Search Results (204)

Although vinegar is technically elaborated by a well-known bioprocess, the behavior and function of the microorganisms responsible for its production still need investigation. In vinegars obtained from raw materials and systems typical of Europe, the acetic acid bacteria species Komagataeibacter europaeus predominates due to its particular adaptive metabolism. This work addresses the study of several adaptation mechanisms of K. europaeus during acetic acid fermentation in a submerged semi-continuous production system. The aim is to analyze the molecular response and behavior of this species to increasing acidity gradients, up to 7–8% w/v acetic acid, applying a comparative proteomic approach in three matrices (synthetic alcoholic medium, dark craft beer, and dry fine wine). A total of 1070 proteins are identified, with 174 showing statistically significant changes in abundance (FDR < 0.05), particularly in pathways related to amino acid biosynthesis, fatty acid metabolism, and stress response. The proteomic patterns differ among substrates, with the synthetic alcohol medium inducing stress-related proteins and the dark craft beer enhancing lipid biosynthesis. These observations provide experimental evidence that the fermentation substrate modulates metabolic adaptation in K. europaeus, offering a rational basis for designing fermentation protocols that enhance bacterial resilience, thereby optimizing vinegar production processes. Full article

A modular strategy for the molecular design of silicone-based antifoaming agents was developed by precisely controlling the architecture of poly (methylhydrosiloxane) (PMHS). Sixteen PMHS variants were synthesized by systematically varying the siloxane chain length (L1–L4), backbone composition (D₃T₁ vs. D₃₀T₁), and terminal group chemistry (H- vs. M-type). These structural modifications resulted in a broad range of Si-H functionalities, which were quantitatively analyzed and correlated with defoaming performance. The PMHS matrices were integrated with high-viscosity PDMS, a nonionic surfactant, and covalently grafted fumed silica—which was chemically matched to each PMHS backbone—to construct formulation-specific defoaming systems with enhanced interfacial compatibility and colloidal stability. Comprehensive physicochemical characterization via FT-IR, ¹H NMR, GPC, TGA, and surface tension analysis revealed a nonmonotonic relationship between Si-H content and defoaming efficiency. Formulations containing 0.1–0.3 wt% Si-H achieved peak performance, with suppression efficiencies up to 96.6% and surface tensions as low as 18.9 mN/m. Deviations from this optimal range impaired performance due to interfacial over-reactivity or reduced mobility. Furthermore, thermal stability and molecular weight distribution were found to be governed by repeat unit architecture and terminal group selection. Compared with conventional EO/PO-modified commercial defoamers, the PMHS-based systems exhibited markedly improved suppression durability and formulation stability in high-viscosity environments. These results establish a predictive structure–property framework for tailoring antifoaming agents and highlight PMHS-based formulations as advanced foam suppressors with improved functionality. This study provides actionable design criteria for high-performance silicone materials with strong potential for application in thermally and mechanically demanding environments such as coating, bioprocessing, and polymer manufacturing. Full article

Tryptophan is synthesized in microorganisms via a five-step enzymatic pathway originating from chorismate, which is a product of the shikimate pathway. As a biosynthetic precursor to a wide range of high-value compounds such as indole-3-acetic acid, indigo, indirubin, and violacein, this pathway has been a central target for metabolic engineering to enhance microbial production. Anthranilate phosphoribosyltransferase (AnPRT) catalyzes the second step of the pathway by transferring a phosphoribosyl group from PRPP to anthranilate, forming phosphoribosyl anthranilate (PRA). AnPRT, the sole member of class IV phosphoribosyltransferases, adopts a unique fold and functions as a homodimer. While the structural basis of AnPRT activity has been elucidated in several organisms, thermostable variants remain underexplored despite their relevance for high-temperature bioprocessing. In this study, the crystal structure of AnPRT from the thermophilic archaeon Methanocaldococcus jannaschii (MjAnPRT) was determined at a 2.16 Å resolution. The enzyme exhibits a conserved dimeric architecture and key catalytic motifs. Comparative structural analysis with mesophilic and hyper thermophilic homologs revealed that MjAnPRT possesses enhanced local stability in catalytically important regions and strengthened inter-subunit interactions. These features likely contribute to its thermostability and provide a valuable framework for the rational design of robust AnPRTs for industrial and synthetic biology applications. Full article

Biotechnological valorization of Flourensia cernua foliage was carried out using fungal solid-state fermentation; several outcomes of this bioprocess were identified which added value to the plant material. F. cernua leaves placed in aluminum trays were inoculated with Aspergillus niger; extracts of this plant were evaluated and the foliage was tested for in vitro digestibility. The solid bioprocess was carried out at 75% humidity for 120 h and after the fermentation, β-glucosidase activity; phenolics and in vitro digestibility were quantified and measured. Two high β-glucosidase production levels were detected at 42 and 84 h with 3192 and 4092 U/L, respectively. Several phenolics of industrial importance were detected with a HPLC-ESI-MS, such as glycosides of luteolin and apigenin. The other outcome was a substantial improvement in anaerobic digestibility. The unfermented sample registered a 30% in vitro degradability, whereas samples subjected to 84 h of fungal fermentation increased degradability by up to 51%. This bioprocess was designed to detect more than one product, which can contribute to an increase in the added value of F. cernua foliage. Full article

Tailoring culture media and supplementation strategies to the specific requirements of a target product is essential for enhancing microbial production efficiency. This work addresses an unexplored aspect of K. phaffii cultivation: optimizing culture media for metabolite production from xylose, diverging from the conventional focus on recombinant protein expression and the use of glycerol or methanol as primary substrates. Ethylene glycol biosynthesis in an engineered K. phaffii strain was improved by evaluating media and nutrient supplementation. Among the seven evaluated formulations, FM22 and d’Anjou were the most effective, with inositol and thiamine dichloride playing key roles in enhancing production. Salt concentrations in both media were optimized using Central Composite Design (CCD), reducing complexity while increasing yields. Ethylene glycol production increased by 54% in FM22 and 21% in d’Anjou, accompanied by a threefold and 26% reduction in the total salt content, respectively. The vitamin solution was streamlined from seven to two components, each at half the standard concentration. Trace element solutions were reduced to 25% of the original volume without compromising productivity. These findings underscore the dual benefit of culture medium optimization: improved ethylene glycol yields and simplified formulations, establishing a foundation for the development of more efficient and cost-effective bioprocesses using K. phaffii. Full article

Hybrid modeling techniques are increasingly important for improving predictive accuracy and control in biomanufacturing, particularly in data-limited conditions. This study develops and experimentally validates a hybrid deep learning model predictive control (MPC) framework for recombinant P. pastoris fed-batch fermentations. Bayesian optimization and grid search techniques were employed to identify the best-performing hybrid model architecture: an LSTM layer with 2 hidden units followed by a fully connected layer with 8 nodes and ReLU activation. This design balanced accuracy (NRMSE 4.93%) and computational efficiency (AICc 998). This architecture was adapted to a new, smaller dataset of bacteriophage Qβ coat protein production using transfer learning, yielding strong predictive performance with low validation (3.53%) and test (5.61%) losses. Finally, the hybrid model was integrated into a novel MPC system and experimentally validated, demonstrating robust real-time substrate feed control in a way that allows it to maintain specific target growth rates. The system achieved predictive accuracies of 6.51% for biomass and 14.65% for product estimation, with an average tracking error of 10.64%. In summary, this work establishes a robust, adaptable, and efficient hybrid modeling framework for MPC in P. pastoris bioprocesses. By integrating automated architecture searching, transfer learning, and MPC, the approach offers a practical and generalizable solution for real-time control and supports scalable digital twin deployment in industrial biotechnology. Full article

Background: Modern viral vector production needs to consider process intensification for higher yields from smaller production volumes. However, innate antiviral immunity triggered in the producer cell may limit virus replication. While commonly used cell lines (e.g., Vero or E1A-immortalised cells) are already compromised in antiviral pathways, the redundancy of innate signaling complicates host cell optimization by genetic engineering. Small molecules that are hypothesized to target antiviral pathways (Viral Sensitizers, VSEs) added to the culture media offer a versatile alternative to genetic modifications to increase permissiveness and, thus, viral yields across multiple cell lines. Methods: To explore how the yield for a chimeric Zika vaccine candidate (YF-ZIK) could be further be increased in an intensified bioprocess, we used spin tubes or an Ambr15 high-throughput microbioreactor system as scale-down models to optimize the dosing for eight VSEs in three host cell lines (AGE1.CR.pIX, BHK-21, and HEK293-F) based on their tolerability. Results: Addition of VSEs to an already optimized infection process significantly increased infectious titers by up to sevenfold for all three cell lines tested. The development of multi-component VSE formulations using a design of experiments approach allowed further synergistic titer increases in AGE1.CR.pIX cells. Scale-up to 1 L stirred-tank bioreactors and 3D-printed mimics of 200 or 2000 L reactors resulted in up to threefold and eightfold increases, respectively. Conclusions: Addition of single VSEs or combinations thereof allowed a further increase in YF-ZIK titers beyond the yield of an already optimized, highly intensified process. The described approach validates the use of VSEs and can be instructive for optimizing other virus production processes. Full article

Bioprocess simulation is a powerful tool for leveraging circular economy principles in the analysis of large-scale bioprocesses, enhancing decision-making for efficient and sustainable production. By simulating different process scenarios, researchers and engineers can evaluate the techno-economic feasibility of different approaches. This approach enables the identification of cost-effective and sustainable solutions, optimizing resource use and minimizing waste, thereby enhancing the overall efficiency and viability of bioprocesses within a circular economy framework. In this review, we provide an overview of circular economy concepts and trends before discussing design methodologies and challenges in large-scale bioprocesses. The analysis highlights the application and advantages of using process simulators like SuperPro Designer v.14 in bioprocess development. Process design methodologies have evolved to use specialized software that integrates chemical and biochemical processes, physical properties, and economic and environmental considerations. By embracing circular economy principles, these methodologies evaluate projects that transform waste into valuable products, aiming to reduce pollution and resources use, thereby shifting from a linear to a circular economy. In process engineering, exciting perspectives are emerging, particularly in large-scale bioprocess simulations, which are expected to contribute to the improvement of bioprocess technology and computer applications. Full article

Spent coffee grounds are the most abundant waste generated during the preparation of coffee beverages, amounting to 60 million tons per year worldwide. Excessive food waste production has become a global issue, emphasizing the need for waste valorization through the bioprocess of solid-state fermentation (SSF) for high added-value compounds. This work aims to identify the operational conditions for optimizing the solid-state fermentation process of spent coffee grounds to recover bioactive compounds (as polyphenols). An SSF process was performed using two filamentous fungi (Trichoderma harzianum and Rhizopus oryzae). An exploratory design based on the Hunter & Hunter method was applied to analyze the effects of key parameters such as inoculum size (spores/mL), humidity (%), and temperature (°C). Subsequently, a Box–Behnken experimental design was carried out to recovery of total polyphenols. DPPH, ABTS, and FRAP assays evaluated antioxidant activity. The maximum concentration of polyphenols was observed in treatment T3 (0.279 ± 0.002 TPC mg/g SCG) using T. harzianum, and a similar result was obtained with R. oryzae in the same treatment (0.250 ± 0.011 TPC mg/g SCG). In the Box–Behnken design, the most efficient treatment for T. harzianum was T12 (0.511 ± 0.017 TPC mg/g SCG), and for R. oryzae, T9 (0.636 ± 0.003 TPC mg/g SCG). These extracts could have applications in the food industry to improve preservation and functionality. Full article

Fed-batch cultivation is a widely used strategy for microbial lipid production, offering flexibility in nutrient control and the potential for high lipid productivity. However, optimizing feeding strategies remains a complex challenge, as it depends on multiple factors, including strain-specific metabolism and process limitations. In this study, we developed a computational framework based on dynamic flux balance analysis and small-scale metabolic models to evaluate and optimize lipid production in Rhodosporidium toruloides strains. We proposed equations to estimate both the carbon and energy source mass feed rate ($F_{in}·s_r$) and its concentration in the feed ($s_r$) based on lipid accumulation targets, and defined minimum feeding flow rate ($F_{in}$) according to process duration. We then assessed the impact of these parameters on commonly used bioprocess metrics—lipid yield, titer, productivity, and intracellular accumulation—across wild-type and engineered strains. Our results showed that the selection of $F_{in}·s_r$ was strongly strain-dependent and significantly influenced strain performance. Moreover, for a given $F_{in}·s_r$, the specific values of $s_r$, and the resulting $F_{in}$, had distinct and non-equivalent effects on performance metrics. This methodology enables the rational pre-selection of feeding strategies and strains, improving resource efficiency and reducing the probability of failed experiments. Full article

The formulation of biosimilar products critically determines their stability, safety, immunogenicity, and market accessibility. This article presents a novel integrative framework for biosimilar formulation that balances scientific, regulatory, and intellectual property dimensions, offering a holistic perspective rarely unified in the literature. It highlights the growing trend toward buffer-free, high-concentration systems that leverage protein self-buffering to improve patient comfort and formulation stability. The article also addresses regulatory flexibility from the FDA and EMA, which allows scientifically justified deviations from reference formulations to ensure pharmaceutical equivalence and minimize immunogenicity. A novelty of this article is its comprehensive analysis of how digital innovations, such as Quality-by-Design, Process-Analytical-Technology, and AI-based in silico simulations, are transforming formulation design and bioprocess optimization to reduce immunogenic risks and enhance bioequivalence. Two important key takeaways emerge: (1) strategic innovation in formulation, especially using buffer-free and high concentration systems, improve product stability and patient tolerability while complying with regulatory standards; and (2) intellectual property challenges, including patent thickets, strongly influence formulation decisions, making early legal-strategic alignment essential for market entry. The article confirms that practical recommendations for the selection of recombinant therapeutic protein formulations can effectively guide developers and regulators toward safer, more efficient, and commercially viable biosimilar products. Full article

The “11th International Congress on Biocatalysis (biocat2024)” was part of a biennial series that unites the fields of biology and chemistry, attracting researchers from the life sciences, engineering, and computer science. This international forum provides an opportunity for scientists worldwide to connect, seek collaboration for future projects, and gain insights into contemporary topics and innovative techniques. Biocat covers a range of compelling subjects and recent advancements in biocatalysis, including enzyme discovery, evolution, and applications. This congress focused on six key topics: AI and computational methods, structure–function analysis and enzyme engineering, enzymatic and whole-cell biotransformations, reaction cascades (electro-, chemo-, and photoenzymatic synergies), bioprocess engineering and the design of smart reactors, and facing climate change through sustainability and a circular bioeconomy. In 2024, we welcomed 344 expert delegates alongside 21 internal attendees, including 154 women and 1 non-binary participant, bringing the total number of participants to an impressive 365. Established researchers and emerging scientists from academia and industry delivered a total of 119 presentations, comprising 59 standard lectures, 60 lightning talks, and 195 posters. Six industry exhibitors showcased their latest products and services, providing an excellent opportunity to strengthen the connection between science and industry. Furthermore, the biocat award, recognized as one of the most prestigious honors in biotechnology, was presented for the eleventh time in the categories of “Science in Academia”, “Lifetime Achievement,” and “Industry”. Full article

Global demands for sustainable energy and advanced therapeutics necessitate innovative interdisciplinary solutions. Integrated biorefining emerges as a strategic response, enabling the co-production of biofuels and pharmaceutical compounds through biomass valorization. This integrated model holds promise in enhancing resource utilization efficiency while ensuring economic viability. Our critical review methodically evaluates seven pivotal methodologies: seven key strategies: microbial metabolites, synthetic biology platforms, biorefinery waste extraction, nanocatalysts, computer-aided design, extremophiles, and plant secondary metabolites. Through systematic integration of these approaches, we reveal pivotal synergies and potential technological innovations that can propel multi-product biorefinery systems. Persistent challenges, particularly in reconciling complex metabolic flux balancing with regulatory compliance requirements, are analyzed. Nevertheless, advancements in systems biology, next-generation bioprocess engineering, and artificial intelligence-enhanced computational modeling present viable pathways for overcoming these obstacles. This comprehensive analysis substantiates the transformative capacity of integrated biorefining in establishing a circular bioeconomy framework, while underscoring the imperative of transdisciplinary cooperation to address existing technical and policy constraints. Full article

Urban solid waste (USW) is a promising alternative source of valuable chemical compounds. It is considered an adsorbent material due to its chemical structure, porosity and electronic charge available to form chemical bonds and can be recovered or transformed for use in bioprocesses and industrial applications. This is the case with cigarette butts (CBs), which consist of thousands of substances that can be chemically converted for various purposes. This work showed high efficiency in the production of cellulose mass from the recycling of CBs, a patented technology in operation at the company Poiato Recicla—SP. The lignin-like solid (LLS)—a material obtained from the recycling of cigarette butts (CBs) by catalytic transfer hydrogenation (CTH), under non-rigorous conditions—showed high efficiency in its conversion into molecules of great interest. In the bio-oil obtained, characterized by analyses such as GCMS and RMN 2D HSQC, a mixture of predominantly hydrocarbons (many of them with cyclic and/or branched chains) was identified in almost all the experiments. This method demonstrates the potential of the TCH process for SSLs and completes the recycling chain designed for CBs, promoting their complete conversion into chemical compounds of greater interest. Full article

Apple fruit is among the most consumed fruits in the world, both in fresh and processed forms (e.g., ready-to-eat fresh slices, juice, jam, cider, and dried slices). During apple consumption/processing, a significant amount of apple residue is discarded. These residues can also be interesting materials to exploit, particularly for direct valorization in the design of added-value foods. In fact, apple waste/by-products are rich in essential components, including sugars, proteins, dietary fibers, and phenolic compounds, as they comprise apple peels, seeds, and pulp (solid residue of juice production). In this sense, the current review paper presents an overview of the nutritional composition of apple waste/by-products, and mainly apple pomace, highlighting their application in producing value-added products through microbial biotechnology. If appropriately managed, apple by-products can generate a variety of useful compounds required in food (as well as in feed, pharmaceutics, and bioenergy). Recent strategies for the synergic use of apple waste/by-products and microbial resources such as lactic acid bacteria and yeasts are discussed. This review contributes to defining a reference framework for valorizing apple waste/by-products from a circular economy perspective through the application of bioprocesses (e.g., fermentation), mainly oriented towards designing foods with improved quality attributes. Full article