Development of a circulation direct sampling and monitoring system for O2 and CO2 concentrations in the gas-liquid phases of shake-flask systems during microbial cell culture

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.

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.

Real-time dissolved carbon dioxide monitoring I: Application of a novel in situ sensor for CO2 monitoring and control

Dissolved carbon dioxide (dCO2 ) is a well-known critical parameter in bioprocesses due to its significant impact on cell metabolism and on product quality attributes. Processes run at small-scale faces many challenges due to limited options for modular sensors for online monitoring and control. Traditional sensors are bulky, costly, and invasive in nature and do not fit in small-scale systems. In this study, we present the implementation of a novel, rate-based technique for real-time monitoring of dCO2 in bioprocesses. A silicone sampling probe that allows the diffusion of CO2 through its wall was inserted inside a shake flask/bioreactor and then flushed with air to remove the CO2 that had diffused into the probe from the culture broth (sensor was calibrated using air as zero-point calibration). The gas inside the probe was then allowed to recirculate through gas-impermeable tubing to a CO2 monitor. We have shown that by measuring the initial diffusion rate of CO2 into the sampling probe we were able to determine the partial pressure of the dCO2 in the culture. This technique can be readily automated, and measurements can be made in minutes. Demonstration experiments conducted with baker's yeast and Yarrowia lipolytica yeast cells in both shake flasks and mini bioreactors showed that it can monitor dCO2 in real-time. Using the proposed sensor, we successfully implemented a dCO2 -based control scheme, which resulted in significant improvement in process performance.

Monitoring of CO2 and O2 concentrations in the headspace of Sakaguchi flasks during liquid culture of microorganism

CO₂ and O₂ in the Sakaguchi flask headspace during culture was monitored via circulation direct monitoring and sampling system (CDMSS), a device with circulation bypass system. In static culture with Saccharomyces cerevisiae (circulation rate, 50 mL/min), a vertical CO₂ concentration gradient (maximum gap ~ 2% (v/v) [height from the bottom of flask 45 mm, 7%; 155 mm, 5%]) in the Sakaguchi flask headspace was observed; no concentration O₂ gradient was observed. However, shake flask culture showed vertical gradient concentrations for both CO₂ and O₂ (maximum gap of CO₂ and O₂ concentrations: 2 and 4% [heights from the bottom of flask 115 mm, 6.0 and 9.5%; 175 mm, 4.0 and 13.5%], respectively). When the CDMSS circulation rate in the Sakaguchi flask headspace was 300 or 400 mL/min, the gaseous environment was uniformly distributed so that no vertical gradient concentration was observed. In shaking culture with Escherichia coli under these conditions, CO₂ was accumulated at high concentrations in the headspace and culture broth (maximum values 8%, in the headspace; 120 mg/L, in the culture broth). Most of the accumulated CO₂ in the headspace could be removed by inserting a column packed with CO₂ adsorbent at the bypass port of the CDMSS gaseous circulation. Thus, dissolved CO₂ was maintained at a lower concentration, and the final UOD (unit optical density) value of culture was increased compared with that of the control. This study is the first to demonstrate that vertical gradients of CO₂ and O₂ concentrations exist in the headspace of Sakaguchi flask during culture.

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.

Effect of intermittent opening of breathable culture plugs and aeration of headspace on the structure of microbial communities in shake-flask culture

In this study, we found that opening breathable culture plugs for 30 s during periodic and aseptic sampling affects the community structure of cultured soil microbes. Similar effects were observed using an automatic aeration flask system that mimics aseptic opening of the breathable culture plug during sampling, but without interruption in shaking. Thus, the observed changes in the microbial consortia appear to be due exclusively to the intermittent ventilation of the flask headspace. To elucidate the mechanism driving this phenomenon, we monitored CO₂ and O₂ concentrations in both headspace and culture broth using the new system termed as circulation direct monitoring and sampling system. The data show that the CO₂ concentration in the culture broth temporarily decreased with the CO₂ concentration in the headspace, strongly suggesting that the effect of intermittent ventilation of the headspace on the microbial consortia depends on CO₂. Importantly, the data also imply that environmental variables during shake flask culture, especially CO₂ concentration, is important for screening aerobic microorganisms.

Erratum to: Development of a circulation direct sampling and monitoring system for O2 and CO2 concentrations in the gas-liquid phases of shake‑flask systems during microbial cell culture

Following publication of the original article (Takahashi et al. 2017), the authors reported that there was a mistake in the legend of Figure 2.