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The discovery of itaconic acid as a product of citric acid pyrolytic distillation in 1837 opened the possibility of using it as a polymer building block. Itaconic acid, featuring two carboxylic acids and an unsaturated group, can potentially be used as a building block in several chemical syntheses, with a particular emphasis on polymer manufacture. The elucidation of biochemical pathways originating from itaconic acid, first in Aspergillus terreus and, recently, in several species of the Ustilago genus, has intensified and diversified research focused on microbe-based itaconic acid production, including at an industrial scale. These efforts include the engineering of naturally producing species/strains along with the exploration of other species that do not naturally produce itaconic acid but may offer potential benefits. The use of renewable wastes or sugar-enriched residues as substrates to produce itaconic acid, from a circular bioeconomy perspective, is another important aspect of the advancements in microbial itaconic acid production. This review provides an overview of the achievements as well as the challenges concerning the engineering of the producing strains/species, substrate selection, optimisation of bioreactor operation, and downstream itaconic acid purification methods. info:eu-repo/semantics/publishedVersion

Aroma and flavour represent the key components of food that improves the organoleptic characteristics of food and enhances the acceptability of food to consumers. Commercial manufacturing of aromatic and flavouring compounds is from the industry's microbial source, but since time immemorial, its concept has been behind human practices. The interest in microbial flavour compounds has developed in the past several decades because of its sustainable way to supply natural additives for the food processing sector. There are also numerous health benefits from microbial bioprocess products, ranging from antibiotics to fermented functional foods. This review discusses recent developments and advancements in many microbial aromatic and flavouring compounds, their biosynthesis and production by diverse types of microorganisms, their use in the food industry, and a brief overview of their health benefits for customers.

Food enzyme immobilization is a technology to mitigate various limitations of free enzymes in food processing. Versatile carriers such as agro-waste based materials, nano materials, and metal organic frameworks are developed to immobilize enzymes with improved enzymological characteristics to enable catalytic reactions to be carried out under sophisticated and extreme processing conditions. New fabrication technologies of immobilized food enzymes, for example, 3D printing and coaxial electrospraying also enhance enzyme functionality. Recent research on food enzyme immobilization is aimed at sustainability, cost-effectiveness, automation, high-throughput, multifunction, and safety. These developments enable new applications in food bioprocessing, food analyses, food control and food packaging, and so on.

During the last years, the use of biosensors in food analysis has gained considerable interest. These analytical devices provide highly selective, sensitive and cost-effective detection of cells, chemical or biochemical compounds that are relevant for food industry. In special, such sensors can be employed to control and monitoring biotechnological processes for food production and transformation. This review provides an overview on the state-of-the-art of electrochemical biosensors with potential use in food bioprocess technology, focusing on those with potential application in fermentation productions.

Nicotinamide adenine dinucleotide(NAD(P)H) is a metabolically interconnected redox cofactor serving as a hydride source for the majority of oxidoreductases, and consequently constituting a significant cost factor for bioprocessing. Much research has been devoted to the development of efficient, affordable, and sustainable methods for the regeneration of these cofactors through chemical, electrochemical, and photochemical approaches. However, the enzymatic approach using formate dehydrogenase is still the most abundantly employed in industrial applications, even though it suffers from system complexity and product purity issues. In this review, we summarize non-enzymatic and enzymatic electrochemical approaches for cofactor regeneration, then discuss recent developments to solve major issues. Issues discussed include Rh-catalyst mediated enzyme mutual inactivation, electron-transfer rates, catalyst sustainability, product selectivity and simplifying product purification. Recently reported remedies are discussed, such as heterogeneous metal catalysts generating H+ as the sole byproduct or high activity and stability redox-polymer immobilized enzymatic systems for sustainable organic synthesis.

Integrated bioprocess strategies may facilitate ethanol production from both C6 and C5 fractions of lignocellulosic feedstocks. We propose a new process concept, SSICF, where sugarcane bagasse is hydrolyzed simultaneously with xylose isomerization and the co-fermentation of C6 and C5 sugars. A commercial cocktail was supplemented with our multi-enzymatic system composed of three recombinant enzymes immobilized in Feroxyhyte magnetic nanoparticles: β-glucosidase, β-xylosidase and xylose isomerase. SSICF was performed using non-GMO Saccharomyces at pH 6.0 and 35 °C for 72 h in a synthetic medium containing cellobiose and xylose, and another medium containing pretreated sugarcane bagasse (PSB). The results of ethanol global yields in SSICF were 77.67% and 73.24% for the synthetic medium and PSB, respectively. In a nutshell, this is the first report of a successful proof-of-concept of SSICF with four rounds of enzyme recycling and a non-GMO yeast, an innovative process with high potential for industrial use.

Microalgae biomass is considered an important feedstock for biofuels and other bioactive compounds due to its faster growth rate, high biomass production and high biomolecules accumulation over first and second-generation feedstock. This research aimed to maximize the specific growth rate of fresh water green microalgae Closteriopsis acicularis, a member of family Chlorellaceae under the effect of pH and phosphate concentration to attain enhanced biomass productivity. This study investigates the individual and cumulative effect of phosphate concentration and pH on specific growth characteristics of Closteriopsis acicularis in autotrophic mode of cultivation for bioethanol production. Central-Composite Design (CCD) strategy and Response Surface Methodology (RSM) was used for the optimization of microalga growth and ethanol production under laboratory conditions. The results showed that high specific growth rate and biomass productivity of 0.342 day−1 and 0.497 g L−1 day−1 respectively, were achieved at high concentration of phosphate (0.115 g L−1) and pH (9) at 21st day of cultivation. The elemental composition of optimized biomass has shown enhanced elemental accumulation of certain macro (C, O, P) and micronutrients (Na, Mg, Al, K, Ca and Fe) except for nitrogen and sulfur. The Fourier transform infrared spectroscopic analysis has revealed spectral peaks and high absorbance in spectral range of carbohydrates, lipids and proteins, in optimized biomass. The carbohydrates content of optimized biomass was observed as 58%, with 29.3 g L−1 of fermentable sugars after acid catalyzed saccharification. The bioethanol yield was estimated as 51 % g ethanol/g glucose with maximum of 14.9 g/L of bioethanol production. In conclusion, it can be inferred that high specific growth rate and biomass productivity can be achieved by varying levels of phosphate concentration and pH during cultivation of Closteriopsis acicularis for improved yield of microbial growth, biomass and bioethanol production.

Rapid technological advances have significantly improved the capability, versatility, and robustness of mass spectrometers which has led to them playing a central role in the development, characterization, and regulatory filings of biopharmaceuticals. Their application spans the entire continuum of drug development, starting with discovery research through product development, characterization, and marketing authorization and continues well into product life cycle management. The scope of application extends beyond traditional protein characterization and includes elements like clone selection, cell culture physiology and bioprocess optimization, investigation support, and process analytical technology. More recently, advances in the MS-based multi-attribute method are enabling the introduction of MS in a cGMP environment for routine release and stability testing. While most applications of MS to date have been for monoclonal antibodies, the successes and learnings should translate to the characterization of next-gen biotherapeutics where modalities like multispecifics could be more prevalent. In this review, we describe the most significant advances in MS and correlate them to the broad spectrum of applications to biotherapeutic development. We anticipate rapid technological improvements to continue that will further accelerate widespread deployment of MS, thereby elevating our overall understanding of product quality and enabling attribute-focused product development.

Precise control over bioreactor operation is desired for optimal productivity and product quality, and there is an increased drive to automation in biomanufacturing. All of these goals require sensors, not only of the basic parameters of temperature, pH, and dissolved oxygen, but of the biomass and substrate concentrations, which directly determine the outcome of the bioprocess. While there are many innovative sensing concepts for biomass and substrate concentrations, this review focuses on sensors that are in-line with the bioreactor, providing data continuously without the removal of sample from the system. The discussion emphasizes the requirements of industry for these sensors, including performance, ease of use, and cost. As the bioeconomy grows, advances in sensing technologies will be needed to achieve the automation of the future for a wider array of bioreactors.

Real-time and near real-time monitoring of cell culture processes are critical to the evolving process analytical technology (PAT) paradigm for upstream bioprocessing. The responses measured from these analytical instruments can enable rapid feedback to perturbations that can otherwise lead to batch failures. Historically, real-time monitoring of bioreactor processes has been relegated to parameters such as pH, dissolved oxygen, and temperature. Other analytical results, such as cell growth and metabolites, are provided through manual daily sampling. In order to reduce sample error and increase throughput, real-time and near real-time instruments have been developed. Here we discuss recent advances in these technologies. This article aims to focus on other developing at-line and in-line technologies that enable monitoring of bioreactor processes, including dielectric spectroscopy, NIR, off-gas spectrometry, integrated at-line HPLC, and nanofluidic devices for monitoring cell growth and health, metabolites, titer, and product quality.

The rapid growth of human civilizations has led to imminent pressures to develop new food products with increased nutritional characteristics and decreased environmental footprints. Filamentous fungi, a class of microorganisms that have been utilized in a wide variety of foods for thousands of years, have recently garnered widespread attention in research communities and commercial ventures seeking to explore new and innovative applications in a diverse array of food products including, but not limited to, their more established applications as alternative proteins. Technological advances in the cultivation and processing of filamentous fungi have created new frontiers in the control of textures, flavors, and nutritional properties of fungi-based foods. This review highlights technological advances in the production of fungi-based foods from cultivation to product manufacturing, presents the current state of the art in fungi-based food products, and offers thoughts on their future trajectories. Emphasis is given to circular bioprocessing concepts for the sustainable utilization of agricultural and food processing byproducts.

The successful commercialization of cell therapies requires thorough planning and consideration of product quality, cost and scale of the manufacturing process. The implementation of automation can be central to a robust and reproducible manufacturing process at industrialized scales. There have been a number of wash-and-concentrate devices developed for cell manufacturing. These technologies have arisen from transfusion medicine, hematopoietic stem cell and biologics manufacturing where operating mechanisms are distinct from manual centrifugation. This review describes the historical origin and fundamental technologies underlying each currently available wash-and-concentrate device as well as their relative advantages and disadvantages in cell therapy applications. Understanding the specific attributes and limitations of these technologies is essential to optimizing cell therapy manufacturing.

Attenuating the biosynthetic potency of camptothecin producing fungi with the multiple subculturing and storage is the major challenge that limits the scaling-up of this approach. Thus, screening for novel fungal isolates with reliable metabolic stability and sustainability for camptothecin production is the objective of this work. Among the recovered isolates, Aspergillus terreus (320 μg/l) and A. flavus (290 μg/l) “endophytes of Ficus elastica” were the most potent camptothecin producing isolates. The chemical identity of extracted camptothecin was resolved from the HPLC, NMR, FTIR and LC–MS analyses, with a strong antiproliferative activity against MCF7 (0.18 μM), LS174 T, HCT29 (0.29−0.43 μM), HEPG-2 (0.73 μM) cell lines. The yield of camptothecin was decreased by about > 60 % by the 7th subculturing for both fungal isolates. Upon using Blackett-Burman design to optimize their nutritional requirements by the fungal isolates, their yield of camptothecin were increased by approximately 2 folds, revealing the essentiality of some carbon, nitrogen and growth elicitors for biosynthesis of camptothecin. Interestingly, the biosynthetic machinery of camptothecin by the 7th generation fungal isolates were completely restored upon addition of 1% surface sterilized leaves of F. elastica, while all the other experimented plant extracts did not display any effect on camptothecin production. So, chemicals signals derived from the plant /or its entire microbiome “microbial communication” triggering the expression of camptothecin biosynthetic gene cluster of these fungi, could be the most conceivable hypothesis explaining the attenuation and restoration processes of camptothecin biosynthesis by target the fungal isolates. This is the first report describing the feasibility of A. terreus and A. flavus “endophytes of F. elastica” for camptothecin production with reliable metabolic and sustainable biosynthetic potency upon addition of the plant host’s entire microbiome, that could be a preliminary platform for scaling-up of camptothecin production.

Recycling of organic waste is not only vital to emerging countries but developed countries too. Presently, a worldwide energy catastrophe is being noticed because of colossal energy requests and constrained capital. Non-sustainable energy sources are draining, and sustainable energy sources are not appropriately being used. There is a prompt backup course of action quest for energy generation. Microbial fuel cells (MFC) innovation, which utilizes micro-organisms to convert the synthetic energy of organic compounds into power, is viewed as a potential alternative option. A promising adaptation of MFC is a plant microbial fuel cell (P-MFC) that implements adistinctive plant-microorganism rhizospheric relationship to transform solar energy into bioelectricity. P-MFC technology is a holistic approach involving various interrelated fields. The system comprises of two structure types; biocontrol and bioprocess structures. Up to 70% of organic matter produced by plants during photosynthesis winds up in the soil as dead root material. The micro-organisms on and around the surface of the roots oxidize these carbon-based exudates, discharge CO2, protons, and electrons. The rhizodeposition at the soil alliance combined with productive designing drives this rhizospheric relationship and eventually contributes towards genuine applications. Thus, this review emphasizes majorly on three criteria; Components and building viewpoints engaged with structuring an effective setup, the efficiency of P-MFC in power generation, and lastly the sustainability of P-MFC.

Background aims Bioartificial liver devices (BALs) are categorized as advanced therapy medicinal products (ATMPs) with the potential to provide temporary liver support for liver failure patients. However, to meet commercial demands, next-generation BAL manufacturing processes need to be designed that are scalable and financially feasible. The authors describe the development and application of a process economics decisional tool to determine the cost of goods (COG) of alternative BAL process flowsheets across a range of industrial scales. Methods The decisional tool comprised an information database linked to a process economics engine, with equipment sizing, resource consumption, capital investment and COG calculations for the whole bioprocess, from cell expansion and encapsulation to fluidized bed bioreactor (FBB) culture to cryopreservation and cryorecovery. Four different flowsheet configurations were evaluated across demands, with cell factories or microcarriers in suspension culture for the cell expansion step and single-use or stainless steel technology for the FBB culture step. Results The tool outputs demonstrated that the lowest COG was achieved with microcarriers and stainless steel technology independent of the annual demand (1500–30 000 BALs/year). The analysis identified the key cost drivers were parameters impacting the medium volume and cost. Conclusions The tool outputs can be used to identify cost-effective and scalable bioprocesses early in the development process and minimize the risk of failing to meet commercial demands due to technology choices. The tool predictions serve as a useful benchmark for manufacturing ATMPs.

Nannochloropsis gaditana is a microalga, constituting cellulose 33 ± 1.3% and hemicellulose 18.2 ± 0.8%; used for the biofuel production. The cellulose in microalgal biomass would contribute to protecting the environment and constitute an attractive renewable raw material for bioethanol production. Ethanol production from N. gaditana microalgal biomass was investigated through Consolidated Bioprocessing (CBP) using Hangateiclostridium thermocellum KSMK1203 bacterial isolate. Screening and optimization of biomass pretreatment with different acids in different dosages, various hydrolysis time at 100 °C were performed and statistically validated using one-way ANOVA for efficient hemicellulose removal from NaClO2-treated N. gaditana biomass. Medium components and process parameters were statistically optimized by Response Surface Methodology. The maximum cellulase of 13.96 ± 1.354 IU/mL and ethanol of 12.90 ± 0.987 g/L were obtained in pretreated N.gaditana biomass. This study demonstrates that N. gaditana is a substitution for vegetal cellulose and these optimized conditions could be successfully used for commercial ethanol production using H. thermocellum KSMK1203.

Anaerobic digestion (AD) is a traditional process that not only manages different sources of organic waste but also generates renewable energy (biomethane) at the same time. However, AD relies on the cooperation of certain microbial communities and is, therefore, vulnerable to process disturbances that may affect biogas production and methane yield. In this context, process monitoring has been receiving attention as a strategy for achieving a stable process and ensuring a high yield of biogas. This review was undertaken to address the recent progress related to contemporary techniques deployed for real-time monitoring of the AD process at different scales. It also points out the necessity of choosing appropriate early-warning indicators and proper monitoring biosystems to achieve accurate information on the bioprocess. Nonetheless, the implementation of online monitoring techniques has been restricted due to its high-cost, which limits its industrial application. On this premise of rigid cost control, further studies are required to make AD real-time monitoring more technically and economically sustainable.

In this study, an effort was made to create a model cell factory of Saccharomyces cerevisiae using bacterial cellulose (BC) and Aspergillus awamori for consolidated bioprocessing (CBP) of starch. This work suggested development of a cell factory for consolidated bioprocessing of starch in one bioreactor, performing three bioprocesses, i.e. production of amylolytic enzymes by fungal culture, hydrolysis of starch and fermentation to ethanol production using S. cerevisiae without its genetic modification. The microorganisms were separately immobilized on different amounts of BC and their mixture was used for the fermentation of 5% w/v starch. The mixture of BC/A. awamori and BC/S. cerevisiae was used for starch fermentation both in wet and freeze-dried (lyophilized) form in the same ratio (3:1). A 1.75-fold increase in maximum ethanol production was observed using freeze-dried BC immobilized biocatalysts compared to wet cell factory. The ethanol production yield was examined progressively by the effect of (i) initial ratios of both freeze-dried BC/S. cerevisiae and BC/A. awamori, (ii) different weight of the freeze-dried cell factory and (iii) A. awamori cells concentration, reaching the 82% of the theoretical yield encouraging us to use this cell factory model for further fermentations of starch in higher concentration. Ethanol production of 26.69 mL/L and the maximum ethanol yield (0.42 g ethanol/g starch) or 82% of the theoretical yield was achieved by increasing cells of A. awamori inoculum during its immobilization on BC to 109 cells/mL. The results of this work are satisfactory compared with other systems of starch fermentation from literature. SEM, TEM and FTIR spectra analysis were carried out in order to prove the successful preparation of cell factory. SEM showed the immobilization of cells on the BC netting, and TEM showed on BC fibrils. Finally, a repeated fermentation batch was performed, proving the operational viability and stability of the cell factory. The results indicated that the objective of designed cell factory was successfully performer, and the results of starch fermentation are promising for the development of an innovation in brewing industry. Likewise, these have prospects of their application in White-Biotechnology.

Genome-scale metabolic models describe cellular metabolism with mechanistic detail. Given their high complexity, such models need to be parameterized correctly to yield accurate predictions and avoid overfitting. Effective parameterization has been well-studied for microbial models, but it remains unclear for higher eukaryotes, including mammalian cells. To address this, we enumerated model parameters that describe key features of cultured mammalian cells – including cellular composition, bioprocess performance metrics, mammalian-specific pathways, and biological assumptions behind model formulation approaches. We tested these parameters by building thousands of metabolic models and evaluating their ability to predict the growth rates of a panel of phenotypically diverse Chinese Hamster Ovary cell clones. We found the following considerations to be most critical for accurate parameterization: (1) cells limit metabolic activity to maintain homeostasis, (2) cell morphology and viability change dynamically during a growth curve, and (3) cellular biomass has a particular macromolecular composition. Depending on parameterization, models predicted different metabolic phenotypes, including contrasting mechanisms of nutrient utilization and energy generation, leading to varying accuracies of growth rate predictions. Notably, accurate parameter values broadly agreed with experimental measurements. These insights will guide future investigations of mammalian metabolism.

Enzymes are core elements of biosynthetic pathways employed in the synthesis of numerous bioproducts. Here, we review enzyme promiscuity, enzyme engineering, enzyme immobilization, and cell-free systems as fundamental strategies of bioprocess development. Initially, promiscuous enzymes are the first candidates in the quest for new activities to power new, artificial, or bypass pathways that expand substrate range and catalyze the production of new products. If the activity or regulation of available enzymes is unsuitable for a process, protein engineering can be applied to improve them to the required level. When cell toxicity and low productivity cannot be engineered away, cell-free systems are an attractive option, especially in combination with enzyme immobilization that allows extended enzyme use. Overall, the above methods support powerful platforms for bioprocess development and optimization.

A great diversity of biological activities has been attributed to peptides. Despite food proteins are essentially considered as sources of dietary amino acids, bioactive peptides can be released during gastrointestinal transit, food fermentation, food maturation, and through enzymatic bioprocessing in vitro. Specific bioactive peptide databases integrated with predictive proteolytic cleavage of proteins are valuable tools allowing a rapid in silico screening of the bioactive potential of dietary proteins. The range of bioactivities generated by hydrolysis of food proteins include antioxidant, antihypertensive, antidiabetic, immunomodulatory, anticancer, and opioid activities. Some of these bioactivities have been also confirmed in vivo, reinforcing their physiological relevance. This review presents a current perspective on the production and main biological activities of peptides derived from food proteins.

Acetic acid hydrolysis is a green and novel approach that can effectively convert lignocellulosic biomass into high-valued xylo-oligosaccharide (XOS). However, the residual acidolysis slurry still contains acetic acid and various monosaccharides. In this study, a sandwich-integration bioprocess (SIBP) method was developed to efficiently remove the residual monosaccharide contaminants by the combination of whole-cell catalysis and electrodialysis separation. Firstly, the acetic acid in acidolysis slurry was separated by electrodialysis to eliminate the strong toxic inhibition on whole-cell catalysis. Secondly, the monosaccharides were oxidized to the corresponding ionogenic acids by whole-cell catalysis. Finally, these ionogenic aldonic acids were removed readily by the second electrodialysis step. Herein, whole-cell catalysis step was combined with two electrodialysis separation steps into SIBP, in which 131.4 g XOS and 79 g aldonic acids were obtained from 1 kg corncob and more than 93.1% acetic acid was recycled.

Parageobacillus thermoglucosidasius is a genetically tractable thermophile that grows rapidly at elevated temperatures, with a doubling time at 65 °C comparable to the shortest doubling times of Escherichia coli. It is capable of using a wide variety of substrates, including carbohydrate oligomers, and has been developed for the industrial production of ethanol. In this study, P. thermoglucosidasius NCIMB11955 has been engineered to produce the sesquiterpene τ-muurolol by introduction of a heterologous mevalonate pathway constructed using genes from several thermophilic archaea together with a recently characterised thermostable τ-muurolol synthase. P. thermoglucosidasius naturally uses the methylerythritol phosphate pathway for production of the terpene precursor, isopentenyl pyrophosphate, while archaea use a version of the mevalonate pathway. By introducing the orthogonal archaeal pathway it was possible to increase the flux through to sesquiterpene biosynthesis. Construction of such a large metabolic pathway created problems with genetic vector introduction and stability, so recombinant plasmids were introduced by conjugation, and a thermostable serine integrase system was developed for integration of large pathways onto the chromosome. Finally, by making the heterologous pathway maltose-inducible we demonstrate that the new strain is capable of using waste bread directly as an autoinduction carbon source for the production of terpenes in a consolidated bioprocess.

International audience; The platform molecule 3-hydroxypropionic acid (3-HP) can be produced using Lactobacillus reuteri through a twostep bioprocess that involves a growth phase followed by a bioconversion phase. The bioproduction is performed by resting cells that convert glycerol into 3-HP and 1,3-propanediol in fed-batch mode. This work aimed at studying the effect of the growth conditions of L. reuteri DSM 17938 during the first step, on the glycerol bioconversion into 3-HP during the second step. A Plackett and Burman design was carried out to test, in controlled bioreactors, the effect of 11 growth conditions simultaneously, at fixed bioconversion conditions. The supplementation of the growth medium with vitamin B12 and cysteine displayed a negative effect on the 3-HP bioproduction. The addition of glucose, phytone peptone, Tween 80, 1,2-propanediol and betaine in the growth medium, together with a low temperature and an optimal pH of 6.0 during the growth phase increased the bioconversion duration from 56 h to 89 h at a glycerol feeding rate of 0.5 g$h L1. A validating experiment displayed that the 3-HP titer, 3-HP production yield and 3-HP specific production rate were significantly improved by 25 %, 150 % and 61 %, respectively.

Temperature is a critical parameter for bioprocess performance, requiring careful optimisation for peak efficiency. Green biohydrogen production via photofermentation by purple nonsulfur bacteria including Rhodopseudomonas palustris has been extensively researched, yet realisation is limited by comparatively low productivity. We thus assessed the growth and hydrogen productivity of two closely-related strains of R. palustris acclimated to higher temperatures, revealing markedly increased strain-dependent optima than the 30 °C previously accepted. Strain CGA009 grew 53% faster at 35 °C, with 2.4-fold higher hydrogen production rate, while at 40 °C strain ATH 2.1.37 displayed 86% faster growth and 4-fold higher production rate, along with improved specific production and substrate conversion efficiency. These results reaffirm the necessity of pre-acclimation when verifying temperature optima and expand the feasible temperature range for advancement of high-rate biohydrogen production. Further, the superior heat resistance and production capability of strain ATH 2.1.37 raises the potential for further efficiency gains from thermotolerant environmental isolates.

An online adaptive deep neural network (DNN) scheme has been introduced for the tracking control of a nonlinear bioprocess with uncertain internal dynamics. First, a detailed controllability analysis is conducted for the Lutein bioprocess to represent the bioprocess as a nonlinear system in affine form. Next, a controller consisting of a DNN-based function approximator is designed for the nonlinear Lutein production bioprocess. It is demonstrated that closed-loop tracking control of a bioprocess for a desired yield profile is possible only with two inputs. The set point trajectory to yield maximum Lutein production is shown by the proposed online adaptive deep NN controller. The proposed controller exhibits self-learning capability under closed loop condition, due to the online learning phase. In other words, no explicit offline learning phase is required and online learning is preferred due to lack of a priori training data for approximating complex nonlinear functions. Simulation results are provided to confirm the performance of the proposed approach.

Downstream processing or product recovery plays a vital role in the development of bioprocesses. To improve the bioprocess efficiency, some unconventional methods are much required. The continuous manufacturing in downstream processing makes the Process Analytical Technologies (PATs) as an important tool. Monitoring and controlling bioprocess are an essential factor for the principles of PAT and quality by design. Spectroscopic methods can apply to monitor multiple analytes in real-time with less sample processing with significant advancements. Raman spectroscopy is an extensively used technique as an analytical and research tool owing to its modest process form, non-destructive, non-invasive optical molecular spectroscopic imaging with computer-based analysis. Generally, its application is essential for the analysis and characterization of biological samples, and it is easy to operate with minimal sample. The innovation on various types of enhanced Raman spectroscopy was designed to enhance the Raman analytical technique. Raman spectroscopy could couple with chemometrics to provide reliable alternative analysis method of downstream process analysis. Thus, this review aims to provide useful insight on the application of Raman spectroscopy for PAT in downstream processing of biotechnology and Raman data analysis in biological fields.

Enzymes have played, and continue to play, important roles in various aspects in food science for decades. With the rapid developments in nanotechnology in recent years, nanozymes comprises both nanomaterials and enzyme catalytic activity have attracted wide attention from food scientists. Even though both traditional enzymes and nanozymes can catalyze enzymatic reactions, their modes of action, activity regulation, acceptance, scope of application, and so on, are considerably different. Recent research progress in enzyme and nanozyme technology in food science suggest that the significant influence of enzymes in food bioprocessing can be further enhanced by the use of nanozymes as tools in food analysis, detection, and quantification.

Bioproduction of medium chain carboxylic acids has recently emerged as an alternative strategy to valorize low-value organic waste and side-streams. Key to this route is chain elongation, an anaerobic microbial process driven by ethanol, lactic acid, or carbohydrates. Because these technologies use wastes as feedstocks, mixed microbial communities are often considered as biocatalysts. Understanding and steering these microbiomes is key to optimize bioprocess performance. From a meta-analysis of publicly available sequencing data, we (i) explore how the current collection of isolated chain elongators compares to microbiome members, (ii) discuss the main beneficial and antagonistic interactions with community partners, and (iii) identify the key research gaps and needs to help understand chain elongation microbiomes, and design/steer these novel bioproduction processes.

Conversion of CO2 into calcium carbonate using microorganism is one of the promising methods of reducing the increased level of CO2 in the atmosphere. In the present study, a novel strain of Corynebacterium flavescens was isolated from cow saliva and screened for CO2 hydration activity. First of all, the effect of C. flavescens on CaCO3 precipitation was studied under optimized conditions. Various factors such as CO2 concentration, protein concentration, pH of the reaction system, and temperature were then optimized for maximum CO2 precipitation into CaCO3 using free cell lysate. After that, C. flavescens cells were immobilized onto highly porous keratin microparticles functionalized with glutaraldehyde (0.6 % v/v) to enhance the CO2 conversion efficiency. Maximum immobilization of bacterial cells was achieved after 25 h at 4 °C under shaking conditions. The covalently immobilized C. flavescens particles showed a 1.35-fold increase in CaCO3 production compared to their free counterparts. Under repeated batch conditions, the relative production of CaCO3 for immobilized and free cells was 53.46 and 22.15 %, respectively, after 10 cycles. This study demonstrated the advantages of keratin microparticles as a support for the immobilization of C. flavescens and the efficient conversion of CO2 to CaCO3.

The cell cultivation process in a bioreactor is a high-value manufacturing process that requires excessive monitoring and control compatibility. The specific cell growth rate is a crucial parameter that describes the online quality of the cultivation process. Most methods and algorithms developed for online estimations of the specific growth rate controls in batch and fed-batch microbial cultivation processes rely on biomass growth models. In this paper, we present a soft sensor – a specific growth rate estimator that does not require a particular bioprocess model. The approach for online estimation of the specific growth rate is based on an online measurement of the oxygen uptake rate. The feasibility of the estimator developed in this study was determined in two ways. First, we used numerical simulations on a virtual platform, where the cell culture processes were theoretically modeled. Next, we performed experimental validation based on laboratory-scale (7, 12, 15 L) bioreactor experiments with three different Escherichia coli BL21 cell strains.

In the area of human-made innovations to improve the quality of life, biocatalysis has already had a great impact and contributed enormously to a growing number of catalytic transformations aimed at the detection and analysis of compounds, the bioconversion of starting materials and the preparation of target compounds at any scale, from laboratory small scale to industrial large scale. The key enabling tools which have been developed in biocatalysis over the last decades also provide great opportunities for further development and numerous applications in various sectors of the global bioeconomy. Systems biocatalysis is a modular, bottom-up approach to designing the architecture of enzyme-catalyzed reaction steps in a synthetic route from starting materials to target molecules. The integration of biocatalysis and sustainable chemistry in vitro aims at ideal conversions with high molecular economy and their intensification. Retrosynthetic analysis in the chemical and biological domain has been a valuable tool for target-oriented synthesis while, on the other hand, diversity-oriented synthesis builds on forward-looking analysis. Bioinformatic tools for rapid identification of the required enzyme functions, efficient enzyme production systems, as well as generalized bioprocess design tools, are important for rapid prototyping of the biocatalytic reactions. The tools for enzyme engineering and the reaction engineering of each enzyme-catalyzed one-step reaction are also valuable for coupling reactions. The tools to overcome interaction issues with other components or enzymes are of great interest in designing multi-step reactions as well as in biocatalytic total synthesis.

The field of metabolic engineering is primarily concerned with improving the biological production of value-added chemicals, fuels and pharmaceuticals through the design, construction and optimization of metabolic pathways, redirection of intracellular fluxes, and refinement of cellular properties relevant for industrial bioprocess implementation. Metabolic network models and metabolic fluxes are central concepts in metabolic engineering, as was emphasized in the first paper published in this journal, "Metabolic fluxes and metabolic engineering" (Metabolic Engineering, 1: 1-11, 1999). In the past two decades, a wide range of computational, analytical and experimental approaches have been developed to interrogate the capabilities of biological systems through analysis of metabolic network models using techniques such as flux balance analysis (FBA), and quantify metabolic fluxes using constrained-based modeling approaches such as metabolic flux analysis (MFA) and more advanced experimental techniques based on the use of stable-isotope tracers, i.e. 13C-metabolic flux analysis (13C-MFA). In this review, we describe the basic principles of metabolic flux analysis, discuss current best practices in flux quantification, highlight potential pitfalls and alternative approaches in the application of these tools, and give a broad overview of pragmatic applications of flux analysis in metabolic engineering practice.

Plant natural products including alkaloids, polyphenols, terpenoids and flavonoids have been reported to exert anticancer activity by targeting various metabolic pathways. The biological pathways regulated by plant products can serve as novel drug targets. Plant natural compounds or their derivatives used for cancer treatment and some novel plant-based compounds which are used in clinical trials were discussed. Callus suspension culture with secondary metabolites can provide a continuous source of plant pharmaceuticals without time and space limitations. Previous research has shown that rice callus suspension culture can kill >95% cancer cells with no significant effect on the growth of normal cells. The role of candidate genes and metabolites which are likely to be involved in the process and their potential to serve as anticancer and anti-inflammatory agents were discussed. Large scale production of plant callus suspension culture and its constituents can be achieved using elicitors which enhance specific secondary metabolites combined with bioprocess technology.

Xenobiotic compounds are synthetic compounds commonly used in industries like dye industries, pharmaceutical industries, pesticides manufacturing, explosives, and other industrial chemicals. These compounds have been released into our ecosystem due to anthropogenic activities and improper waste disposal and cause consequential damage due to their lethal nature. A massive number of enzymes from plants and microorganisms have been reportedly involved in the biodegradation of toxic organic contaminants. Bioremediation is an economical and sustainable part of biotechnology that is dependent on microbial enzymes. Research in this topic would contribute towards the development of advanced bioprocess technology for the reduction of the toxicity of the pollutants and also to acquire beneficiary novel compounds.

New technologies have allowed researchers to better design, build, and analyze complex consortia. These developments are fueling a wider implementation of consortium-based bioprocessing by leveraging synthetic biology, delivering on the field's multitudinous promises of higher efficiencies, superior resiliency, augmented capabilities, and modular bioprocessing. Here we chronicle current progress by presenting a range of screening, computational, and biomolecular tools enabling robust population control, efficient division of labor, and programmatic spatial organization; furthermore, we detail corresponding advancements in areas including machine learning, biocontainment, and standardization. Additionally, we show applications in myriad sectors, including medicine, energy and waste sustainability, chemical production, agriculture, and biosensors. Concluding remarks outline areas of growth that will promote the utilization of complex community structures across the biotechnology spectrum.

Since the approval of the first biotherapeutic protein produced from CHO cells in 1987, researchers have been studying how to improve protein titer and product quality, mainly through cell line development and bioprocess optimization. With recent advances in genetic editing methods (CRISPR/Cas systems) together with large scale systems biology data, further improvements have been made. Here we outline recent progress in protein production from CHO cells through genetic editing and look to the future of improvements through synthetic biology approaches. We describe new work in the expansion of the genetic parts toolkit, including novel promoters, terminators, transcription factors, and genetic circuits, and how these synthetic parts will be used synergistically to continue improvements to protein production.

The ability to utilize agricultural waste products is one of the many reasons why bioprocessing using Escherichia coli is an attractive alternative to unsustainable fossil fuel-based methods for chemical synthesis. However, mixed sugar co-utilization is a challenge for E. coli due to the effects of carbon catabolite repression (CCR), which dictates a preference for the consumption of glucose over secondary sugars through the mechanisms of inducer exclusion and transcriptional regulation. To overcome these obstacles, metabolic engineers have developed strategies to relax the effects of CCR through both global and sugar-specific methods. Understanding the feed conditions as well as the engineering opportunities for CCR relaxation can allow for the development of a strain with maximized productivity and growth.

Bacterial cellulose (BC) is a biopolymer of great significance to the medical, pharmaceutical, and food industries. However, a high concentration of carbon sources (mainly glucose) and other culture media components is usually required to promote a significant yield of BC, which increases the bioprocess cost. Thus, optimization strategies (conventional or statistical) have become relevant for the cost-effective production of bacterial cellulose. Additionally, this biopolymer may present new properties through modifications with exogenous compounds. The present review, explores and discusses recent studies (last five years) that report the optimization of BC production and its yield as well as in situ and ex situ modifications, resulting in improved mechanical, antioxidant, and antimicrobial properties of BC for new applications.

Current trends in the biopharmaceutical market such as the diversification of therapies as well as the increasing time-to-market pressure will trigger the rethinking of bioprocess development and production approaches. Thereby, the importance of development time and manufacturing costs will increase, especially for microbial production. In the present review, we investigate three technological approaches which, to our opinion, will play a key role in the future of biopharmaceutical production. The first cornerstone of process development is the generation and effective utilization of platform knowledge. Building processes on well understood microbial and technological platforms allows to accelerate early-stage bioprocess development and to better condense this knowledge into multi-purpose technologies and applicable mathematical models. Second, the application of verified scale down systems and in silico models for process design and characterization will reduce the required number of large scale batches before dossier submission. Third, the broader availability of mathematical process models and the improvement of process analytical technologies will increase the applicability and acceptance of advanced control and process automation in the manufacturing scale. This will reduce process failure rates and subsequently cost of goods. Along these three aspects we give an overview of recently developed key tools and their potential integration into bioprocess development strategies.

International audience; Irrespective use of chemical pesticides has led, over the last decades, to several problems such as soil, water and food sources pollution, and generation of a selective pressure causing the emergence of pest resistance. Consequently, researchers have been focusing more on the use of biological control as an alternative strategy. Bacillus thuringiensis (Bt) is one of the most widely studied bacteria in industrial biotechnology and commercialized as an environmentally sustainable biopesticide. Therefore, a huge interest has been allocated for research on this bacterium and several scientific studies have been published on the issue. In this review, we tried to evaluate the scientific production over the last thirty years, for the first time, in terms of number and geographical origin, focusing particularly on B. thuringiensis kurstaki (Btk). It is worth emphasizing that the Btk process engineering involving factors affecting growth, sporulation and toxin formation yields by Bt has not been fully investigated in previous reviews. To this end, the second section of this review provided an updated survey about these conditions, such as nutritional requirements, culture media and fermentation technologies. Relevant information was collected in comparative tables that could be very useful for the scientific community interested in Btk-based biopesticides.

This review aims to highlight the bioprocessing strategies behind one of the most commercially produced enzymes in the biotechnological market, pectinase. Significant steps in the upstream processing of this enzyme include its source, the selection of the substrate, the reaction conditions and the overall reactor design, all of which will be discussed in great detail. Past literature which has contributed to the viability of this design will be highlighted with the intention of generating a comparative review that accounts not only for the contributions of previous research but also for what needs to be done in the future to further increase the productivity of this vital industrial process. There is an incredibly wide net of application based research and industry which currently depends on the bioprocessing of pectinase, these will thereby benefit greatly from the concepts of process intensification and optimisation which are at the forefront of this review and will likely be inspired by the outlined steps that need to be taken to further improve this process.

In the context of increasing demand for novel pharmaceutical high-value compounds and their natural sources, endophytic fungi from medicinal plants are being recently explored for diverse bioactive metabolites. We report bioprocess optimization and biochemical characterization of the endo-metabolome possessing broad-spectrum antimicrobial and antioxidant activities, from an endophytic fungus Cercospora sp. PM018 that was isolated from Lal-bisalyakarani (Aerva javanica Juss. Ex.Schult, an Indian indigenous medicinal plant). Potato dextrose medium having pH 4.0 and incubation temperature of 30 °C were found to be optimal for the enhanced bioactivities of the endo-metabolome after 12 days of fungal growth. In the antibiotic-potentiating assay, fractional inhibitory concentration

Mammalian cell cultures are widely used in the biopharmaceutical industry to produce monoclonal antibodies, vaccines, and growth factors, etc. Cell death is an essential biological process for physiological growth and development, but it is a major problem in biopharmaceutical production in bio-industry. Cell death within bioreactor occurs due to various intracellular and extracellular stresses. These stresses negatively affect the culture longevity, overall product quality, and yield. Among all cell death types, apoptosis accounts for most of the cellular death in the bioreactor. The implementation and development of various strategies to prevent the cellular death are crucial for robust bioprocess development. Cell death during culture can be prevented or inhibited by supplementing media with specific chemicals, synthetic inhibitors, and genetic cell engineering approaches. In this review, we classified and described different types of cell death and their molecular mechanisms and summarized the cell death inhibition approaches implemented to inhibit cell death for various applications.

Biochemical production faces economic and environmental challenges that need to be overcome to enable a viable and sustainable bioeconomy. We propose an assessment framework that consistently combines environmental and economic indicators to support optimized biochemical production at early development stages. We define internally consistent system boundaries and a comprehensive set of quantitative indicators from life cycle assessment (LCA) and techno-economic assessment (TEA) to combine environmental and economic performance in a single score. Our framework enables the identification of trade-offs across environmental and economic aspects over the entire biochemical life cycle. This approach provides input for the optimization of future biochemicals in terms of overall sustainability, to overcome prevailing obstacles in the development of biochemical production processes.

Quantitative unit operation models for the optimization and refinement of modern late-stage biopharmaceutical drug manufacturing processes have recently attracted increasing attention. The supplementary benefits of these models include increased process robustness and control in combination with a more stringent design of the bioprocess due to a reduced number of exploratory experiments. In addition to unit operations, further efforts also focus on digital bioprocess replicas, which are straightforward combinations of unit operation and process models from inoculum to the fill and finish phase. In this review, we shed more light on digital bioprocess replicas in addition to standard unit operation models and discuss their strengths and weaknesses. We comment on the current usage of these approaches for late stage processes and outline the associated benefits, challenges and limitations.

Combined soda and enzyme-catalyzed extrusion pretreatment (bioextrusion) of barley straw was evaluated for bioethanol production. The effect of the enzyme dose on the bioextrudate was for the first time analyzed. The enzyme load (5–10 FPU/g DM) had a significant impact on the solubilization of sugars during bioextrusion and also affected the saccharification yield at long incubation times. The solids concentration (17–25% w/w) in the extended incubation of bioextrudates was also studied and its effect on the carbohydrate conversion and sugar release was evaluated. An enzyme dose of 10 FPU/g dry matter and a solids content of 20% (w/w) were selected as the best conditions to submit the bioextrudate to a liquefaction plus simultaneous saccharification and co-fermentation (LSSCF) process using a modified S. cerevisiae strain. At the end of the process, an ethanol concentration close to 38 g/l was obtained, corresponding to a production of 15.8 g ethanol/100 g raw barley straw.

The natural world blends microenvironments to create a continuum of spatial niches wherein microbial consortia participate in metabolic exchanges. The capability with which nature selects a consortium to complement a given niche is often taken for granted. Not by Shahab et al. (2020), however, who created a synthetic microbial consortium to mediate a multi-step bioprocess in a single bioreactor system. The concept affords a fair degree of modularity in the choice of biocatalyst and a reasonable level of process control, thus making it an engineering tool.

Synthetic methylotrophy aims to engineer methane and methanol utilization pathways in platform hosts like Escherichia coli for industrial bioprocessing of natural gas and biogas. While recent attempts to engineer synthetic methylotrophs have proved successful, autonomous methylotrophy, i.e. the ability to utilize methane or methanol as sole carbon and energy substrates, has not yet been realized. Here, we address an important limitation of autonomous methylotrophy in E. coli: the inability of the organism to synthesize several amino acids when grown on methanol. By activating the stringent/stress response via ppGpp overproduction, or DksA and RpoS overexpression, we demonstrate improved biosynthesis of proteinogenic amino acids via endogenous upregulation of amino acid synthesis pathway genes. Thus, we were able to achieve biosynthesis of several limiting amino acids from methanol-derived carbon, in contrast to the control methylotrophic E. coli strain. This study addresses a key limitation currently preventing autonomous methylotrophy in E. coli and possibly other synthetic methylotrophs and provides insight as to how this limitation can be alleviated via stringent/stress response activation.