Abstract:

Biosynthesis has become an important way of green manufacturing of chemicals. Traditionally, microbial synthesis of chemicals mainly uses a single strain. However, mono-culture often has the following problems:(1) Introduction of complex pathways causes heavy metabolic burden, (2) the cell microenvironment cannot fulfil the functional expression of all enzymes in the pathways, and (3) the mutual interference between modules of different pathways. Inspired by the natural symbiosis, researchers have developed co-culture technology. By cultivating two or more different cells in the same system, they can fully simulate the natural symbiosis environment, realizing the exchange of energy, materials and signals between different species and achieving the purpose of division of labor and metabolic compartmentation. This technology shows outstanding advantages in reduction of the metabolic burden and provision of suitable environment for different enzymes. Co-culture strategy can also be applied in the aspect of utilizing complex (e.g. lignocellulose), mixed (e.g. glucose/xylose/arabinose) or nonconventional (methane, CO and CO₂) carbon sources. Synthesis of the target products competes with the native metabolism for precursors, energy and other resources. Introduction of long pathways in a single strain may cause severe metabolic burden. Splitting and distributing pathways to different cells can alleviate such burden. In addition, each module can be optimized independently, and the balance between the modules can be achieved by adjusting the proportion of strains. Studies have shown that co-culture can significantly affect microbial metabolism and activate silent biosynthetic pathways. In recent years, hundreds of new compounds including polyketones, macrolides and diterpenes have been discovered through co-culture techniques. As an emerging technology, microbial co-culture still has many challenges in the prediction and control of the proportion of different strains. This review lists recent successful cases of microbial co-culture to produce chemicals, summarizes the research progress on regulating the strain proportion through quorum sensing and predicting the dynamic changes through computer simulation tools. Finally, the prospects and challenges in this emerging technology is also discussed.

Key words: co-culture, biosynthesis, division of labor, quorum sensing, computational simulation

摘要：

生物合成已成为化学品绿色制造的重要方式。传统上，微生物合成化学品以单菌株培养为主。然而，单培养经常存在引入复杂途径造成沉重代谢负担、细胞微环境无法满足所有酶的功能性表达以及不同途径模块之间相互干扰等问题。借鉴自然界中普遍存在的共生现象，研究者开发了共培养技术，通过在同一体系中培养两种或多种细胞，以充分模拟自然共生环境，实现不同物种之间能量、物质及信号的交流，达到劳动分工以及代谢分区的目的。该技术在减轻宿主代谢负担、提供适宜的酶催化环境以及底物共利用方面表现出突出优势。不过作为一种新兴技术，微生物共培养技术在菌群稳定性、物种兼容性以及菌群比例调控等方面还存在一些挑战。本文列举了近年来微生物共培养划分长途径减轻代谢负担以及利用复杂、混合、非常规底物生产化学品和扩大化学品多样性的成功案例，总结了通过群体感应调控菌群比例以及通过计算机模拟工具预测菌群动态变化的研究进展，并对设计复杂稳定可控的共培养体系在高效生产化学品方面的应用前景和挑战进行了讨论。共培养技术有望成为合成复杂化学品的重要策略，并推动合成生物学的发展。

关键词: 共培养, 生物合成, 劳动分工, 群体感应, 计算机模拟