Table_2_Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics.XLSX

Species utilizing the same resources often fail to coexist for extended periods of time. Such competitive exclusion mechanisms potentially underly microbiome dynamics, causing breakdowns of communities composed of species with similar genetic backgrounds of resource utilization. Although genes responsible for competitive exclusion among a small number of species have been investigated in pioneering studies, it remains a major challenge to integrate genomics and ecology for understanding stable coexistence in species-rich communities. Here, we examine whether community-scale analyses of functional gene redundancy can provide a useful platform for interpreting and predicting collapse of bacterial communities. Through 110-day time-series of experimental microbiome dynamics, we analyzed the metagenome-assembled genomes of co-occurring bacterial species. We then inferred ecological niche space based on the multivariate analysis of the genome compositions. The analysis allowed us to evaluate potential shifts in the level of niche overlap between species through time. We hypothesized that community-scale pressure of competitive exclusion could be evaluated by quantifying overlap of genetically determined resource-use profiles (metabolic pathway profiles) among coexisting species. We found that the degree of community compositional changes observed in the experimental microbiome was correlated with the magnitude of gene-repertoire overlaps among bacterial species, although the causation between the two variables deserves future extensive research. The metagenome-based analysis of genetic potential for competitive exclusion will help us forecast major events in microbiome dynamics such as sudden community collapse (i.e., dysbiosis).

物种在利用相同资源时常因竞争而无法长期共存。此类竞争排斥机制可能构成了微生物组动态变化的基础，导致具有相似资源利用遗传背景的物种组成的群落崩溃。尽管在先驱研究中已对少数物种间负责竞争排斥的基因进行了探讨，但将基因组学与生态学整合以理解物种丰富群落中的稳定共存仍然是一项重大挑战。本研究旨在探究社区尺度上功能基因冗余的社区分析是否能为解释和预测细菌群落崩溃提供有用平台。通过110天的实验微生物组动态时间序列分析，我们研究了共现细菌物种的宏基因组组装基因组。随后，我们基于基因组组成的多元分析推断生态位空间。该分析使我们能够评估物种间生态位重叠水平随时间的潜在变化。我们假设，通过量化共存物种间由遗传决定的资源利用特征（代谢途径特征）的重叠，可以评估社区尺度竞争排斥的压力。我们发现，实验微生物组中观察到的社区组成变化程度与细菌物种间基因库重叠的程度相关，尽管这两个变量之间的因果关系仍有待未来深入研究。基于宏基因组的竞争排斥遗传潜力分析将有助于我们预测微生物组动态中的重大事件，如突发群落崩溃（即，菌群失调）。