Astrid Cappuyns

Optimal fed batch experiment design for estimation of monod kinetics of Azospirillum brasilense: from theory to practice.

In this paper the problem of reliable and accurate parameter estimation for unstructured models is considered. It is illustrated how a theoretically optimal design can be successfully translated into a practically feasible, robust, and informative experiment. The well‐known parameter estimation problem of Monod kinetic parameters is used as a vehicle to illustrate our approach. As known for a long time, noisy batch measurements do not allow for unique and accurate estimation of the kinetic parameters of the Monod model. Techniques of optimal experiment design are, therefore, exploited to design informative experiments and to improve the parameter estimation accuracy. During the design process, practical feasibility has to be kept in mind. The designed experiments are easy to implement in practice and do not require additional monitoring equipment. Both design and experimental validation of informative fed batch experiments are illustrated with a case study, namely, the growth of the nitrogen‐fixing bacteria Azospirillum brasilense.

Individual and Combined Effects of pH and Lactic Acid Concentration on Listeria innocua Inactivation: Development of a Predictive Model and Assessment of Experimental Variability

ABSTRACT In food technology, organic acids (e.g., lactic acid, acetic acid, and citric acid) are popular preservatives. The purpose of this study was to separate the individual effects of the influencing factors pH and undissociated lactic acid on Listeria innocua inactivation. Therefore, the inactivation process was investigated under controlled, initial conditions of pH (pH0) and undissociated lactic acid ([LaH]0). The resulting inactivation curves consisted of a (sometimes negligible) shoulder period followed by a descent phase. In a few cases, a tailing phase was observed. Depending on the conditions, the descent phase contained one or two log-linear parts or had a convex or concave shape. In addition, the inactivation process was characterized by a certain variability, dependent on the severity of the conditions. Furthermore, in the neighborhood of the growth/no growth interface sometimes contradictory observations occurred. Overall, the individual effects of the influencing factors pH and undissociated lactic acid could clearly be distinguished and were also apparent based on fluorescence microscopy. Appropriate model types were developed and enabled prediction of which conditions of pH0 and [LaH]0 are necessary to obtain a predetermined inactivation (number of decimal reductions) within a predetermined time range.

Heat stress adaptation of Escherichia coli under dynamic conditions: effect of inoculum size*

Aims:  When subjected to dynamic temperatures surpassing the expected maximum growth temperature, Escherichia coli K12 MG1655 shows disturbed growth curves. These irregular population dynamics were explained by considering two subpopulations, i.e. a thermoresistant and a thermosensitive one ( Van Derlinden et al. 2010a ). In this paper, the influence of the initial cell concentration on the subpopulations’ dynamics is evaluated.

In Situ Production of Prebiotic AXOS by Hyperthermophilic Xylanase B from Thermotoga maritima in High-Quality Bread

ABSTRACT In situ enrichment of bread with arabinoxylan-oligosaccharides (AXOS) through enzymic degradation of wheat flour arabinoxylan (AX) by the hyperthermophilic xylanase B from Thermotoga maritima (rXTMB) was studied. The xylanolytic activity of rXTMB during breadmaking was essentially restricted to the baking phase. This prevented problems with dough processability and bread quality that generally are associated with thorough hydrolysis of the flour AX during dough mixing and fermentation. rXTMB action did not affect loaf volume. Bread with a dry matter AXOS content of 1.5% was obtained. Further increase in bread AXOS levels was achieved by combining rXTMB with xylanases from Pseudoalteromonas haloplanktis or Bacillus subtilis. Remarkably, such a combination synergistically increased the specific bread loaf volume. Assuming an average daily consumption of 180 g of fresh bread, the bread AXOS levels suffice to provide a substantial part of the AXOS intake leading to desired physiological effects in hu...

Analysis of the lag phase to exponential growth transition by incorporating inoculum characteristics

During the last decade, individual-based modelling (IbM) has proven to be a valuable tool for modelling and studying microbial dynamics. As each individual is considered as an independent entity with its own characteristics, IbM enables the study of microbial dynamics and the inherent variability and heterogeneity. IbM simulations and (single-cell) experimental research form the basis to unravel individual cell characteristics underlying population dynamics. In this study, the IbM framework MICRODIMS, i.e., MICRObial Dynamics Individual-based Model/Simulator, is used to investigate the system dynamics (with respect to the model and the system modelled). First, the impact of the time resolution on the simulation accuracy is discussed. Second, the effect of the inoculum state and size on emerging individual dynamics, such as individual mass, individual age and individual generation time distribution dynamics, is studied. The distributions of individual characteristics are more informative during the lag phase and the transition to the exponential growth phase than during the exponential phase. The first generation time distributions are strongly influenced by the inoculum state. All inocula with a pronounced heterogeneity, except the inocula starting from a uniform distribution, exhibit commonly observed microbial behaviour, like a more spread first generation time distribution compared to following generations and a fast stabilisation of biomass and age distributions.

A dynamic model for diauxic growth, overflow metabolism, and AI-2-mediated cell-cell communication of Salmonella Typhimurium based on systems biology concepts.

The last decades, the research on bacterial cell–cell communication or quorum sensing has been quite intense. Quorum sensing allows bacteria to coordinate their behavior and to act as one entity. Quorum sensing controls microbiological functions of medical, agricultural and industrial importance and a better understanding of the underlying mechanisms and the conditions under which the signaling occurs, offers possibilities for new applications. In this article a dynamic model for diauxic growth, overflow metabolism and AI‐2‐mediated cell–cell communication of Salmonella Typhimurium is presented. The growth, and the production and uptake of the AI‐2 signaling molecule of S. Typhimurium are investigated in a controlled environment (bioreactor). In a first stage a model is developed to describe diauxic growth and overflow metabolism. This model is extended in a second stage to describe AI‐2 dynamics of S. Typhimurium in relation to the growth kinetics and biomass concentration. It is illustrated how this model can be employed to test hypotheses concerning AI‐2 dynamics on the basis of macroscopic data. Biotechnol. Bioeng. 2009;102: 280–293.

Growth kinetics of listeria isolated from salmon and salmon processing environment: single strains versus cocktails.

The growth dynamics of Listeria monocytogenes strains isolated from salmon or a salmon processing environment and two reference Listeria innocua strains were investigated at refrigerated and close-to-optimal growth temperatures. Estimates for the growth rates and the lag-phase duration at 4, 8, 12, and 30°C were obtained for optical density measurements by using different growth parameter estimation methods, i.e., the serial dilution (SD) method and the relative rate to detection (RRD) method. Both single L. innocua and L. monocytogenes strains and mixtures of L. monocytogenes strains (cocktails) were studied. Both methods show an increase in maximum growth rate (μ(max)) of Listeria with increasing temperatures. Generally, single-strain growth rate estimates were quite similar for both species, although L. monocytogenes showed slightly higher μ(max) estimates at 4°C. The SD method gave the highest estimates for the growth rate, i.e., the estimates from the RRD method were 10 to 20% lower. This should lead to caution when using the latter method for Listeria, particularly at lower temperatures. Overall, the SD method is preferred as this method yields μ(max) estimates close to the biological value and provides estimates for the duration of lag time (λ). For discrimination between different strains, λ appeared to be a more suitable parameter than μ(max). This effect was most prominent for L. innocua. Significant differences were observed between μ(max) and/or λ of L. monocytogenes cocktails and single strains at all temperatures investigated. At 4°C, the average growth rate of cocktails was higher than that of single strains. At 8 and 30°C, this trend was reversed. The average λ of single strains were more than twice as long as those of cocktails at 4°C. At 8 and 30°C, the λ of cocktails were significantly slower than those of single strains, but the variation was considerably less and the differences were less pronounced.

A Prototype Model for Indole-3-Acetic Acid (IAA) Production by Azospirillum brasilense SP245

Abstract Given the vital role of nitrogen for plant growth on the one hand, versus the severe impact on the environment of extensive use of inorganic nitrogen fertilizers on the other hand, the need for alternative fertilization becomes apparent. In this respect, the nitrogen fixing bacteria of the genus Azospirillum offer interesting perspectives since inoculation of the plant roots with these bacteria positively affects plant growth. Studies have shown that the growth promoting power of the bacteria can probably be attributed more to the production of the auxin indole-3-acetic acid (IAA) than to the nitrogen fixation qualities of the genus. The aim of this study is therefore to characterize and quantify the IAA production of Azospirillum brasilense Sp245 on a macroscopic level as to exploit the resulting model in optimal experiment design studies. The data obtained from these optimal experiments should be rich enough to aid in further unravelling the studied IAA production mechanism.

Quantifying lactic acid induced inhibition and inactivation of Yersinia enterocolitica in mixed cultures

Abstract In food technology, models describing microbial proliferation in food products are a helpful tool to predict the food safety. In general, the available models consider the micro-organisms in pure culture. As such, microbial interactions are ignored, which may lead to a discrepancy between model predictions and the actual microbial evolution. In this study, a model describing the lactic acid induced inhibition of the pathogenic Yersinia enterocolitica in mixed culture was extended to describe also the subsequent inactivation. In the development of a suitable model structure to describe the inactivation process, biological knowledge was incorporated. The extended model was able to predict the evolution of Y. enterocolitica in coculture as well as in monoculture.

Modelling methyl tertiary butyl ether and tertiary butyl alcohol biodegradation by a bacterial consortium

The widespread use of methyl tertiary butyl ether (MTBE) as an additive in gasoline has resulted in serious soil and groundwater pollution. To tackle MTBE contamination in groundwater, bioremediation is considered a cost-effective and energy-efficient option. The design of an efficient, reliable and reproducible bioremediation strategy requires a thorough understanding of the (microbial) degradation kinetics of both MTBE and tertiary butyl alcohol (TBA), that is, the main intermediate during bioremediation of MTBE. To assist the design procedure, this research focuses on building a mathematical model to describe MTBE/TBA degradation kinetics by a bacterial consortium, that is, the VITO M-consortium. For the presented case study, the information obtained from experimental data is combined with knowledge regarding the biodegradation reactions in order to obtain a low-complexity, accurate mathematical model. The resulting model accurately describes MTBE/TBA degradation and has successfully been validated on independent experimental data. Since the model is of the mass balance type, it can easily be extended to other types of operation by defining the transport terms of the new system. This makes the model a very useful tool in the design procedure for large-scale bioremediation strategies. Furthermore, the model provides insight into the MTBE/TBA degradation kinetics and biodegradation mechanisms by hypothesis testing.