Shaken flasks by resonant acoustic mixing versus orbital mixing: Mass transfer coefficient kLa characterization and Escherichia coli cultures comparison

Gas supply apparatus using rotational motion of shaking incubator for flask culture of aerobic microorganisms

Shake flask cultivation, a cornerstone in bioprocess research encounters limitations in supplying sufficient oxygen and exchanging gases, restricting its accuracy in assessing microbial growth and metabolic activity. In this communication, we introduce an innovative gas supply apparatus that harnesses the rotational motion of a shaking incubator to facilitate continuous air delivery, effectively overcoming these limitations. We measured the mass transfer coefficient (kLa) and conducted batch cultures of Corynebacterium glutamicum H36LsGAD using various working volumes to assess its performance. Results demonstrated that the gas supply apparatus significantly outperforms conventional silicone stoppers regarding oxygen delivery, with kLa values of 2531.7 h-1 compared to 20.25 h-1 at 230 rpm. Moreover, in batch cultures, the gas supply apparatus enabled substantial improvements in microbial growth, maintaining exponential growth even at larger working volumes. Compared to the existing system, an increase in final cell mass by a factor of 3.4-fold was observed when utilizing 20% of the flask's volume, and a remarkable 9-fold increase was achieved when using 60%. Furthermore, the gas supply apparatus ensured consistent oxygen supply and efficient gas exchange within the flask, overcoming challenges associated with low working volumes. This approach offers a simple yet effective solution to enhance gas transfer in shake flask cultivation, bridging the gap between laboratory-scale experiments and industrial fermenters. Its broad applicability holds promise for advancing research in bioprocess optimization and scale-up endeavors.

A forced aeration system for microbial culture of multiple shaken vessels suppresses volatilization

Shake-flask culture, an aerobic submerged culture, has been used in various applications involving cell cultivation. However, it is not designed for forced aeration. Hence, this study aimed to develop a small-scale submerged shaking culture system enabling forced aeration into the medium. A forced aeration control system for multiple vessels allows shaking, suppresses volatilization, and is attachable externally to existing shaking tables. Using a specially developed plug, medium volatilization was reduced to less than 10%, even after 45 h of continuous aeration (~ 60 mL/min of dry air) in a 50 mL working volume. Escherichia coli IFO3301 cultivation with aeration was completed within a shorter period than that without aeration, with a 35% reduction in the time-to-reach maximum bacterial concentration (26.5 g-dry cell/L) and a 1.25-fold increase in maximum concentration. The maximum bacterial concentration achieved with aeration was identical to that obtained using the Erlenmeyer flask, with a 65% reduction in the time required to reach it.

Thermoinducible E. coli for Recombinant Protein Production in Inclusion Bodies

The temperature-inducible λpL/pR-cI857 expression system has been widely used to produce recombinant proteins (RPs), especially when it is necessary to avoid the addition of exogenous materials to induce the expression of recombinant genes, preventing contamination of bioprocesses. The temperature increase favors the formation of inclusion bodies (IBs). The temperature upshift could change the metabolism, productivities, cell viability, IBs architecture, and the host cell proteins inside IBs, affecting downstream to obtain the final product. In this contribution, we focus on the relationship between the bioprocesses using temperature increase as inducer, the heat shock response associated with temperature up-shift, the RP accumulation, and the formation of IBs. Here, we describe how to produce IBs and how culture conditions can modulate the composition and architecture of IBs by modifying the induction temperature in RP production.

Control of carbon dioxide concentration in headspace of multiple flasks using both non-electric bellows pump and shaking incubator

Current methods of controlling gas in the headspace involve constant speed aeration and proportional-integral-differential (PID) controlled aeration using improved monitoring devices or gas cylinders. However, these approaches are restricted and inconvenient to use. In this study, we propose a method to control the CO₂ concentration in the headspace while maintaining the convenience of shake-flask culture. A combination of a non-electric bellows pump for shake-flask (NeBP-sf) and a CO₂ incubator was used to control the flask gas phase by shaking without additional external power. The CO₂ half-life, as an indicator of the ventilation ability of the system, was measured using a circulation direct monitoring and sampling system, and the NeBP-sf was optimised. The ventilation capacity varied depending on the shaking speed, and under optimal conditions, was 10 min compared with 45 min when only a breathable culture plug was used. In conventional microbial shaking culture, the CO₂ concentration in the flask gas phase remained higher than the 5% set-value with a maximum of 9%, resulting in a large concentration difference with the set point. Therefore, the ventilation capacity of the conventional shake-flask culture was insufficient for aerobic culture. Cultivation of Escherichia coli and Lactiplantibacillus plantarum using the system showed no significant difference between the set point and real point values. Thus, the system combined an NeBP-sf and a gas incubator built-in shaking table to achieve the reproducibility of gas control while maintaining a high level of convenience.

Analysis of porous breathable stopper and development of PID control for gas phase during shake-flask culture with microorganisms

We evaluated the ventilation ability of two types (plug-type and cap-type) of culture-stoppers having standard air permeability. The culture-stoppers were evaluated using the circulation direct monitoring and sampling system with CO₂ concentration in the gas phase of a shake-flask culture as an index. The half-lives of CO₂ in the headspace of the shake flask with the plug-type and cap-type stoppers were about 51.5 min and about 30.3 min, respectively. Based on these half-lives, we formulated a model equation to simulate the behaviour of CO₂ with different culture-stoppers. After validating the model equation by shake-flask culture with Saccharomyces cerevisiae, we investigated the effect of different ventilation abilities of the culture-stoppers on the growth of Pelomonas saccharophila and Escherichia coli: the sensitivity of the culture-stopper to the ventilation ability was dependent on the microorganism species. In the case of P. saccharophila, when the plug-type culture-stopper was combined with controlled CO₂ concentration (6%) in the flask, the maximum yield increased by twofold compared to that of the control. This study shows the importance of ventilation in headspace and conventional culture-stoppers during the shake-flask culture of microorganisms. The problems that may occur between the conventional shake-flask culture approach using a breathable culture-stopper and the next-generation shake-flask culture without a conventional culture-stopper were clarified from the evaluation of gas-permeable culture-stoppers. The importance of controlled gaseous phase in the headspace during shake-flask culture of the microorganisms was also elucidated. KEY POINTS: • Ventilation capacity of culture-stoppers was evaluated using the CO₂ half-life concentration. • Behaviour of microorganisms varies with the type of culture-stopper. • Developed a PID system for control of CO₂ in flask gas phase to enhance the shake-flask culture.

Analysis of the influence of flame sterilization included in sampling operations on shake-flask cultures of microorganisms

Shake-flask cultures of microorganisms involve flame sterilization during sampling, which produces combustion gas with high CO₂ concentrations. The gaseous destination has not been deeply analyzed. Our aim was to investigate the effect of flame sterilization on the headspace of the flask and on the shake-flask culture. In this study, the headspace CO₂ concentration was found to increase during flame sterilization ~0.5–2.0% over 5–20 s empirically using the Circulation Direct Monitoring and Sampling System. This CO₂ accumulation was confirmed theoretically using Computational Fluid Dynamics; it was 9% topically. To evaluate the influence of CO₂ accumulation without interference from other sampling factors, the flask gas phase formed by flame sterilization was reproduced by aseptically supplying 99.8% CO₂ into the headspace, without sampling. We developed a unit that can be sampled in situ without interruption of shaking, movement to a clean bench, opening of the culture-plug, and flame sterilization. We observed that the growth behaviour of Escherichia coli, Pelomonas saccharophila, Acetobacter pasteurianus, and Saccharomyces cerevisiae was different depending on the CO₂ aeration conditions. These results are expected to contribute to improving microbial cell culture systems.

Analysis and effect of conventional flasks in shaking culture of Escherichia coli

The circulation direct monitoring and sampling system (CDMSS) is used as a monitoring device for CO₂ and O₂ concentrations of bypass type in shake-culture flask. The CDMSS could measure k_La, an index for evaluating the performance of aerobic culture incubators, and k_G, an indicator of the degree of CO₂ ventilation in the flask gas phase. We observed that cylindrical flasks provided a different culture environment, yielded a much higher k_G than the Erlenmeyer and Sakaguchi flasks, and yielded k_La equivalent to that by Erlenmeyer flask by setting the ring-type baffle appropriately. Baffled cylindrical flask used for Escherichia coli K12 IFO3301 shake culture maintained lower CO₂ concentrations in the headspace than conventional flasks; therefore, CO₂ accumulation in the culture broth could be suppressed. Cell growth in baffled cylindrical flask (with k_La equivalent to that of the Erlenmeyer flask) was about 1.3 and 1.4 times that in the Erlenmeyer and Sakaguchi flasks, respectively. This study focused on the batch culture at the flask scale and designed the headspace environment with low CO₂ accumulation. Therefore, we conclude that redesign of flasks based on k_La and k_G may contribute to a wide range of fields employing microorganism culture.

From field sampling to pneumatic bioreactor mycelia production of the ectomycorrhizal mushroom Laccaria trichodermophora

In order to increase survival rates of greenhouse seedlings destined for restoration and conservation programs, successful mycorrhization of the seedlings is necessary. To reforest forest ecosystems, host trees must be inoculated with ectomycorrhizal fungi and, in order to guarantee a sufficient supply of ectomycorrhizal inoculum, it is necessary to develop technologies for the mass production of ectomycorrhizal fungi mycelia. We selected the ectomycorrhizal fungus Laccaria trichodermophora, due to its ecological traits and feasible mycelia production in asymbiotic conditions. Here, we report the field sampling of genetic resources, as well as the highly productive nutritional media and cultivation parameters in solid cultures. Furthermore, in order to achieve high mycelial production, we used strain screening and evaluated pH, carbon source concentration, and culture conditions of submerged cultures in normal and baffled shake flasks. The higher productivity culture conditions in shake flasks were selected for evaluation in a pneumatic bioreactor, using modified BAF media with a 10 g/L glucose, pH 5.5, 25 °C, and a volumetric oxygen transfer coefficient (K_La) of 36 h^-1. Under those conditions less biomass (12-37 %) was produced in the pneumatic bioreactor compared with the baffled shake flasks. This approach shows that L. trichodermophora can generate a large biomass concentration and constitute the biotechnological foundation of its mycelia mass production.

Recombinant production of ESAT-6 antigen in thermoinducible Escherichia coli: the role of culture scale and temperature on metabolic response, expression of chaperones, and architecture of inclusion bodies

The heat-inducible expression system has been widely used to produce recombinant proteins in Escherichia coli. However, the rise in temperature affects cell growth, activates the bacterial Heat-Shock Response (HSR), and promotes the formation of insoluble protein aggregates known as inclusion bodies (IBs). In this work, we evaluate the effect of the culture scale (shake flasks and bioreactors) and induction temperature (39 and 42 °C) on the kinetic behavior of thermoinducible recombinant E. coli ATCC 53606 producing rESAT-6 (6-kDa early-secretory antigenic target from Mycobacterium tuberculosis), compared with cultures grown at 30 °C (without induction). Also, the expression of the major E. coli chaperones (DnaK and GroEL) was analyzed. We found that almost twice maximum biomass and rESAT-6 production were obtained in bioreactors (~ 3.29 g/L of biomass and ~ 0.27 g/L of rESAT-6) than in shake flasks (~ 1.41 g/L of biomass and ~ 0.14 g/L of rESAT-6) when induction was carried out at 42 °C, but similar amounts of rESAT-6 were obtained from cultures induced at 39 °C (~ 0.14 g/L). In all thermo-induced conditions, rESAT-6 was trapped in IBs. Furthermore, DnaK was preferably expressed in the soluble fraction, while GroEL was present in IBs. Importantly, IBs formed at 39 °C, in both shake flasks and bioreactors, were more susceptible to degradation by proteinase-K, indicating a lower amyloid content compared to IBs formed at 42 °C. Our work presents evidence that the culture scale and the induction temperature modify the E. coli metabolic response, expression of chaperones, and structure of the IBs during rESAT-6 protein production in a thermoinducible system.

Dynamic headspace analysis using online measurements: Modeling of average and initial concentration

Dynamic headspace sampling is an important technique for the analysis of consumer products, the study of biological samples and environmental water analyses. This paper shows the influence of experimental conditions, such as the sampling time, sampling flow rate, headspace volume, liquid volume and Henry coefficient on the measured average concentration values. A corresponding closed expression as function of these variables is introduced in order to quantify the deviation of the initial headspace concentration. The proposed bi-exponential function embeds different current existing models for recovery calculation in dynamic sampling analyses in one single expression. A fully automated and user-friendly Excel^® file to investigate or to model the dynamic headspace sampling results is added to everyone's easy use.

Novel electrodynamic oscillation technique enables enhanced mass transfer and mixing for cultivation in micro-bioreactor

Micro-bioreactors (MBRs) have become an indispensable part for modern bioprocess development enabling automated experiments in parallel while reducing material cost. Novel developments aim to further intensify the advantages as dimensions are being reduced. However, one factor hindering the scale-down of cultivation systems is to provide adequate mixing and mass transfer. Here, vertical oscillation is demonstrated as an effective method for mixing of MBRs with a reaction volume of 20 μL providing adequate mass transfer. Electrodynamic exciters are used to transduce kinetic energy onto the cultivation broth avoiding additional moving parts inside the applied model MBR. The induced vertical vibration leads to oscillation of the liquid surface corresponding to the frequency and displacement. On this basis, the resonance frequency of the fluid was identified as the most decisive factor for mixing performance. Applying this vertical oscillation method outstanding mixing times below 1 s and exceptionally high oxygen transport with volumetric mass transfer coefficients (k_L a) above 1,000/hr can be successfully achieved and controlled. To evaluate the applicability of this vertical oscillation mixing for low volume MBR systems, cultivations of Escherichia coli BL21 as proof-of-concept were performed. The dissolved oxygen was successfully online monitored to assure any avoidance of oxygen limitations during the cultivation. The here presented data illustrate the high potential of the vertical oscillation technique as a flexible measure to adapt mixing times and oxygen transfer according to experimental demands. Thus, the mixing technique is a promising tool for various biological and chemical micro-scale applications still enabling adequate mass transfer.

The metabolic switch can be activated in a recombinant strain of Streptomyces lividans by a low oxygen transfer rate in shake flasks

Background

In Streptomyces, understanding the switch from primary to secondary metabolism is important for maximizing the production of secondary metabolites such as antibiotics, as well as for optimizing recombinant glycoprotein production. Differences in Streptomyces lividans bacterial aggregation as well as recombinant glycoprotein production and O-mannosylation have been reported due to modifications in the shake flask design. We hypothetized that such differences are related to the metabolic switch that occurs under oxygen-limiting conditions in the cultures.

Results

Shake flask design was found to affect undecylprodigiosin (RED, a marker of secondary metabolism) production; the RED yield was 12 and 385 times greater in conventional normal Erlenmeyer flasks (NF) than in baffled flasks (BF) and coiled flasks (CF), respectively. In addition, oxygen transfer rates (OTR) and carbon dioxide transfer rates were almost 15 times greater in cultures in CF and BF as compared with those in NF. Based on these data, we obtained respiration quotients (RQ) consistent with aerobic metabolism for CF and BF, but an RQ suggestive of anaerobic metabolism for NF.

Conclusion

Although the metabolic switch is usually related to limitations in phosphate and nitrogen in Streptomyces sp., our results reveal that it can also be activated by low OTR, dramatically affecting recombinant glycoprotein production and O-mannosylation and increasing RED synthesis in the process.

Electronic supplementary material

The online version of this article (10.1186/s12934-018-1035-3) contains supplementary material, which is available to authorized users.

Practices of shake-flask culture and advances in monitoring CO2 and O2

About 85 years have passed since the shaking culture was devised. Since then, various monitoring devices have been developed to measure culture parameters. O₂ consumed and CO₂ produced by the respiration of cells in shaking cultures are of paramount importance due to their presence in both the culture broth and headspace of shake flask. Monitoring in situ conditions during shake-flask culture is useful for analysing the behaviour of O₂ and CO₂, which interact according to Henry's law, and is more convenient than conventional sampling that requires interruption of shaking. In situ monitoring devices for shake-flask cultures are classified as direct or the recently developed bypass type. It is important to understand the characteristics of each type along with their unintended effect on shake-flask cultures, in order to improve the existing devices and culture conditions. Technical developments in the bypass monitoring devices are strongly desired in the future. It is also necessary to understand the mechanism underlying conventional shake-flask culture. The existing shaking culture methodology can be expanded into next-generation shake-flask cultures constituting a novel culture environment through a judicious selection of monitoring devices depending on the intended purpose of shake-flask culture. Construction and sharing the databases compatible with the various types of the monitoring devices and measurement instruments adapted for shaking culture can provide a valuable resource for broadening the application of cells with shake-flask culture.

Production of a recombinant phospholipase A2 in Escherichia coli using resonant acoustic mixing that improves oxygen transfer in shake flasks

Background

Shake flasks are widely used during the development of bioprocesses for recombinant proteins. Cultures of recombinant Escherichia coli with orbital mixing (OM) have an oxygen limitation negatively affecting biomass growth and recombinant-protein production. With the aim to improve mixing and aeration in shake flask cultures, we analyzed cultures subjected to OM and the novel resonant acoustic mixing (RAM) by applying acoustic energy to E. coli BL21-Gold (DE3): a producer of recombinant phospholipase A2 (rPLA2) from Micrurus laticollaris snake venom.

Results

Comparing OM with RAM (200 rpm vs. 7.5g) at the same initial volumetric oxygen transfer coefficient (k_La ≈ 80 h⁻¹) ~69% less biomass was obtained with OM compared with RAM. We analyzed two more conditions increasing agitation until maximal speed (12.5 and 20g), and ~1.6- and ~1.4-fold greater biomass was obtained as compared with cultures at 7.5g. Moreover, the specific growth rate was statistically similar in all cultures carried out in RAM, but ~1.5-fold higher than that in cultures carried out under OM. Almost half of the glucose was consumed in OM, whereas between 80 and 100% of the glucose was consumed in RAM cultures, doubling biomass per glucose yields. Differential organic acid production was observed, but acetate production was prevented at the maximal RAM (20g). The amount of rPLA2 in both, OM and RAM cultures, represented 38 ± 5% of the insoluble protein. A smaller proportion of α-helices and β-sheet of purified inclusion bodies (IBs) were appreciated by ATR-FTIR from cultures carried out under OM, than those from RAM. At maximal agitation by RAM, internal E. coli localization patterns of protein aggregation changed, as well as, IBs proteolytic degradation, in conjunction with the formation of small external vesicles, although these changes did not significantly affect the cell survival response.

Conclusions

In moderate-cell-density recombinant E. coli BL21-Gold (DE3) cultures, the agitation increases in RAM (up to the maximum) was not enough to avoid the classical oxygen limitation that happens in OM shake flasks. However, RAM presents a decrease of oxygen limitation, resulting in a favorable effect on biomass growth and volumetric rPLA2 production. While under OM a higher recombinant protein yield was obtained.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0746-1) contains supplementary material, which is available to authorized users.

Kinetic analysis of Fe3+reduction coupled with nitrate removal by Klebsiella sp. FC61 under different conditions

Klebsiellasp. FC61, a newly found iron-reducing bacterium, has the ability of simultaneously reducing Fe³⁺and nitrate under different pH and temperature conditions.