跨系统 SynCom 入门综述：设计、接种、评估与伦理边界

图示信息：Figure 1. Dual continuums of “question” and “system” for SynCom research. Research questions using SynComs can range from fundamental questions or basic science, that is, trying to understand the rules and functioning underpinning different systems, to applied questions. Here communities are designed to fulfill certain purposes, for example, [AU: please complete this sentence using a brief example from the figure]. Likewise, the system being used can be placed on a continuum from environmental to free living and host-associated microbial communities. Mehlferber et al. Page 14 Nat Microbiol. Author manuscript; available in PMC 2024 December 20. 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-2038349.pdf，PDF 第 14 页；图像来自 PDF 内部可匹配 Figure caption 的图像块。

图示信息：Figure 2. Flow diagram of approaches used when designing, evaluating and deploying a SynCom. (A) All studies begin by designing the community (green). SynCom design can proceed from either Bottom-up (increase complexity through iterations) or Top-down (reduce complexity through iterations) approaches. When designing communities it is important to consider the number of strains needed to be relevant, as well as the sourcing of those strains. (B) Strains are then prepared and used for inoculation (yellow). Important considerations include the strain growth conditions, applied concentration, experimental system and methods of inoculation. (C) After a SynCom has been implemented, it is critical to evaluate if it provides relevant information about the system being modeled. To do so, the questions must first be well defined, after which the relevant features can be assessed by tracking the composition and functioning of the community. (D) When designing and Mehlferber et al. Page 15 Nat Microbiol. Author manuscript; available in PMC 2024 December 20. Author Manuscript Author Manuscript Author Manuscript Author Manuscript

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-2038349.pdf，PDF 第 15 页；图像来自 PDF 内部可匹配 Figure caption 的图像块。

图示信息：Figure 3. Examples of bottom-up and top-down design approaches for SynComs. (A) Bottom-up approaches can include selecting strains that represent the phylogenetic diversity of the natural community at some level, identifying strains that perform some functions of interest in the natural community, or through the prediction of key interactions in the community that a researcher might want to model. (B) Top-down designs can employ host or environmental filtering. This is where a larger community is applied into the study environment and only those strains that pass some growth or persistence metrics are included. It can also be achieved through the recapitulation of key features in community interaction networks or through a sequential drop out, where strains are sequentially removed in order to select the minimal complexity required to model the interactions of interest. In practice these approaches are not mutually exclusive, and researchers can choose to employ a combination of bottom-up or top-down strain selection approaches to define their communities. Mehlferber et al. Page 17 Nat Microbiol. Author manuscript; available in PMC 2024 December 20. Author Manuscript Author Manuscr

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-2038349.pdf，PDF 第 17 页；图像来自 PDF 内部可匹配 Figure caption 的图像块。