Ecological rules for the assembly of microbiome communities

Area of Science:

• Microbial Ecology
• Systems Biology
• Host-Microbe Interactions

Background:

• The human microbiome is established each generation, with symbiont order critical for health.
• Factors governing microbial community assembly remain largely unknown.
• Understanding assembly is key to managing host-microbe relationships.

Purpose of the Study:

• To develop ecological theory for predicting microbial community assembly.
• To identify key factors influencing the success of microbiome development.
• To explore the role of inter-species dependencies and host factors.

Main Methods:

• Developed "assembly maps" to visualize feasible microbial community formation pathways.
• Applied ecological theory to model the assembly process.
• Analyzed published data on preterm infant and human microbiome assembly.

Main Results:

• Revealed a tradeoff: ecological dependencies predict assembly and offer benefits but can also create colonization barriers.
• Demonstrated that interdependent species may fail to establish if they require each other for initial colonization.
• Found that host feeding mechanisms, like breast milk, can overcome assembly barriers.

Conclusions:

• Microbiome assembly is governed by both microbe-to-microbe and host-to-microbe interactions.
• Ecological dependencies shape the predictable order of microbial symbiont arrival.
• Host interventions can facilitate successful microbiome establishment.