Department of Genome Sciences, University of Washington, Seattle, WA, 98102, USA.
Department of Computer Science and Engineering, University of Washington, Seattle, WA, 98102, USA.
Microbiome. 2018 Mar 2;6(1):45. doi: 10.1186/s40168-018-0425-4.
The species composition of a microbial community is rarely fixed and often experiences fluctuations of varying degrees and at varying frequencies. These perturbations to a community's taxonomic profile naturally also alter the community's functional profile-the aggregate set of genes encoded by community members-ultimately altering the community's overall functional capacities. The magnitude of such functional changes and the specific shift that will occur in each function, however, are strongly dependent on how genes are distributed across community members' genomes. This gene distribution, in turn, is determined by the taxonomic composition of the community and would markedly differ, for example, between communities composed of species with similar genomic content vs. communities composed of species whose genomes encode relatively distinct gene sets. Combined, these observations suggest that community functional robustness to taxonomic perturbations could vary widely across communities with different compositions, yet, to date, a systematic study of the inherent link between community composition and robustness is lacking.
In this study, we examined how a community's taxonomic composition influences the robustness of that community's functional profile to taxonomic perturbation (here termed taxa-function robustness) across a wide array of environments. Using a novel simulation-based computational model to quantify this taxa-function robustness in host-associated and non-host-associated communities, we find notable differences in robustness between communities inhabiting different body sites, including significantly higher robustness in gut communities compared to vaginal communities that cannot be attributed solely to differences in species richness. We additionally find between-site differences in the robustness of specific functions, some of which are potentially related to site-specific environmental conditions. These taxa-function robustness differences are most strongly associated with differences in overall functional redundancy, though other aspects of gene distribution also influence taxa-function robustness in certain body environments, and are sufficient to cluster communities by environment. Further analysis revealed a correspondence between our robustness estimates and taxonomic and functional shifts observed across human-associated communities.
Our analysis approach revealed intriguing taxa-function robustness variation across environments and identified features of community and gene distribution that impact robustness. This approach could be further applied for estimating taxa-function robustness in novel communities and for informing the design of synthetic communities with specific robustness requirements.
微生物群落的物种组成很少是固定不变的，往往会经历不同程度和不同频率的波动。这些群落分类群谱的扰动自然也会改变群落的功能谱——即群落成员所编码的基因的总和——最终改变群落的整体功能能力。然而，这种功能变化的幅度以及每个功能将发生的具体转变，强烈依赖于基因在群落成员基因组中的分布方式。这种基因分布反过来又由群落的分类组成决定，如果群落由基因组内容相似的物种组成，与由基因组编码相对独特基因集的物种组成的群落相比，其基因分布将有明显不同。综上所述，这些观察结果表明，群落对分类扰动的功能稳健性可能因组成不同的群落而有很大差异，但迄今为止，缺乏对群落组成与稳健性之间内在联系的系统研究。
在这项研究中，我们研究了群落的分类组成如何影响群落功能谱对分类扰动的稳健性（此处称为分类-功能稳健性），研究涵盖了广泛的环境。我们使用一种新的基于模拟的计算模型来量化宿主相关和非宿主相关群落中的这种分类-功能稳健性，我们发现栖息在不同身体部位的群落之间存在显著的稳健性差异，包括与阴道群落相比，肠道群落的稳健性显著更高，而这种差异不能仅归因于物种丰富度的差异。我们还发现不同部位之间特定功能的稳健性存在差异，其中一些可能与特定的环境条件有关。这些分类-功能稳健性差异与整体功能冗余性的差异密切相关，尽管基因分布的其他方面也会影响某些身体环境中的分类-功能稳健性，并且足以根据环境对群落进行聚类。进一步的分析揭示了我们的稳健性估计与人类相关群落中观察到的分类和功能转变之间的对应关系。
我们的分析方法揭示了不同环境中引人入胜的分类-功能稳健性变化，并确定了影响稳健性的群落和基因分布特征。这种方法可以进一步应用于估计新群落的分类-功能稳健性，并为具有特定稳健性要求的合成群落的设计提供信息。
