How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes
How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes
复制标题
微生物如何塑造它们的群落？
DOI：
10.1016/j.gpb.2018.09.003
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发表时间：
2019-02-01
影响因子：
9.5
通讯作者：
Zhu, Huaiqiu
中科院分区：
文献类型：
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作者：
Jiang, Xiaoqing;Li, Xin;Zhu, Huaiqiu
探索维持微生物群落结构的机制对于了解生物膜发育或微生物群失调非常重要。在本文中，我们提出了一种基于功能基因的组成预测（FCP）模型来预测微生物群落内的种群结构组成。该模型可以很好地预测酸性矿山排水 (AMD) 微生物群等低复杂性群落和人类肠道微生物群等复杂群落的群落组成。此外，我们将群落结构塑造（CSS）基因定义为对于塑造微生物群落至关重要的功能基因。我们利用 FCP 模型鉴定了 AMD 和人类肠道微生物样本中的 CSS 基因，并发现 CSS 基因随条件而变化。与微生物的必需基因相比，CSS基因显着富集了涉及可移动遗传元件、细胞运动和防御机制的基因，表明CSS基因的功能集中于通信和应对环境因素的策略。我们进一步发现，是少数人而不是多数人有助于维持社区结构。与健康对照样本相比，我们发现疾病组中一些与氨基酸、核苷酸和脂多糖代谢相关的功能基因更有可能是CSS基因。 CSS 基因可以帮助我们理解关键的细胞过程，并有助于寻找可添加的基因电路来维持人工的自我可持续的群落。我们的研究表明功能基因对于微生物群落的组装很重要。
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.