微生物组工程 DBTL 综述：通用原则与最佳实践

图示信息：Figure 1. The design-build-test-learn cycle for microbiome engineering. The figure presents key aspects and approaches of each phase of the design-build-test-learn (DBTL) cycle. The cycle starts with a defined engineering objective that determines the design and produces an engineered microbiome that performs the desired function(s). Lawson et al. Page 34 Nat Rev Microbiol. Author manuscript; available in PMC 2021 July 30. Author Manuscript Author Manuscript Author Manuscript Author Manuscript

论文结果 / 观点：该图支撑作者把微生物组工程组织为 DBTL 闭环的观点：工程目标驱动设计，构建后的群落需要测试与学习反馈。

研究意义 / 边界：这张图用于支持作者的概念框架或案例归纳；实际迁移到其他系统时，仍需结合成员来源、环境条件、稳定性和功能验证。

来源：nihms-1724630.pdf，PDF 第 34 页；图像来自 PDF 内部可匹配 Figure caption 的图像块。

图示信息：Figure 2. Top-down and bottom-up approaches to design microbiomes. The left panel illustrates a bottom-up design workflow starting from pure isolates. Physiological characterization of individual organisms is performed, and metabolic modeling is used to design consortia for desired function (produce light blue compound from dark blue compound). Genetic engineering and synthetic biology strategies are used to optimize system function (identifying gene editing targets that re-route metabolic flux away from toxin (purple) and towards desired product; designing of toxin reporter strain). The right panel illustrates a top- down design starting with an inoculum containing uncultivated microorganisms from the environment. Community characterization of mixed microbiome is performed, and bioprocess modeling (mass balance analysis including kinetics and microbial growth) is used to develop selection strategies to achieve desired function (produce light blue compound from dark blue compound). Reactor engineering design is used to optimize system function. The middle panel shows an integrated top-down bottom-up design. Combinations of uncultivated consortia and defined cultures are selected to

论文结果 / 观点：该图支撑作者对 top-down 与 bottom-up 两类设计路径的比较，说明菌株来源、纯培养表征和自然群落筛选会影响可控性与生态相关性。

研究意义 / 边界：这张图用于支持作者的概念框架或案例归纳；实际迁移到其他系统时，仍需结合成员来源、环境条件、稳定性和功能验证。

来源：nihms-1724630.pdf，PDF 第 35 页；图像来自 PDF 内部可匹配 Figure caption 的图像块。

图示信息：Figure 3. Building self-assembled and synthetic microbiomes. (a) This example shows a protocol for assembling synthetic microbiomes from multiple microbiome sources. Complex microbiomes can be taken apart into key functional members using automated microfluidic cell sorting techniques. Isolated or enriched members can then be recombined into synthetic consortia using liquid handling robotics for downstream screening and/or cultivation. (b) Microbiome assembly can also be achieved through environmental selection via bioreactor manipulation or biostimulation (top) or using bioaugmentation with defined cultures (bottom). (c) Another option is microbiome assembly through directed adaptation and/or evolution of the microbiome to acquire or optimize a desired function. (d) In situ microbiome engineering can be used to add new functions to microbiomes residing in the environment. Lawson et al. Page 36 Nat Rev Microbiol. Author manuscript; available in PMC 2021 July 30. Author Manuscript Author Manuscript Author Manuscript Author Manuscript

论文结果 / 观点：该图支撑“群落构建后必须验证功能”的观点，强调组学、示踪、功能测定或模型不能脱离实验验证。

研究意义 / 边界：这张图用于支持作者的概念框架或案例归纳；实际迁移到其他系统时，仍需结合成员来源、环境条件、稳定性和功能验证。

来源：nihms-1724630.pdf，PDF 第 36 页；图像来自 PDF 内部可匹配 Figure caption 的图像块。

图示信息：Figure 4. Testing microbiome function. (a) Isotopic tracers combined with metaproteome can also be used to measure microbiome metabolic flux by analyzing isotopic labelling patterns of short peptides rather than amino acids (metabolome). (b) Biorthogonal non-canonical amino acid tagging (BONCAT) is a method for rapid profiling of the anabolic processes (growth) in situ using either fluorescent detection or metaproteomics. (c) Metagenomics, metatranscriptomics, metaproteomics, and metabolomics can be integrated to reconstruct and analysis metabolic network expression in microbiomes. (d) An automated microbioreactor platform enables high-throughput analysis of microbiome processes across diverse conditions (for example, with changing environmental or physiological variables). The platform can integrate tools for detailed functional analysis of individual microbiome members to complex communities. HPG: the amino acid homopropargylglycine. Lawson et al. Page 37 Nat Rev Microbiol. Author manuscript; available in PMC 2021 July 30. Author Manuscript Author Manuscript Author Manuscript Author Manuscript

论文结果 / 观点：该图把群落互作落实到代谢物、电子或营养物交换，是理解共培养功能涌现的关键证据。

研究意义 / 边界：这张图用于支持作者的概念框架或案例归纳；实际迁移到其他系统时，仍需结合成员来源、环境条件、稳定性和功能验证。

来源：nihms-1724630.pdf，PDF 第 37 页；图像来自 PDF 内部可匹配 Figure caption 的图像块。

图示信息：Figure 5. Learning fundamental principles for microbiome engineering. (a) Model laboratory ecosystems can be used for controlled experiments with simplified microbiomes and environmental properties, representing an in-between of pure lab conditions (such as test tubes or flasks) and complex natural environments (such as soil or the ocean). Continuous cross-examination between laboratory-scale models and natural complex ecosystems will be needed for developing engineering principles and practices that are robust in real systems, while also tractable in the lab. This will require close collaboration between multiple stakeholders, including researchers and end-users (such as hospitals or treatment plants) that have expertise and experience with issues specific to each scale. Key principles that need to be learned to enable systematic microbiome engineering are microbial interaction Lawson et al. Page 38 Nat Rev Microbiol. Author manuscript; available in PMC 2021 July 30. Author Manuscript Author Manuscript Author Manuscript Author Manuscript

论文结果 / 观点：该图说明作者把模型系统、数据学习和生态机制总结作为下一轮工程设计的依据。

研究意义 / 边界：这张图用于支持作者的概念框架或案例归纳；实际迁移到其他系统时，仍需结合成员来源、环境条件、稳定性和功能验证。

来源：nihms-1724630.pdf，PDF 第 38 页；图像来自 PDF 内部可匹配 Figure caption 的图像块。