On the Origins and Control of Community Types in the Human Microbiome

TL;DR

This study uses a dynamic systems approach to explain the existence of community types in the human microbiome and proposes control strategies to steer microbial communities towards desired healthy states.

Contribution

It demonstrates that heterogeneity in interspecific interactions can explain community types and introduces a control method to manipulate microbiome composition.

Findings

Heterogeneity in interactions explains community types.

Control of strongly interacting species can steer microbiomes.

Control strategy works even without distinct community types.

Abstract

Microbiome-based stratification of healthy individuals into compositional categories, referred to as "community types", holds promise for drastically improving personalized medicine. Despite this potential, the existence of community types and the degree of their distinctness have been highly debated. Here we adopted a dynamic systems approach and found that heterogeneity in the interspecific interactions or the presence of strongly interacting species is sufficient to explain community types, independent of the topology of the underlying ecological network. By controlling the presence or absence of these strongly interacting species we can steer the microbial ecosystem to any desired community type. This open-loop control strategy still holds even when the community types are not distinct but appear as dense regions within a continuous gradient. This finding can be used to develop viable therapeutic strategies for shifting the microbial composition to a healthy configuration