Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, USA.
J Appl Microbiol. 2021 Dec;131(6):2899-2917. doi: 10.1111/jam.15155. Epub 2021 Jun 22.
While gas-fermenting acetogens have been engineered to secrete non-native metabolites such as butyrate, acetate remains the most thermodynamically favourable product. An alternative to metabolic engineering is to exploit native capabilities for CO-to-acetate conversion by coculturing an acetogen with a second bacterium that provides efficient acetate-butyrate conversion.
We used dynamic metabolic modelling to computationally evaluate the CO-to-butyrate conversion capabilities of candidate coculture systems by exploiting the diversity of human gut bacteria for anaerobic synthesis of butyrate from acetate and ethanol. A preliminary screening procedure based on flux balance analysis was developed to identify 48 gut bacteria which satisfied minimal growth rate and acetate-to-butyrate conversion requirements when cultured on minimal medium containing acetate and a simple sugar not consumed by the paired acetogen. A total of 170 acetogen/gut bacterium/sugar combinations were dynamically simulated for continuous growth using a 70/30 CO/CO feed gas mixture and minimal medium computationally determined for each combination.
While coculture systems involving the acetogens Eubacterium limosum or Blautia producta yielded low butyrate productivities and CO-to-ethanol conversion had minimal impact on system performance, dynamic simulations predicted a large number of promising coculture designs with Clostridium ljungdahlii or C. autoethanogenum as the CO-to-acetate converter. Pairings with the gut bacterium Clostridium hylemonae or Roseburia hominis were particularly promising due to their ability to generate high butyrate productivities over a range of dilution rates with a variety of sugars. The higher specific acetate secretion rate of C. ljungdahlii proved more beneficial than the elevated growth rate of C. autoethanogenum for coculture butyrate productivity.
Our study demonstrated that metabolic modelling could provide useful insights into coculture design that can guide future experimental studies. More specifically, our predictions generated several favourable designs, which could serve as the first coculture systems realized experimentally.
虽然已经对产甲烷发酵的产乙酸菌进行了工程改造，以分泌非天然代谢物，如丁酸盐，但乙酸盐仍然是热力学上最有利的产物。代谢工程的一种替代方法是通过共培养产乙酸菌和第二种能够将 CO 转化为乙酸盐的细菌来利用其将 CO 转化为乙酸盐的天然能力。
我们使用动态代谢建模，通过利用人类肠道细菌的多样性，从乙酸盐和乙醇厌氧合成丁酸盐，计算评估候选共培养系统将 CO 转化为丁酸盐的能力。开发了一种基于通量平衡分析的初步筛选程序，以确定 48 种肠道细菌，当在含有乙酸盐和简单糖（产乙酸菌不消耗）的最小培养基中培养时，这些细菌能够满足最小生长速率和乙酸盐到丁酸盐的转化率要求。总共对 170 种产乙酸菌/肠道细菌/糖组合进行了动态模拟，这些组合使用 70/30 CO/CO 进料气体混合物连续生长，并为每种组合计算了最小培养基。
虽然涉及产乙酸菌 Eubacterium limosum 或 Blautia producta 的共培养系统产生的丁酸盐产率较低，但 CO 到乙醇的转化率对系统性能的影响最小，但动态模拟预测了大量有前途的共培养设计，其中包括 Clostridium ljungdahlii 或 C. autoethanogenum 作为 CO 到乙酸盐的转换器。与肠道细菌 Clostridium hylemonae 或 Roseburia hominis 的配对特别有希望，因为它们能够在各种糖存在的不同稀释率下产生高丁酸盐产率。与 C. autoethanogenum 相比，Clostridium ljungdahlii 的特定乙酸盐分泌率更高，这对共培养丁酸盐产率更有利。
我们的研究表明，代谢建模可以为共培养设计提供有用的见解，从而指导未来的实验研究。更具体地说，我们的预测产生了一些有利的设计，这些设计可以作为第一个共培养系统进行实验验证。
