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Neutral Models of Microbiome Evolution.

Qinglong Zeng1, Jeet Sukumaran1, Steven Wu1

  • 1Biology Department, Duke University, Durham, North Carolina, United States of America.

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Summary
This summary is machine-generated.

Microbiome evolution is explored using an agent-based framework. High parental contribution reduces microbiome diversity, while environmental microbial pools maintain diversity over evolutionary time.

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Area of Science:

  • Microbial Ecology
  • Evolutionary Biology
  • Computational Biology

Background:

  • Host-associated microbial communities (microbiomes) are extensively studied for their links to host health and ecology.
  • Research has primarily focused on microbiome composition and distribution, with less attention to evolutionary dynamics.

Purpose of the Study:

  • To develop an agent-based framework for studying microbiome evolution on an evolutionary timescale.
  • To investigate the impact of host acquisition models and environmental microbial assembly on microbiome diversity.

Main Methods:

  • An agent-based framework incorporating neutral models for host microbiome acquisition.
  • Integration of a Wright-Fisher genealogical model to simulate host evolution.
  • Modeling of microbial community assembly from parental and environmental sources.

Main Results:

  • Parental contribution significantly influences microbiome diversity; higher contribution leads to lower diversity.
  • A small but constant environmental microbial pool can sustain high microbiome diversity.
  • The framework allows for hypothesis generation regarding microbiome assembly processes over evolutionary time.

Conclusions:

  • Microbiome evolution is shaped by the balance between parental inheritance and environmental microbial exposure.
  • The developed framework provides a novel approach to understanding long-term microbiome dynamics.
  • Future research can utilize this model to explore specific evolutionary scenarios of microbiome assembly.