant variations were also observed between the two differently glycosylated enzymes. We conclude that the biotechnological value of an enzyme can be optimized for a specific application by carefully selecting the production host.

Aspergillus oryzae spore germination is enhanced by non-thermal atmospheric pressure plasma

Poor and unstable culture growth following isolation presents a technical barrier to the efficient application of beneficial microorganisms in the food industry. Non-thermal atmospheric pressure plasma is an effective tool that could overcome this barrier. The objective of this study was to investigate the potential of plasma to enhance spore germination, the initial step in fungal colonization, using Aspergillus oryzae, a beneficial filamentous fungus used in the fermentation industry. Treating fungal spores in background solutions of phosphate buffered saline (PBS) and potato dextrose broth (PDB) with micro dielectric barrier discharge plasma using nitrogen gas for 2 and 5 min, respectively, significantly increased the germination percentage. Spore swelling, the first step in germination, was accelerated following plasma treatment, indicating that plasma may be involved in loosening the spore surface. Plasma treatment depolarized spore membranes, elevated intracellular Ca²⁺ levels, and activated mpkA, a MAP kinase, and the transcription of several germination-associated genes. Our results suggest that plasma enhances fungal spore germination by stimulating spore swelling, depolarizing the cell membrane, and activating calcium and MAPK signaling.