Two-species community design of lactic acid bacteria for optimal production of lactate,Computational and Structural Biotechnology Journal

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Two-species community design of lactic acid bacteria for optimal production of lactate
Computational and Structural Biotechnology Journal ( IF 4.4 ) Pub Date : 2021-11-09 , DOI: 10.1016/j.csbj.2021.11.009
Maziya Ibrahim _{1,

2,

3} , Karthik Raman _{1,

2,

3}

Affiliation

Microbial communities that metabolise pentose and hexose sugars are useful in producing high-value chemicals, resulting in the effective conversion of raw materials to the product, a reduction in the production cost, and increased yield. Here, we present a computational analysis approach called CAMP (Co-culture/Community Analyses for Metabolite Production) that simulates and identifies appropriate communities to produce a metabolite of interest. To demonstrate this approach, we focus on the optimal production of lactate from various Lactic Acid Bacteria. We used genome-scale metabolic models (GSMMs) belonging to , and species from the Virtual Metabolic Human (VMH; ) resource and well-curated GSMMs of WCSF1 and JCM 1112. We analysed 1176 two-species communities using a constraint-based modelling method for steady-state flux-balance analysis of communities. Flux variability analysis was used to detect the maximum lactate flux in the communities. Using glucose or xylose as substrates separately or in combination resulted in either parasitism, amensalism, or mutualism being the dominant interaction behaviour in the communities. Interaction behaviour between members of the community was deduced based on variations in the predicted growth rates of monocultures and co-cultures. Acetaldehyde, ethanol, acetate, among other metabolites, were found to be cross-fed between community members. WCSF1 was found to be a member of communities with high lactate yields. community optimisation strategies to predict reaction knock-outs for improving lactate flux were implemented. Reaction knock-outs of acetate kinase, phosphate acetyltransferase, and fumarate reductase in the communities were found to enhance lactate production.

中文翻译：

用于优化乳酸生产的两种乳酸菌群落设计

代谢戊糖和己糖的微生物群落可用于生产高价值化学品，从而将原材料有效转化为产品，降低生产成本并提高产量。在这里，我们提出了一种称为 CAMP（代谢物生产的共培养/群落分析）的计算分析方法，该方法模拟并识别适当的群落以产生感兴趣的代谢物。为了演示这种方法，我们重点关注各种乳酸菌的乳酸的最佳生产。我们使用了属于的基因组规模代谢模型 (GSMM)，以及来自虚拟代谢人类 (VMH;) 资源的物种以及 WCSF1 和 JCM 1112 精心策划的 GSMM。我们使用基于约束的建模方法分析了 1176 个两物种群落用于社区的稳态通量平衡分析。通量变异分析用于检测群落中的最大乳酸通量。单独或组合使用葡萄糖或木糖作为底物导致寄生、共生或互利共生成为群落中的主要相互作用行为。社区成员之间的互动行为是根据单一培养和共培养的预测增长率的变化推断出来的。乙醛、乙醇、乙酸盐以及其他代谢物被发现在社区成员之间交叉喂养。 WCSF1被发现是乳酸产量高的群落的成员。实施了预测反应敲除以改善乳酸通量的群落优化策略。研究发现，群落中乙酸激酶、磷酸乙酰转移酶和富马酸还原酶的反应敲除可以提高乳酸产量。

更新日期：2021-11-09

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