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How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes / 基因组蛋白质组与生物信息学报·英文版
Genomics, Proteomics & Bioinformatics ; (4): 91-105, 2019.
Article in English | WPRIM | ID: wpr-772955
ABSTRACT
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.
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Full text: Available Index: WPRIM (Western Pacific) Main subject: Water Pollution / Genes, Microbial / Microbiota / Gastrointestinal Microbiome / Genetics / Mining / Models, Genetic Type of study: Prognostic study Limits: Humans Language: English Journal: Genomics, Proteomics & Bioinformatics Year: 2019 Type: Article

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Full text: Available Index: WPRIM (Western Pacific) Main subject: Water Pollution / Genes, Microbial / Microbiota / Gastrointestinal Microbiome / Genetics / Mining / Models, Genetic Type of study: Prognostic study Limits: Humans Language: English Journal: Genomics, Proteomics & Bioinformatics Year: 2019 Type: Article