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

Microbiome-based stratification of healthy individuals into compositional categories, referred to as “enterotypes” or “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.Author Summary: We coexist with a vast number of microbes that live in and on our bodies, and play important roles in physiology and disease. Two interesting phenomena have been observed in the human microbiome. The first is the stratification of healthy individuals based on the relative abundances of their microbes, which holds promise for drastically improving personalized medicine. The second is the astounding success of fecal microbial transplantation in treating certain diseases related to disordered microbiomes. Surprisingly, both phenomena have not been analytically or quantitatively understood, despite a few early qualitative attempts. This work shows that through a dynamic systems and control theoretical approach the success of fecal microbial transplantation can be explained and that the microbiome-based stratification can be as simple as the existence of strongly interacting species.