Macroecological dynamics of gut microbiota

Abstract

The gut microbiome is now widely recognized as a dynamic ecosystem that plays an important role in health and disease1. While current sequencing technologies make it possible to estimate relative abundances of host-associated bacteria over time2, 3, the biological processes governing their dynamics remain poorly understood. Therefore, as in other ecological systems4, 5, it is important to identify quantitative relationships describing global aspects of gut microbiota dynamics. Here we use multiple high-resolution time series data obtained from humans and mice6-8 to demonstrate that despite their inherent complexity, gut microbiota dynamics can be characterized by several robust scaling relationships. Interestingly, these patterns are highly similar to those previously observed across diverse ecological communities and economic systems, including the temporal fluctuations of animal and plant populations9-12 and the performance of publicly traded companies13. Specifically, we find power law relationships describing short- and long-term changes in gut microbiota abundances, species residence and return times, and the connection between the mean and variance of species abundances. The observed scaling relationships are altered in mice receiving different diets and affected by context-specific perturbations in humans. We use these macroecological relationships to reveal specific bacterial taxa whose dynamics are significantly affected by dietary and environmental changes. Overall, our results suggest that a quantitative macroecological framework will be important for characterizing and understanding complex dynamics of microbial communities.