Neutral models of short-term microbiome dynamics with host subpopulation structure and migration limitation

Area of Science:

• Microbiome research
• Ecological modeling
• Evolutionary biology

Background:

• Limited formal models exist for studying short-term microbiome dynamics within a unified ecological and evolutionary framework.
• Previous work developed a long-term neutral framework but could not explore dynamics within a single host generation.

Purpose of the Study:

• To develop a computational, agent-based, forward-time framework for microbiome dynamics within a single host generation.
• To investigate the influence of neutral processes, host genealogy, and population structure on microbiome evolution.

Main Methods:

• Developed a computational framework incorporating neutral assembly, microbe acquisition (parental/environmental), and a Moran genealogical model.
• Included host subpopulation structure and migration to influence microbiome recruitment.
• Simulated microbiome dynamics within a single host generation.

Main Results:

• Microbiome diversity within hosts increases with environmental contribution.
• Microbiome diversity between hosts increases with parental inheritance.
• Host population structure and dispersal limitation alter within- and between-host diversity patterns.
• Overall population microbiome diversity remained temporally stable.

Conclusions:

• Presents a novel computational framework integrating host genealogy, microbe recruitment, and dispersal limitation for short-term microbiome dynamics.
• Demonstrates that neutral microbiome dynamics are significantly influenced by transmission mode and shared environment.