Exploring the mechanisms of maintaining microbial community structure is important to understand biofilm development or microbiota dysbiosis. In this paper, we propose a functional gene-based composition prediction (FCP) model to predict the population structure composition within a microbial community. The model predicts the community composition well in both a low-complexity community as acid mine drainage (AMD) microbiota, and a complex community as human gut microbiota. Furthermore, we define community structure shaping (CSS) genes as functional genes crucial for shaping the microbial community. We have identified CSS genes in AMD and human gut microbiota samples with FCP model and find that CSS genes change with the conditions. Compared to essential genes for microbes, CSS genes are significantly enriched in the genes involved in mobile genetic elements, cell motility, and defense mechanisms, indicating that the functions of CSS genes are focused on communication and strategies in response to the environment factors. We further find that it is the minority, rather than the majority, which contributes to maintaining community structure. Compared to health control samples, we find that some functional genes associated with metabolism of amino acids, nucleotides, and lipopolysaccharide are more likely to be CSS genes in the disease group. CSS genes may help us to understand critical cellular processes and be useful in seeking addable gene circuitries to maintain artificial self-sustainable communities. Our study suggests that functional genes are important to the assembly of microbial communities.
长期以来，微生物种群动力学致力于探索微生物群落的多样性和复杂性，是微生物生态学研究关注的一个重要科学问题。近年来，基于对微生物群落进行高通量测序的宏基因组学技术得到迅速的发展，很好地避开了绝大多数微生物难以在现有实验室条件和技术下进行培养这一难题，同时也为微生物种群动力学研究提供了新的途径和方法。从高通量测序数据出发，目前大多数微生物种群动力学模型主要使用16S rRNA数据进行物种水平的分析。本文从宏基因组的全基因组测序数据出发，进行基因及功能注释、物种注释并得到以物种和功能为分类单元的特征，结合环境因子信息，提出了一个基于功能相互作用关系进而量化种群适应度的FCP模型（Functional gene-based Composition Prediction model）。数据检测表明，FCP模型在一个简单的（酸矿水微生物群落）和复杂的（人肠道菌群）微生物系统中均能很好地预测微生物群落在不同环境下的种群结构及其变化。从FCP模型出发，我们可进一步从分子水平上分析基因缺失对群落结构造成的影响，由此定义了对群落结构稳定至关重要的功能基因——CSS基因（Community Structure Shaping genes）。运用FCP模型，本文设计了一个鉴定CSS基因的方法，并将其应用于酸矿水微生物群落和人肠道菌群。结果显示，CSS基因在生物膜成熟过程中发生了显著变化。在早期样本中，CSS基因富含与环境压力相关的具有防御机制的功能基因；随着生物膜逐渐成熟，膜形成和控制细胞运动的功能类基因显著增加，表明微生物群落在生态演替过程发生了生理变化。与人们熟悉的微生物必需基因（Essential Genes）相比，CSS基因的特点在于显著地富集于移动元件、细胞运动和防御机制等功能，很好地描述了微生物群落对于环境特别是极端环境的适应性。值得关注的是，群落中各物种对于CSS基因的贡献分析结果表明，群落中的低丰度菌，而不是主导菌，对群落结构稳定发挥着重要的作用。此外，我们发现人肠道菌群中CSS基因的数量远高于酸矿水微生物。患病组的CSS基因与健康对照组相比有着明显的不同，而且也得到了相关文献的支持。





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