New milliliter-scale stirred tank bioreactors for the cultivation of mycelium forming microorganisms

Online 2D Fluorescence Monitoring in Microtiter Plates Allows Prediction of Cultivation Parameters and Considerable Reduction in Sampling Efforts for Parallel Cultivations of Hansenula polymorpha

Multi-wavelength (2D) fluorescence spectroscopy represents an important step towards exploiting the monitoring potential of microtiter plates (MTPs) during early-stage bioprocess development. In combination with multivariate data analysis (MVDA), important process information can be obtained, while repetitive, cost-intensive sample analytics can be reduced. This study provides a comprehensive experimental dataset of online and offline measurements for batch cultures of Hansenula polymorpha. In the first step, principal component analysis (PCA) was used to assess spectral data quality. Secondly, partial least-squares (PLS) regression models were generated, based on spectral data of two cultivation conditions and offline samples for glycerol, cell dry weight, and pH value. Thereby, the time-wise resolution increased 12-fold compared to the offline sampling interval of 6 h. The PLS models were validated using offline samples of a shorter sampling interval. Very good model transferability was shown during the PLS model application to the spectral data of cultures with six varying initial cultivation conditions. For all the predicted variables, a relative root-mean-square error (RMSE) below 6% was obtained. Based on the findings, the initial experimental strategy was re-evaluated and a more practical approach with minimised sampling effort and elevated experimental throughput was proposed. In conclusion, the study underlines the high potential of multi-wavelength (2D) fluorescence spectroscopy and provides an evaluation workflow for PLS modelling in microtiter plates.

Microbioreactor (micro-Matrix) potential in aerobic and anaerobic conditions with different industrially relevant microbial strains

Microscale fermentation systems are important high throughput tools in clone selection, and bioprocess set up and optimization, since they provide several parallel experiments in controlled conditions of pH, temperature, agitation, and gas flow rate. In this work we evaluated the performance of biotechnologically relevant strains with different respiratory requirements in the micro‐Matrix microbioreactor. In particular Escherichia coli K4 requires well aerated fermentation conditions to improve its native production of chondroitin‐like capsular polysaccharide, a biomedically attractive polymer. Results from batch and fed‐batch experiments demonstrated high reproducibility with those obtained on 2 L reactors, although highlighting a pronounced volume loss for longer‐term experiments. Basfia succiniciproducens and Actinobacillus succinogenes need CO₂ addition for the production of succinic acid, a building block with several industrial applications. Different CO₂ supply modes were tested for the two strains in 24 h batch experiments and results well compared with those obtained on lab‐scale bioreactors. Overall, it was demonstrated that the micro‐Matrix is a useful scale‐down tool that is suitable for growing metabolically different strains in simple batch process, however, a series of issues should still be addressed in order to fully exploit its potential.

Microbioreactor-assisted cultivation workflows for time-efficient phenotyping of protein producing Aspergillus niger in batch and fed-batch mode

In recent years, many fungal genomes have become publicly available. In combination with novel gene editing tools, this allows for accelerated strain construction, making filamentous fungi even more interesting for the production of valuable products. However, besides their extraordinary production and secretion capacities, fungi most often exhibit challenging morphologies, which need to be screened for the best operational window. Thereby, combining genetic diversity with various environmental parameters results in a large parameter space, creating a strong demand for time-efficient phenotyping technologies. Microbioreactor systems, which have been well established for bacterial organisms, enable an increased cultivation throughput via parallelization and miniaturization, as well as enhanced process insight via non-invasive online monitoring. Nevertheless, only few reports about microtiter plate cultivation for filamentous fungi in general and even less with online monitoring exist in literature. Moreover, screening under batch conditions in microscale, when a fed-batch process is performed in large-scale might even lead to the wrong identification of optimized parameters. Therefore, in this study a novel workflow for Aspergillus niger was developed, allowing for up to 48 parallel microbioreactor cultivations in batch as well as fed-batch mode. This workflow was validated against lab-scale bioreactor cultivations to proof scalability. With the optimized cultivation protocol, three different micro-scale fed-batch strategies were tested to identify the best protein production conditions for intracellular model product GFP. Subsequently, the best feeding strategy was again validated in a lab-scale bioreactor.

Miniaturization and 3D Printing of Bioreactors: A Technological Mini Review

Many articles have been published on scale-down concepts as well as additive manufacturing techniques. However, information is scarce when miniaturization and 3D printing are applied in the fabrication of bioreactor systems. Therefore, garnering information for the interfaces between miniaturization and 3D printing becomes important and essential. The first goal is to examine the miniaturization aspects concerning bioreactor screening systems. The second goal is to review successful modalities of 3D printing and its applications in bioreactor manufacturing. This paper intends to provide information on anaerobic digestion process intensification by fusion of miniaturization technique and 3D printing technology. In particular, it gives a perspective on the challenges of 3D printing and the options of miniature bioreactor systems for process high-throughput screening.

The ejector loop reactor: Application for microbial fermentation and comparison with a stirred-tank bioreactor

Ejector loop reactors (ELR) are successfully used in industrial chemical processes for gas/liquid reactions. They achieve higher mass transfer rates compared to the stirred-tank reactor (STR) at comparable specific power input. Insufficient oxygen transport and shear stress induced growth inhibition are limiting parameters during microbial fermentation. Due to its better mass transfer characteristics, the ELR was expected to have beneficial effects on biomass and recombinant protein production. One concern, however, was whether the ELR's shear stress characteristics would have a negative effect. This study evaluated the suitability of using the Buss-Loop® Reactor (BLR), one of the most advanced ELR technologies, as a bioreactor. The well-studied STR was used as a reference. A lab scale BLR was adapted for microbial fermentation. Mass transfer rates and specific power inputs were within the same order of magnitude in the ELR and the reference STR. Maximum k L a values of 207 and 205 h^-1 at power inputs of 6.9 and 9.7 W/L were measured in the ELR and STR, respectively. During batch fermentation of Escherichia coli K12 MG1655, maximum cell densities were higher in the ELR (OD600 of 22) than in the STR (OD600 of 18). Green fluorescence protein (GFP) production with pGS1 was comparable; however, more GFP was released into the media in the ELR. This indicates higher cell disruption compared to the STR. Despite this drawback of the first prototype, our work clearly demonstrates the potential of the ELR as a system for microbial fermentations.

Generic Protocol for Optimization of Heterologous Protein Production Using Automated Microbioreactor Technology

A core business in industrial biotechnology using microbial production cell factories is the iterative process of strain engineering and optimization of bioprocess conditions. One important aspect is the improvement of cultivation medium to provide an optimal environment for microbial formation of the product of interest. It is well accepted that the media composition can dramatically influence overall bioprocess performance. Nutrition medium optimization is known to improve recombinant protein production with microbial systems and thus, this is a rewarding step in bioprocess development. However, very often standard media recipes are taken from literature, since tailor-made design of the cultivation medium is a tedious task that demands microbioreactor technology for sufficient cultivation throughput, fast product analytics, as well as support by lab robotics to enable reliability in liquid handling steps. Furthermore, advanced mathematical methods are required for rationally analyzing measurement data and efficiently designing parallel experiments such as to achieve optimal information content. The generic nature of the presented protocol allows for easy adaption to different lab equipment, other expression hosts, and target proteins of interest, as well as further bioprocess parameters. Moreover, other optimization objectives like protein production rate, specific yield, or product quality can be chosen to fit the scope of other optimization studies. The applied Kriging Toolbox (KriKit) is a general tool for Design of Experiments (DOE) that contributes to improved holistic bioprocess optimization. It also supports multi-objective optimization which can be important in optimizing both upstream and downstream processes.

Significance of Heavy-Ion Beam Irradiation-Induced Avermectin B1a Production by Engineered Streptomyces avermitilis

Heavy-ion irradiation technology has advantages over traditional methods of mutagenesis. Heavy-ion irradiation improves the mutation rate, broadens the mutation spectrum, and shortens the breeding cycle. However, few data are currently available regarding its effect on Streptomyces avermitilis morphology and productivity. In this study, the influence of heavy-ion irradiation on S. avermitilis when cultivated in approximately 10 L stirred-tank bioreactors was investigated. The specific productivity of the avermectin (AVM) B1a-producing mutant S. avermitilis 147-G₅8 increased notably, from 3885 to 5446 μg/mL, approximately 1.6-fold, compared to the original strain. The mycelial morphology of the mutant fermentation processes was microscopically examined. Additionally, protein and metabolite identification was performed by using SDS-PAGE, 2- and 3-dimensional electrophoresis (2DE and 3DE). The results showed that negative regulation gene deletion of mutants led to metabolic process upregulating expression of protein and improving the productivity of an avermectin B1a. The results showed that the heavy-ion beam irradiation dose that corresponded to optimal production was well over the standard dose, at approximately 80 Gy at 220 AMeV (depending on the strain). This study provides reliable data and a feasible method for increasing AVM productivity in industrial processes.

Oxygen transfer characteristics of miniaturized bioreactor systems

Since their introduction in 2001 miniaturized bioreactor systems have made great advances in function and performance. In this article the dissolved oxygen (DO) transfer performance of submilliliter microbioreactors, and 1–10 mL minibioreactors was examined. Microbioreactors have reached k_La values of 460 h^-1, and are offering instrumentation and some functionality comparable to production systems, but at high throughput screening volumes. Minibioreactors, aside from one 1,440 h^-1k_La system, have not offered as high rates of DO transfer, but have demonstrated superior integration with automated fluid handling systems. Microbioreactors have been typically limited to studies with E. coli, while minibioreactors have offered greater versatility in this regard. Further, mathematical relationships confirming the applicability of k_La measurements across all scales have been derived, and alternatives to fluorescence lifetime DO sensors have been evaluated. Finally, the influence on reactor performance of oxygen uptake rate (OUR), and the possibility of its real-time measurement have been explored. Biotechnol. Bioeng. 2013; 110: 1005–1019. © 2012 Wiley Periodicals, Inc.

Novel approach of high cell density recombinant bioprocess development: optimisation and scale-up from microliter to pilot scales while maintaining the fed-batch cultivation mode of E. coli cultures

Background

Bioprocess development of recombinant proteins is time consuming and laborious as many factors influence the accumulation of the product in the soluble and active form. Currently, in most cases the developmental line is characterised by a screening stage which is performed under batch conditions followed by the development of the fed-batch process. Performing the screening already under fed-batch conditions would limit the amount of work and guarantee that the selected favoured conditions also work in the production scale.

Results

Here, for the first time, high throughput multifactorial screening of a cloning library is combined with the fed-batch technique in 96-well plates, and a strategy is directly derived for scaling to bioreactor scale. At the example of a difficult to express protein, an RNase inhibitor, it is demonstrated that screening of various vector constructs and growth conditions can be performed in a coherent line by (i) applying a vector library with promoters and ribosome binding sites of different strength and various fusion partners together with (ii) an early stage use of the fed-batch technology. It is shown that the EnBase^® technology provides an easy solution for controlled cultivation conditions in the microwell scale. Additionally the high cell densities obtained provide material for various analyses from the small culture volumes. Crucial factors for a high yield of the target protein in the actual case were (i) the fusion partner, (ii) the use of of a mineral salt medium together with the fed-batch technique, and (iii) the preinduction growth rate. Finally, it is shown that the favorable conditions selected in the microwell plate and shake flask scales also work in the bioreactor.

Conclusions

Cultivation media and culture conditions have a major impact on the success of a screening procedure. Therefore the application of controlled cultivation conditions is pivotal. The consequent use of fed-batch conditons from the first screening phase not only shortens the developmental line by guarantying that the selected conditions are relevant for the scale up, but in our case also standard batch cultures failed to select the right clone or conditions at all.