How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes  

作　　者：Xiaoqing Jiang Xin Li Longshu Yang Chunhong Liu Qi Wang Weilai Chi Huaiqiu Zhu 

机构地区：[1]State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University [2]Center for Quantitative Biology, Peking University [3]Peking University-Tsinghua University-National Institute of Biological Sciences Joint Biological (PTN) PhD Program and College of Life Sciences, Peking University [4]Center for Protein Science, Peking University

出　　处：《Genomics, Proteomics & Bioinformatics》2019年第1期91-105,共15页基因组蛋白质组与生物信息学报（英文版）

基　　金：supported by the National Key R&D Program of China (Grant No. 2017YFC1200205);the National Natural Science Foundation of China (Grant Nos. 31671366 and 91231119);the Special Research Project of ‘Clinical Medicine + X’ by Peking University, China awarded to HZ

摘　　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.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.

关 键 词：METAGENOMICS Dynamics MODEL Community structure Acid mine drainage Human GUT MICROBIOTA 

分 类 号：Q[生物学]