The ecology of the microbiome: Networks, competition, and stability

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Science  06 Nov 2015:
Vol. 350, Issue 6261, pp. 663-666
DOI: 10.1126/science.aad2602

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What makes the gut microbiome stable?

Classically, we think of our microbiome as stable, benign, and cooperative. Recent experimental work is beginning to unpick essential functions that can be attributed to the stable microbiota of humans. To be able to manipulate the microbiome to improve health, we need to understand community structure and composition and we need models to quantify and predict stability. Coyte et al. applied concepts and tools from community ecology to gut microbiome assembly. Independently developed models converged on a surprising answer: A high diversity of species is likely to coexist stably when the system is dominated by competitive, rather than cooperative, interactions.

Science, this issue p. 663


The human gut harbors a large and complex community of beneficial microbes that remain stable over long periods. This stability is considered critical for good health but is poorly understood. Here we develop a body of ecological theory to help us understand microbiome stability. Although cooperating networks of microbes can be efficient, we find that they are often unstable. Counterintuitively, this finding indicates that hosts can benefit from microbial competition when this competition dampens cooperative networks and increases stability. More generally, stability is promoted by limiting positive feedbacks and weakening ecological interactions. We have analyzed host mechanisms for maintaining stability—including immune suppression, spatial structuring, and feeding of community members—and support our key predictions with recent data.

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