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

Publication date: Available online 23 April 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Xiaoqing Jiang, Xin Li, Longshu Yang, Chunhong Liu, Qi Wang, Weilai Chi, Huaiqiu ZhuAbstractExploring 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 lipopolysaccha...
Source: Genomics, Proteomics and Bioinformatics - Category: Bioinformatics Source Type: research