School of Food and Advanced Technology, Massey University, Palmerston North, New Zealand.
Riddet Institute, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand.
BMC Bioinformatics. 2021 Jan 6;22(1):3. doi: 10.1186/s12859-020-03923-6.
Hydrogen cross-feeding microbes form a functionally important subset of the human colonic microbiota. The three major hydrogenotrophic functional groups of the colon: sulphate-reducing bacteria (SRB), methanogens and reductive acetogens, have been linked to wide ranging impacts on host physiology, health and wellbeing.
An existing mathematical model for microbial community growth and metabolism was combined with models for each of the three hydrogenotrophic functional groups. The model was further developed for application to the colonic environment via inclusion of responsive pH, host metabolite absorption and the inclusion of host mucins. Predictions of the model, using two existing metabolic parameter sets, were compared to experimental faecal culture datasets. Model accuracy varied between experiments and measured variables and was most successful in predicting the growth of high relative abundance functional groups, such as the Bacteroides, and short chain fatty acid (SCFA) production. Two versions of the colonic model were developed: one representing the colon with sequential compartments and one utilising a continuous spatial representation. When applied to the colonic environment, the model predicted pH dynamics within the ranges measured in vivo and SCFA ratios comparable to those in the literature. The continuous version of the model simulated relative abundances of microbial functional groups comparable to measured values, but predictions were sensitive to the metabolic parameter values used for each functional group. Sulphate availability was found to strongly influence hydrogenotroph activity in the continuous version of the model, correlating positively with SRB and sulphide concentration and negatively with methanogen concentration, but had no effect in the compartmentalised model version.
Although the model predictions compared well to only some experimental measurements, the important features of the colon environment included make it a novel and useful contribution to modelling the colonic microbiota.
氢供体微生物是人类结肠微生物组中具有重要功能的亚群。结肠中三大主要产氢功能群：硫酸盐还原菌（SRB）、产甲烷菌和还原乙酸菌，它们与宿主生理学、健康和福祉的广泛影响有关。
将现有的微生物群落生长和代谢数学模型与三种产氢功能群的模型相结合。该模型通过纳入响应 pH 值、宿主代谢物吸收和宿主黏蛋白，进一步发展为适用于结肠环境的模型。使用两个现有的代谢参数集对模型进行预测，并将预测值与现有的粪便培养数据集进行比较。模型的准确性因实验和测量变量而异，在预测高相对丰度功能群（如拟杆菌）和短链脂肪酸（SCFA）产生方面最为成功。开发了两种结肠模型版本：一种代表具有连续隔室的结肠，另一种利用连续空间表示。当应用于结肠环境时，该模型预测了体内测量范围内的 pH 动态和与文献中可比的 SCFA 比值。连续模型版本模拟了微生物功能群的相对丰度与测量值相当，但预测对每个功能群使用的代谢参数值敏感。硫酸盐的可用性被发现强烈影响连续模型版本中的产氢生物活性，与 SRB 和硫化物浓度呈正相关，与产甲烷菌浓度呈负相关，但在隔室模型版本中没有影响。
尽管模型预测与一些实验测量值相比效果良好，但该模型纳入了结肠环境的重要特征，是对结肠微生物组建模的一个新颖而有用的贡献。
