Control points for design of taxonomic composition in synthetic human gut communities.
Control points for design of taxonomic composition in synthetic human gut communities.
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DOI：
10.1016/j.cels.2023.11.007
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发表时间：
2023-12-20
期刊：
影响因子：
9.3
通讯作者：
中科院分区：
文献类型：
--
作者：
微生物群落在许多部门提供了巨大的潜力，但在系统控制方面仍然具有挑战性。我们开发了一个两阶段的方法来指导合成微生物群的分类组成，通过精确地操纵介质成分和初始物种丰度。通过结合高通量实验和计算建模，我们展示了预测和设计10个成员合成人类肠道群落的多样性的能力。我们揭示，控制单一培养生长的关键环境因素可以被利用来引导微生物群落达到所需的状态。此外，系统变化的初始丰度驱动群落集合的变化，并通过动态生态模型推断物种间的成对相互作用。这些相互作用与条件介质实验总体上是一致的，表明对高丰富度群落的特定扰动可以为建立动态生态模型提供丰富的信息。这个模型随后被用来设计在较长时期内表现出低或高时间分类变异性的低丰富度群落。补充资料中包括了本文件透明的同行审查过程的记录。介质和接种条件是群落组成的控制点来设计群落的时间行为，我们使用动态计算模型单一培养信息加速群落设计目标统计设计实验和模型导航高维设计空间微生物群落具有巨大的应用潜力，从医疗保健到农业，但缺乏系统的方法来控制这些复杂的系统。Connors等人。开发一种两阶段模型指导的方法，根据介质成分和初始物种丰度精确地操纵群落组成。
Microbial communities offer vast potential across numerous sectors but remain challenging to systematically control. We develop a two-stage approach to guide the taxonomic composition of synthetic microbiomes by precisely manipulating media components and initial species abundances. By combining high-throughput experiments and computational modeling, we demonstrate the ability to predict and design the diversity of a 10-member synthetic human gut community. We reveal that critical environmental factors governing monoculture growth can be leveraged to steer microbial communities to desired states. Furthermore, systematically varied initial abundances drive variation in community assembly and enable inference of pairwise inter-species interactions via a dynamic ecological model. These interactions are overall consistent with conditioned media experiments, demonstrating that specific perturbations to a high-richness community can provide rich information for building dynamic ecological models. This model is subsequently used to design low-richness communities that display low or high temporal taxonomic variability over an extended period. A record of this paper’s transparent peer review process is included in the supplemental information. Media and inoculation conditions are control points for community composition To design community temporal behaviors, we used a dynamic computational model Monoculture information expedites community design goals Statistical design of experiments and models navigate high-dimensional design space Microbial communities have tremendous potential for applications ranging from healthcare to agriculture, but systematic approaches for controlling these complex systems are lacking. Connors et al. develop a two-stage model-guided approach to precisely manipulate community composition as a function of media components and initial species abundances.
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DOI：
10.1038/s41396-020-00751-7
发表时间：
2021-01
期刊：
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影响因子：
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影响因子：
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