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Artificial intelligence (AI) technology is booming up a new industrial revolution, and its successful application is rapidly spreading from the information industry to many other fields. The traditional fermentation industry also faces more opportunities and great challenges for reforming. First of all, the rapid development of synthetic biotechnology has greatly enhanced the availability and efficiency for obtaining high-performance strains, which poses great opportunities to the traditional fermentation optimization and scale-up technology. It is urgent to upgrade fermentation optimization technology to cope with the requirement for high-throughput verification of strain performance. Secondly, the development of fermentation equipment technology has laid a good foundation for advancing fermentation optimization technology. The application of AI technology, especially the digital twin and knowledge graph technology, will further boost the upgrade of the traditional fermentation technology. This review summarizes the challenges of fermentation optimization technology in the era of synthetic biology, the core technology of fermentation optimization and scale-up, the equipment technology of high-throughput fermentation, data visualization technology, as well as the application of digital twin and knowledge graph in fermentation optimization and scale-up. This review also prospects future industrial fermentation technology, and the associated new requirements for personnel training.

Industrial bioprocess is a complex systematic process and bio-manufacturing can be realized on the basis of understanding the metabolism process of living cells. In this article, the multi-scale optimization principle and practice of industrial fermentation process are reviewed, including multi-scale optimizing theory and equipment, on-line sensing technology for cellular macroscopic metabolism, and correlated analysis of physiological parameters. Furthermore, intelligent control of industrial bioprocess is further addressed, in terms of new sensing technology for intracellular physiological metabolism, big database establishment and data depth calculation, intelligent decision.

Penicillin is one of the best known pharmaceuticals and is also an important member of the β-lactam antibiotics. Over the years, ambitious yields, titers, productivities, and low costs in the production of the β-lactam antibiotics have been stepwise realized through successive rounds of strain improvement and process optimization. Penicillium chrysogenum was proven to be an ideal cell factory for the production of penicillin, and successful approaches were exploited to elevate the production titer. However, the industrial production of penicillin faces the serious challenge that environmental gradients, which are caused by insufficient mixing and mass transfer limitations, exert a considerably negative impact on the ultimate productivity and yield. Scale-down studies regarding diverse environmental gradients have been carried out on bacteria, yeasts, and filamentous fungi as well as animal cells. In accordance, a variety of scale-down devices combined with fast sampling and quenching protocols have been established to acquire the true snapshots of the perturbed cellular conditions. The perturbed metabolome information stemming from scale-down studies contributed to the comprehension of the production process and the identification of improvement approaches. However, little is known about the influence of the flow field and the mechanisms of intracellular metabolism. Consequently, it is still rather difficult to realize a fully rational scale-up. In the future, developing a computer framework to simulate the flow field of the large-scale fermenters is highly recommended. Furthermore, a metabolically structured kinetic model directly related to the production of penicillin will be further coupled to the fluid flow dynamics. A mathematical model including the information from both computational fluid dynamics and chemical reaction dynamics will then be established for the prediction of detailed information over the entire period of the fermentation process and thereby for the optimization of penicillin production, and subsequently also benefiting other fermentation products.

This minireview mainly aims at the study of S-adenosyl-L-methionine (SAM) production by microbial fermentation. A brief introduction of the biological role and application of SAM was presented. In general, SAM production can be improved by breeding of the producing strain through the conventional mutation or genetic engineering approach in the molecular or cellular scale, by optimization of culture conditions in the cellular scale or bioreactor engineering scale, or by multiscale approach. The productivity of SAM fermentation has been improved greatly through the efforts of many researchers using the methods previously mentioned. The SAM-producing strains used extensively are Pichia pastoris and Saccharomyces cerevisiae. The effect of SAM on antibiotic production was also exemplified. The skill and scheme beneficial to the improvement of SAM production involves the enhancement of SAM synthetase (methionine adenosyltransferase) activity and selection of engineered constitutive promoters with appropriate strength; seeking for and eliminating the rate-limiting factors in SAM synthesis, namely, knocking off the genes that transform SAM and L-methionine (L-Met) to cysteine; release the feedback inhibition of SAM to methylenetetrahydrofolate reductase; blocking the transsulfuration pathway by interfering the responsible enzymes; enhancing ATP level through pulsed feeding of glycerol; and optimizing the L-Met feeding strategy. Precise control of gene expression and quantitative assessment of physiological parameters in engineered P. pastoris were highlighted. Finally, a discussion of the prospect of SAM production was presented.

Effects of impeller configuration on fungal physiology and cephalosporin C production were investigated by an industrial strain Acremonium chrysogenum in a 12 m(3) bioreactor equipped with conventional and novel impeller configuration, respectively. The cell growth and oxygen uptake rate (OUR) profiles were little affected by the impeller configurations. However, differing impeller combinations significantly affected the morphology, which in turn influenced cephalosporin C production. Under the novel impeller configuration, the production of cephalosporin C was 10% higher and an excessive amount of dispersed arthrospores was also observed. Computational fluid dynamics (CFD) simulation further revealed that poor mass and energy exchange as well as inhomogeneous environment existed in the bioreactor equipped with conventional impeller configuration. For equivalent power dissipation, the volume oxygen transfer coefficient (K(L)a) could be enhanced by 15% compared with that of conventional impeller configuration. Power consumption was dramatically decreased by 25% by using novel impeller configuration., (Copyright © 2012 Elsevier B.V. All rights reserved.)

Oxytetracycline (OTC) is a widely used antibiotic, which is commercially produced by Streptomyces rimosus. The type II minimal polyketide synthases (minimal PKS) genes of the oxytetracycline biosynthesis cluster in S. rimosus, consisting of oxyA, oxyB and oxyC, are involved in catalyzing 19-C chain building by the condensation of eight malonyl-CoA groups to form the starting polyketide. This study aimed to investigate the effects of overexpression of the minimal PKS gene in a model S. rimosus strain (M4018) and in an industrial overproducer (SR16) by introduction of a second copy of the gene into the chromosome. Increased levels of oxyA, oxyB and oxyC gene transcription were monitored using reverse transcription quantitative real-time PCR. Overexpression of the minimal PKS gene elicited retardation of cell growth and a significant improvement in OTC production in corresponding mutants (approximately 51.2% and 32.9% in M4018 and SR16 mutants respectively). These data indicate that the minimal PKS plays an important role in carbon flux redirection from cell growth pathways to OTC biosynthesis pathways., (Copyright © 2012 Elsevier Inc. All rights reserved.)

The effects of light/dark cycle, mixing pattern and partial pressure of H2 on the growth and hydrogen production of Rhodobacter sphaeroides ZX-5 were investigated. The results from light/dark cycle culture showed that little or no hydrogen production was observed during the dark periods, and the hydrogen production immediately recovered once illumination was resumed. Also, it was found that the optimum condition of shaking velocity was 120 rpm for hydrogen photo-fermentation. Meanwhile, shaking during H2 production phase (i.e., cell growth stationary phase) of photo-fermentation played a crucial role on effectively enhancing the phototrophic hydrogen production, rather than that during cell exponential growth phase. The other factor evaluated was hydrogen partial pressure in the culture system. The substrate conversion efficiency increased from 86.07% to 95.56% along with the decrease of the total pressure in the photobioreactor from 1.082×10(5) to 0.944×10(5) Pa, which indicated that reduction of H2 partial pressure by lowering the operating pressure substantially improved H2 production in an anaerobic, photo-fermentation process., (Copyright © 2010 Elsevier Ltd. All rights reserved.)

The developments of the systems biotechnology and its application in the industrial process open up new horizons to industrial biotechnology. The unprecedented understanding of the relationships between cellular behaviors and the surrounding environments during the bioprocess has been achieved. In this paper, we review new advances in the strain improvement, bioprocess control and optimization. The holistic viewpoints and ideas applied in industrial bioprocesses and their future prospects are discussed by illustrating some successful cases.

Abstract The fermentation process is dynamically changing, and the metabolic status can be grasped through real-time monitoring of environmental parameters. In this study, a real-time and on-line monitoring experiment platform for substrates and products detection was developed based on non-contact type near-infrared (NIR) spectroscopy technology. The prediction models for monitoring the fermentation process of lactic acid, sophorolipids (SLs) and sodium gluconate (SG) were established based on partial least-squares regression and internal cross-validation methods. Through fermentation verification, the accuracy and precision of the NIR model for the complex fermentation environments, different rheological properties (uniform system and multi-phase inhomogeneous system) and different parameter types (substrate, product and nutrients) have good applicability, and R 2 was greater than 0.98, exhibiting a good linear relationship. The root mean square error of prediction shows that the model has high credibility. Through the control of appropriate glucose concentration in SG fermentation as well as glucose and oil concentrations SLs fermentation by NIR model, the titers of SG and SLs were increased to 11.8% and 26.8%, respectively. Although high cost of NIR spectrometer is a key issue for its wide application in an industrial scale. This work provides a basis for the application of NIR spectroscopy in complex fermentation systems.

The Valley of Death confronts industrial biotechnology with a significant challenge to the commercialization of products. Fortunately, with the integration of computation, automation and artificial intelligence (AI) technology, the industrial biotechnology accelerates to cross the Valley of Death. The Fourth Industrial Revolution (Industry 4.0) has spurred advanced development of intelligent biomanufacturing, which has evolved the industrial structures in line with the worldwide trend. To achieve this, intelligent biomanufacturing can be structured into three main parts that comprise digitalization, modeling and intellectualization, with modeling forming a crucial link between the other two components. This paper provides an overview of mechanistic models, data-driven models and their applications in bioprocess development. We provide a detailed elaboration of the hybrid model and its applications in bioprocess engineering, including strain design, process control and optimization, as well as bioreactor scale-up. Finally, the challenges and opportunities of biomanufacturing towards Industry 4.0 are also discussed. [ABSTRACT FROM AUTHOR]

Abstract Background The otrC gene of Streptomyces rimosus was previously annotated as an oxytetracycline (OTC) resistance protein. However, the amino acid sequence analysis of OtrC shows that it is a putative ATP-binding cassette (ABC) transporter with multidrug resistance function. To our knowledge, none of the ABC transporters in S. rimosus have yet been characterized. In this study, we aimed to characterize the multidrug exporter function of OtrC and evaluate its relevancy to OTC production. Results In order to investigate OtrC’s function, otrC is cloned and expressed in E. coli The exporter function of OtrC was identified by ATPase activity determination and ethidium bromide efflux assays. Also, the susceptibilities of OtrC-overexpressing cells to several structurally unrelated drugs were compared with those of OtrC-non-expressing cells by minimal inhibitory concentration (MIC) assays, indicating that OtrC functions as a drug exporter with a broad range of drug specificities. The OTC production was enhanced by 1.6-fold in M4018 (P = 0.000877) and 1.4-fold in SR16 (P = 0.00973) duplication mutants, while it decreased to 80% in disruption mutants (P = 0.0182 and 0.0124 in M4018 and SR16, respectively). Conclusions The results suggest that OtrC is an ABC transporter with multidrug resistance function, and plays an important role in self-protection by drug efflux mechanisms. This is the first report of such a protein in S. rimosus, and otrC could be a valuable target for genetic manipulation to improve the production of industrial antibiotics.

• Compared to other delivery systems, the specific colonization ability of Escherichia coli Nissle 1917 (ECN) at the tumor site enables active targeting and enhances drug delivery efficiency. • Surface encapsulation of ECN with TA@Fe3+, which not only enhances the efficiency of drug loading (90%) without affecting viability of ECN but also enables the drug release behavior of the tumor microenvironment-responsive system, effectively avoids drug premature leakage. • The first report on the lytic circuit responding to the hypoxic microenvironment within tumors, inducing ECN bacteria lysis in vivo and thus enhancing the biosafety profile of the system. • The lytic ECN releases relevant antigens, triggering the TLR4 signaling pathway and promoting the macrophage polarization of M2 towards the M1 phenotype, ultimately reversing the tumor immune-suppressive microenvironment and enhancing the anti-tumor efficacy. The utilization of bacteria as a drug delivery system represents a promising strategy for tumor therapy, owing to their inherent ability to selectively colonize and induce apoptosis of tumor cells at the solid tumor. However, the occurrence of dose-dependent toxicity has led to the failure of clinical trials. Unfortunately, the implementation of a singular bacterial treatment strategy for tumor therapy is inherently limited. In this study, we developed a living drug delivery material named DOX@TA@ECN (D@T@E) by utilizing Fe3+ and tannin acid (TA) as a cross-linking network to encapsulate doxorubicin (DOX) and form a protective coating on the surface of Escherichia coli Nissle 1917 (ECN). In an acidic tumor microenvironment, D@T@E disintegrated the coating to release DOX through the highly expressed H 2 O 2. To enhance biosafety, the D@T@E was equipped with a hypoxic lytic circuit (Pvhb-Lysis) to regulate the number of ECN in vivo (D@T@E-PL). The hypoxic promotor of Vitreoscilla hemoglobin protein (Pvhb) were activied to induce expression of lysis protein (PhiX174E) in the tumor hypoxic microenvironment (3 %), resulting in ECN lysis and subsequent elimination by the immune system. Additionally, D@T@E-PL pass lysis to release relevant antigens (DNA and flagellin). This antigen promotes the polarization of M2-type tumor-promoting macrophages towards M1-type anti-tumor macrophages at the tumor microenvironment by activating Toll-like receptor 4 (TLR4), eliciting immune-mediated anti-tumor responses. The in vivo findings demonstrated that D@T@E-PL intelligent material demonstrated enhanced biosecurity through the lytic circuit and effectively suppressed tumor growth, thereby achieving a dual therapeutic approach combining chemotherapy and immunotherapy for tumor inhibition. [ABSTRACT FROM AUTHOR]

Abstract: S-Adenosyl-l-methionine (SAM) is an important molecule for normal cell function and survival. To enhance methionine adenosyltransferase (MAT, EC2.5.1.6) activity and thus SAM production in recombinant Pichia pastoris, MAT genes from Escherichia coli, Saccharmyces cerevisiae, and Streptomyces spectabilis were recombined by DNA shuffling. The shuffled genes were transformed into P. pastoris GS115 to construct recombinant strains and screened for high MAT activity and enhanced SAM production mutants. In the two best recombinant strains, the MAT activities were respectively 201% and 65% higher than the recombinant strains containing the starting MAT genes, and the SAM concentration increased by 103% and 65% respectively. The analysis on the deduced sequences of five representative MAT variants showed that the K18R mutation probably resulted in the increased activity of the best MAT, which may provide new insights into structure-enzyme activity relationship of MAT and might shed light on the further rational evolution of MAT. Finally, a 6.14gl−1 of SAM production was reached in a 500l bioreactor with the best recombinant strain GS115/DS56, which showed a favorable foreground in industrial scale production of SAM. [Copyright &y& Elsevier]