A computational framework for resolving the microbiome diversity conundrum

Area of Science:

• Microbiome Research
• Ecology
• Evolutionary Biology

Background:

• Host microbiome composition is critical for host wellbeing and survival.
• Significant variation exists in microbiome composition among healthy individuals, posing a challenge to understanding its role in fitness.
• Gnotobiotic models demonstrate the microbiome's importance, yet arbitrary microbial introductions can rescue deleterious phenotypes, creating a paradox.

Purpose of the Study:

• To resolve the 'microbial beta-diversity conundrum' concerning host fitness and microbiome composition.
• To explain the paradox of microbiome importance versus variability and rescue effects.
• To investigate the influence of host population dynamics on microbiome-host interactions.

Main Methods:

• Computational framework simulating host and microbiome population dynamics over multiple generations.
• Modeling of microbial beta-diversity and its impact on host fitness.
• Analysis of factors including host population size, mode of microbial contribution to fitness, and microbiome richness.

Main Results:

• Host fitness can be entirely dependent on microbiome composition.
• Microbiome composition may have minimal impact on population-level natural selection dynamics.
• Solutions to the conundrum involve host population size, microbial contribution mechanisms, and microbiome richness.

Conclusions:

• The microbial beta-diversity conundrum can be resolved by considering population dynamics and specific ecological factors.
• Host fitness is intricately linked to microbiome composition, but this relationship does not necessarily drive population-level evolutionary trajectories.
• Understanding host-microbiome interactions requires a multi-generational, population-level perspective.