In nature, microbes do not exist in isolation but co-exist in a variety of ecological and biological environments and on various host organisms. Due to their close proximity, these microbes interact among themselves, and also with the hosts in both positive and negative manners. Moreover, these interactions may modulate dynamically upon external stimulus as well as internal community changes. This demands systematic techniques such as mathematical modeling to understand the intrinsic community behavior. Here, we reviewed various approaches for metabolic modeling of microbial communities. If detailed species-specific information is available, segregated models of individual organisms can be constructed and connected via metabolite exchanges; otherwise, the community may be represented as a lumped network of metabolic reactions. The constructed models can then be simulated to help fill knowledge gaps, and generate testable hypotheses for designing new experiments. More importantly, such community models have been developed to study microbial interactions in various niches such as host microbiome, biogeochemical and bioremediation, waste water treatment and synthetic consortia. As such, the metabolic modeling efforts have allowed us to gain new insights into the natural and synthetic microbial communities, and design interventions to achieve specific goals. Finally, potential directions for future development in metabolic modeling of microbial communities were also discussed.

中文翻译：

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用于健康、环境和生物技术应用的微生物群落相互作用的代谢建模

在自然界中，微生物不是孤立存在的，而是共存于各种生态和生物环境以及各种宿主生物体中。由于它们非常接近，这些微生物之间会相互影响，也会以积极和消极的方式与宿主相互作用。此外，这些互动可能会根据外部刺激和内部社区变化动态调节。这需要系统的技术，如数学建模来理解内在的社区行为。在这里，我们回顾了微生物群落代谢建模的各种方法。如果可以获得详细的物种特定信息，则可以通过代谢物交换构建和连接个体生物的分离模型；否则，社区可能被表示为代谢反应的集总网络。然后可以模拟构建的模型以帮助填补知识空白，并为设计新实验生成可测试的假设。更重要的是，此类群落模型已被开发用于研究宿主微生物组、生物地球化学和生物修复、废水处理和合成联盟等各种生态位中的微生物相互作用。因此，代谢建模工作使我们能够获得对天然和合成微生物群落的新见解，并设计干预措施以实现特定目标。最后，还讨论了微生物群落代谢模型未来发展的潜在方向。此类群落模型已被开发用于研究各种生态位中的微生物相互作用，例如宿主微生物组、生物地球化学和生物修复、废水处理和合成菌群。因此，代谢建模工作使我们能够获得对天然和合成微生物群落的新见解，并设计干预措施以实现特定目标。最后，还讨论了微生物群落代谢模型未来发展的潜在方向。此类群落模型已被开发用于研究各种生态位中的微生物相互作用，例如宿主微生物组、生物地球化学和生物修复、废水处理和合成菌群。因此，代谢建模工作使我们能够获得对天然和合成微生物群落的新见解，并设计干预措施以实现特定目标。最后，还讨论了微生物群落代谢模型未来发展的潜在方向。