微生物组表达影响宿主生物学的多种功能。功能范围取决于微生物组的组成,由于中立的程序集进程,它可以在主机的生存期内更改,宿主介导的选择,和环境条件。迄今为止,微生物组组装的确切动态,潜在的决定因素,对宿主相关功能的影响仍然知之甚少。这里,我们使用了线虫秀丽隐杆线虫和一个完全测序的确定的群落,在受控实验条件下,研究蠕虫宿主寿命的主要部分的微生物组动态和功能。细菌群落组成最初显示出剧烈下降的随机性,在稍后的时间点增加,表明在年轻动物中的选择性效应,而不是在老年动物中更随机的过程。与直接底物和无宿主对照环境相比,成体微生物组富含苍白杆菌属和肠杆菌。使用途径分析,新陈代谢,和生态建模,我们进一步发现,在宿主相关微生物组中,终生组装动力学增加了竞争策略和肠道相关功能,表明定殖细菌对蠕虫有益。总的来说,我们的研究引入了一个基于随机的微生物组组装动力学研究框架,生态,和代谢模型,对确定宿主相关微生物组组成和功能的过程产生新的见解。
目的:微生物组在宿主生物学中起着至关重要的作用。其功能取决于在宿主的一生中可以改变的微生物组组成。迄今为止,微生物组组装的动力学和由此产生的功能仍需要更好地理解。本研究引入了一种新的方法,通过对微生物群落变化的随机过程和代谢特征的相关性进行建模来表征微生物组组装的功能后果。该方法应用于线虫秀丽隐杆线虫在其一生的大部分时间内获得的实验时间序列数据。随机过程起到了次要的作用,而有益细菌以及肠道相关功能在宿主中富集。这表明宿主可能主动塑造其微生物组的组成。总的来说,这项研究为研究微生物组组装动力学提供了一个框架,并对秀丽隐杆线虫的微生物组功能产生了新的见解。
The microbiome expresses a variety of functions that influence host biology. The range of functions depends on the microbiome\'s composition, which can change during the host\'s lifetime due to neutral assembly processes, host-mediated selection, and environmental conditions. To date, the exact dynamics of microbiome assembly, the underlying determinants, and the effects on host-associated functions remain poorly understood. Here, we used the nematode Caenorhabditis elegans and a defined community of fully sequenced, naturally associated bacteria to study microbiome dynamics and functions across a major part of the worm\'s lifetime of hosts under controlled experimental conditions. Bacterial community composition initially shows strongly declining levels of stochasticity, which increases during later time points, suggesting selective effects in younger animals as opposed to more random processes in older animals. The adult microbiome is enriched in genera Ochrobactrum and Enterobacter compared to the direct substrate and a host-free control environment. Using pathway analysis, metabolic, and ecological modeling, we further find that the lifetime assembly dynamics increase competitive strategies and gut-associated functions in the host-associated microbiome, indicating that the colonizing bacteria benefit the worm. Overall, our study introduces a framework for studying microbiome assembly dynamics based on stochastic, ecological, and metabolic models, yielding new insights into the processes that determine host-associated microbiome composition and function.
OBJECTIVE: The microbiome plays a crucial role in host biology. Its functions depend on the microbiome composition that can change during a host\'s lifetime. To date, the dynamics of microbiome assembly and the resulting functions still need to be better understood. This study introduces a new approach to characterize the functional consequences of microbiome assembly by modeling both the relevance of stochastic processes and metabolic characteristics of microbial community changes. The approach was applied to experimental time-series data obtained for the microbiome of the nematode Caenorhabditis elegans across the major part of its lifetime. Stochastic processes played a minor role, whereas beneficial bacteria as well as gut-associated functions enriched in hosts. This indicates that the host might actively shape the composition of its microbiome. Overall, this study provides a framework for studying microbiome assembly dynamics and yields new insights into C. elegans microbiome functions.