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This study reveals pairwise microbial interactions drive gut microbiome assembly. A novel model predicts community dynamics, showing negative and positive interactions ensure species coexistence and stability.

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Area of Science:

  • Microbiology
  • Systems Biology
  • Ecology

Background:

  • The ecological principles governing the human gut microbiota's assembly and stability are not fully understood.
  • Predicting the behavior of complex microbial communities from simpler interactions remains a challenge.

Purpose of the Study:

  • To develop a generalizable model-guided framework for predicting higher-dimensional microbial consortia from lower-order assemblage data.
  • To decipher microbial interactions within a diverse human gut microbiome synthetic community.

Main Methods:

  • A model-guided framework was developed to predict microbial community dynamics.
  • Time-resolved measurements of lower-order assemblages were used to infer interactions.
  • Extracellular metabolite measurements were used to understand metabolic capabilities and interaction bases.

Main Results:

  • Pairwise interactions were identified as the primary drivers of multi-species community dynamics.
  • The inferred ecological network showed a high proportion of negative and frequent positive interactions.
  • A positive and negative interaction topology was found to enable robust coexistence through negative feedback loops.

Conclusions:

  • The developed framework successfully defined the ecological roles of key human gut species.
  • The study illuminated fundamental design principles for constructing stable microbial communities.
  • Negative interactions were shown to generate history-dependent responses in community assembly.