Tack Ignace L M M, Nimmegeers Philippe, Akkermans Simen, Hashem Ihab, Van Impe Jan F M
BioTeC+, Department of Chemical Engineering, KU Leuven, Ghent, Belgium.
Front Microbiol. 2017 Dec 13;8:2509. doi: 10.3389/fmicb.2017.02509. eCollection 2017.
Clustered microbial communities are omnipresent in the food industry, e.g., as colonies of microbial pathogens in/on food media or as biofilms on food processing surfaces. These clustered communities are often characterized by metabolic differentiation among their constituting cells as a result of heterogeneous environmental conditions in the cellular surroundings. This paper focuses on the role of metabolic differentiation due to oxygen gradients in the development of cell communities, whereby low local oxygen concentrations lead to cellular secretion of weak acid products. For this reason, a metabolic model has been developed for the facultative anaerobe covering the range of aerobic, microaerobic, and anaerobic environmental conditions. This metabolic model is expressed as a multiparametric programming problem, in which the influence of low extracellular pH values and the presence of undissociated acid cell products in the environment has been taken into account. Furthermore, the developed metabolic model is incorporated in MICRODIMS, an in-house developed individual-based modeling framework to simulate microbial colony and biofilm dynamics. Two case studies have been elaborated using the MICRODIMS simulator: (i) biofilm growth on a substratum surface and (ii) submerged colony growth in a semi-solid mixed food product. In the first case study, the acidification of the biofilm environment and the emergence of typical biofilm morphologies have been observed, such as the mushroom-shaped structure of mature biofilms and the formation of cellular chains at the exterior surface of the biofilm. The simulations show that these morphological phenomena are respectively dependent on the initial affinity of pioneer cells for the substratum surface and the cell detachment process at the outer surface of the biofilm. In the second case study, a no-growth zone emerges in the colony center due to a local decline of the environmental pH. As a result, cellular growth in the submerged colony is limited to the colony periphery, implying a linear increase of the colony radius over time. MICRODIMS has been successfully used to reproduce complex dynamics of clustered microbial communities.
聚集的微生物群落广泛存在于食品工业中，例如，作为食品介质中/上的微生物病原体菌落或食品加工表面上的生物膜。由于细胞周围环境条件的异质性，这些聚集的群落通常以其组成细胞之间的代谢分化为特征。本文重点研究了由于氧梯度导致的代谢分化在细胞群落发育中的作用，即局部低氧浓度导致细胞分泌弱酸产物。因此，针对兼性厌氧菌开发了一种代谢模型，该模型涵盖了需氧、微需氧和厌氧环境条件范围。这个代谢模型被表示为一个多参数规划问题，其中考虑了低细胞外pH值的影响以及环境中未解离酸性细胞产物的存在。此外，所开发的代谢模型被纳入MICRODIMS，这是一个内部开发的基于个体的建模框架，用于模拟微生物菌落和生物膜动力学。使用MICRODIMS模拟器详细阐述了两个案例研究：（i）基质表面上的生物膜生长和（ii）半固体混合食品产品中的淹没菌落生长。在第一个案例研究中，观察到了生物膜环境的酸化以及典型生物膜形态的出现，例如成熟生物膜的蘑菇状结构以及生物膜外表面细胞链的形成。模拟结果表明，这些形态现象分别取决于先锋细胞对基质表面的初始亲和力以及生物膜外表面的细胞脱离过程。在第二个案例研究中，由于环境pH值的局部下降，菌落在中心出现了一个无生长区。结果，淹没菌落中的细胞生长仅限于菌落周边，这意味着菌落半径随时间呈线性增加。MICRODIMS已成功用于再现聚集微生物群落的复杂动态。
