Community Divergence Predicts the Stability of the Human Microbiome

Chris Smillie, Massachusetts Institute of Technology

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The stability of the human microbiome underpins key aspects of human health, including metabolism, immune tolerance and disease, yet the determinants of stability remain unknown. The diversity-stability hypothesis – that increased species diversity begets ecosystem stability – has been the focus of debate for decades because empirical tests have yielded contradictory results. Here, we identify a new metric, community divergence, which is a stronger determinant of stability than is species diversity in 1,274 microbial communities from 18 body sites, ranging from subgingival plaque to the gastrointestinal tract. Using this metric, we derive a simple mechanism to explain the apparently contradictory correlations between species diversity and stability across different habitats (r2 = 0.90; P = 1×10-6), thus explaining key aspects of the diversity-stability debate. These findings may guide the development of clinical interventions against diseases associated with microbiome instability such as obesity, diabetes, autoimmune disease and cancer.

Abstract Author(s): Smillie, C.S., Friedman, J., Smith, M.B., and Alm, E.J.