Models of microbiome evolution incorporating host and microbial selection

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.