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Models of microbiome evolution incorporating host and microbial selection.

Qinglong Zeng1,2, Steven Wu3, Jeet Sukumaran4

  • 1Department of Biology, Duke University, Durham, NC, USA.

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Selection on microbes strongly impacts microbiome diversity and microbial fitness. Host selection has weaker effects on microbiome diversity, influencing host fitness only under specific conditions of microbial inheritance.

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Area of Science:

  • Microbial Ecology
  • Evolutionary Biology
  • Computational Biology

Background:

  • Empirical studies indicate reciprocal selection between hosts and microbes.
  • A lack of explicit frameworks exists to model host-microbe co-evolution under selection.
  • Previous work established a computational framework for neutral evolution of host-associated microbiomes.

Purpose of the Study:

  • To extend a computational framework to model host and microbial selection dynamics.
  • To investigate the impact of different types of selection on microbiome diversity and host/microbial fitness.
  • To analyze the interplay between host-mediated and trait-mediated microbial selection.

Main Methods:

  • Developed a computational framework incorporating host and microbial selection.
  • Modeled microbial traits influencing host and microbial fitness.
  • Simulated three types of selection: host selection, trait-mediated microbial selection, and host-mediated microbial selection.

Main Results:

  • Microbiome diversity is significantly influenced by selection acting on microbes.
  • Host selection impacts microbiome diversity only with substantial parental microbial contribution.
  • Host fitness increases under host selection only with strong parental contribution or concomitant host-mediated microbial selection.

Conclusions:

  • Presented a computational framework integrating diverse selective processes in microbiome evolution.
  • Demonstrated strong effects of microbial selection on microbiome diversity and fitness.
  • Showed that host selection generally has weaker outcomes on microbiome diversity compared to microbial selection.