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

Xiaoqing Jiang1, Xin Li2, Longshu Yang1

  • 1State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China; Center for Quantitative Biology, Peking University, Beijing 100871, China.

Genomics, Proteomics & Bioinformatics
|April 27, 2019
PubMed
Summary

We developed a functional gene-based model to predict microbial community composition. This model identified community structure shaping genes, revealing their role in environmental adaptation and highlighting the importance of minority genes in maintaining microbial communities.

Keywords:
Acid mine drainageCommunity structureDynamics modelHuman gut microbiotaMetagenomics

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Area of Science:

  • Microbial Ecology
  • Systems Biology
  • Bioinformatics

Background:

  • Understanding microbial community structure is crucial for fields like biofilm development and microbiota dysbiosis.
  • Functional genes play a key role in microbial community assembly and dynamics.
  • Existing models often focus on species composition rather than functional gene contributions.

Purpose of the Study:

  • To develop a functional gene-based composition prediction (FCP) model for microbial communities.
  • To identify and characterize community structure shaping (CSS) genes.
  • To investigate the role of CSS genes in different microbial environments and their potential implications for health and synthetic biology.

Main Methods:

  • Development and application of a functional gene-based composition prediction (FCP) model.
  • Identification of community structure shaping (CSS) genes in acid mine drainage (AMD) and human gut microbiota.
  • Comparative analysis of CSS genes with essential microbial genes and their enrichment in specific functional categories.
  • Analysis of CSS gene differences between healthy and diseased human gut microbiota samples.

Main Results:

  • The FCP model accurately predicts community composition in both low-complexity (AMD) and high-complexity (human gut) microbial communities.
  • CSS genes were identified and found to be condition-dependent, enriched in mobile genetic elements, cell motility, and defense mechanisms.
  • Minority functional genes, not the majority, were found to be critical for maintaining community structure.
  • In disease states, CSS genes associated with amino acid, nucleotide, and lipopolysaccharide metabolism were more prevalent compared to healthy controls.

Conclusions:

  • Functional genes are fundamental to microbial community assembly and maintenance.
  • CSS genes are key players in microbial community dynamics, involved in environmental adaptation and inter-microbe interactions.
  • The identification of CSS genes offers insights into microbial ecology and has potential applications in engineering self-sustainable artificial communities.