Dual-substrate utilization by Bordetella pertussis

The growth of Pichia pastoris Mut+ on methanol-glycerol mixtures fits to interactive dual-limited kinetics: model development and application to optimised fed-batch operation for heterologous protein production

The methanol-glycerol co-feeding during the induction stage for heterologous protein production in Pichia pastoris has shown significant productive applications. Available model analysis applied to this dual-limited condition is scarce and normally does not consider the interaction effects between the substrates. In this work, a dual-limited growth model of P. pastoris considering an interactive kinetic effect was applied to an optimised fed-batch process production of heterologous Rhizopus oryzae lipase (ROL). In the proposed model, the growth kinetics on glycerol is fully expressed, whereas methanol kinetics is modulated by the co-metabolisation of glycerol, resulting in an enhancing effect of glycerol-specific growth rate. The modelling approach of fed-batch cultures also included the methanol volatilisation caused by the aeration that was found to be a not-negligible phenomenon. The model predicts the ability of P. pastoris to keep control of the methanol concentration in the broth during ROL-optimised production process in fed batch and fits satisfactorily the specific cell growth rate and ROL production. Implications of interaction effect are discussed applying the general procedure of modelling approach.

Probing the Genome-Scale Metabolic Landscape of Bordetella pertussis, the Causative Agent of Whooping Cough

Whooping cough is a highly contagious respiratory disease caused by Bordetella pertussis Despite widespread vaccination, its incidence has been rising alarmingly, and yet, the physiology of B. pertussis remains poorly understood. We combined genome-scale metabolic reconstruction, a novel optimization algorithm, and experimental data to probe the full metabolic potential of this pathogen, using B. pertussis strain Tohama I as a reference. Experimental validation showed that B. pertussis secretes a significant proportion of nitrogen as arginine and purine nucleosides, which may contribute to modulation of the host response. We also found that B. pertussis can be unexpectedly versatile, being able to metabolize many compounds while displaying minimal nutrient requirements. It can grow without cysteine, using inorganic sulfur sources, such as thiosulfate, and it can grow on organic acids, such as citrate or lactate, as sole carbon sources, providing in vivo demonstration that its tricarboxylic acid (TCA) cycle is functional. Although the metabolic reconstruction of eight additional strains indicates that the structural genes underlying this metabolic flexibility are widespread, experimental validation suggests a role of strain-specific regulatory mechanisms in shaping metabolic capabilities. Among five alternative strains tested, three strains were shown to grow on substrate combinations requiring a functional TCA cycle, but only one strain could use thiosulfate. Finally, the metabolic model was used to rationally design growth media with >2-fold improvements in pertussis toxin production. This study thus provides novel insights into B. pertussis physiology and highlights the potential, but also the limitations, of models based solely on metabolic gene content.IMPORTANCE The metabolic capabilities of Bordetella pertussis, the causative agent of whooping cough, were investigated from a systems-level perspective. We constructed a comprehensive genome-scale metabolic model for B. pertussis and challenged its predictions experimentally. This systems approach shed light on new potential host-microbe interactions and allowed us to rationally design novel growth media with >2-fold improvements in pertussis toxin production. Most importantly, we also uncovered the potential for metabolic flexibility of B. pertussis (significantly larger range of substrates than previously alleged; novel active pathways allowing growth in minimal, nearly mineral nutrient combinations where only the carbon source must be organic), although our results also highlight the importance of strain-specific regulatory determinants in shaping metabolic capabilities. Deciphering the underlying regulatory mechanisms appears to be crucial for a comprehensive understanding of B. pertussis's lifestyle and the epidemiology of whooping cough. The contribution of metabolic models in this context will require the extension of the genome-scale metabolic model to integrate this regulatory dimension.

Online automatic tuning and control for fed-batch cultivation

Performance of controllers applied in biotechnological production is often below expectation. Online automatic tuning has the capability to improve control performance by adjusting control parameters. This work presents automatic tuning approaches for model reference specific growth rate control during fed-batch cultivation. The approaches are direct methods that use the error between observed specific growth rate and its set point; systematic perturbations of the cultivation are not necessary. Two automatic tuning methods proved to be efficient, in which the adaptation rate is based on a combination of the error, squared error and integral error. These methods are relatively simple and robust against disturbances, parameter uncertainties, and initialization errors. Application of the specific growth rate controller yields a stable system. The controller and automatic tuning methods are qualified by simulations and laboratory experiments with Bordetella pertussis.

Improving the cellular pertussis vaccine: increased potency and consistency

Although Europe, Canada and the US have switched from cellular to acellular pertussis vaccines, most developing countries will continue to use the more cost effective cellular vaccine. Consistency of production however is the typical problem inherent to cellular vaccines. Optimising the production process of cellular pertussis bulk suspensions using product potency as a measure is not possible, since the mandatory animal test to measure potency has little discriminatory power. To circumvent this problem, this study focussed on measuring process parameters related to consistency and potency instead, even though the extent of those relationships could not be quantified. Critical evaluation and modification of individual process steps lead to 2 optimised production processes, NVP-96 and NVP-THIJS. These were compared to the original NVP production process in terms of antigen and biomass content, potency, toxicity and immunogenicity in mice. The batch to batch variation for both optimised products was clearly less than the original product for all parameters tested. The biomass content of the NVP-THIJS product was 15% lower than that of the NVP-96 product, while the immunogenicity in mice was twofold to threefold higher. The stability of the NVP-THIJS product remained higher than the NVP-96 product over a period of 2 years, while the decline of the potency of both suspensions was comparable.

Constant specific growth rate in fed-batch cultivation of Bordetella pertussis using adaptive control

Monitoring and control of production processes for biopharmaceuticals have become standard requirements to support consistency and quality. In this paper, a constant specific growth rate in fed-batch cultivation of Bordetella pertussis is achieved by a newly designed specific growth rate controller. The performance of standard control methods is limited because of the time-varying characteristics due to the exponentially increasing biomass and volume. To cope with the changing dynamics, a stable model reference adaptive controller is designed which adapts the controller settings as volume and biomass increase. An important asset of the design is that dissolved oxygen is the only required online measurement. An original design without considering the dissolved oxygen dynamics resulted experimentally in oscillatory behaviour. Hence, in contrast to common believes, it is essential to include dissolved oxygen dynamics. The robustness of this novel design was tested in simulation. The validity of the design was confirmed by laboratory experiments for small-scale production of B. pertussis. The controller was able to regulate the specific growth rate at the desired set point, even during a long fed-batch cultivation time with exponentially increasing demands for substrates and oxygen.

A dual-substrate steady-state model for biological hydrogen production in an anaerobic hydrogen fermentation process

Biological hydrogen production from anaerobic waste fermentation possesses potential benefits in simultaneously reducing organic wastes and generating sustainable energy sources. Three kinetic-based steady-state models for anaerobic fermentation of multiple substrates, including glucose and peptone, were evaluated. Experimental results obtained from a continuous stirred tank reactor (CSTR) were primarily used for model evaluation. The dual-substrate steady-state model developed and the associated kinetic parameters estimated in this study successfully described the anaerobic growth of hydrogen-producing bacteria. The model was able to capture the general trends of consumption of substrates and accumulation of products, including formate, acetate, butyrate, and hydrogen, at dilution rates (D) between 0.06 and 0.69/h. According to the model, the adverse effects of endogeneous and peptone metabolism on net hydrogen production can be minimized by increasing D. For the operational conditions of D > 0.69/h, however, substantial washout of hydrogen-producing bacteria from the CSTR was observed, and it resulted in a rapid drop in hydrogen production rate as well.