A macroecological description of alternative stable states reproduces intra- and inter-host variability of gut microbiome

The most fundamental questions in microbial ecology concern the diversity and variability of communities. Their composition varies widely across space and time, as a result of a nontrivial combination of stochastic and deterministic processes. The interplay between nonlinear community dynamics and environmental fluctuations determines the rich statistical structure of community variability. We analyze long time series of individual human gut microbiomes and compare intra- and intercommunity dissimilarity under a macroecological framework. We show that most taxa have large but stationary fluctuations over time, while a minority of taxa display rapid changes in average abundance that cluster in time, suggesting the presence of alternative stable states. We disentangle interindividual variability in a stochastic component and a deterministic one, the latter recapitulated by differences in carrying capacities. Last, by combining environmental fluctuations and alternative stable states, we introduce a model that quantitatively predicts the statistical properties of both intra- and interindividual community variability, therefore summarizing variation in a unique macroecological framework.

Automated summary

The study focused on the diversity and variability of microbial communities, revealing that most taxa exhibit stable fluctuations while a minority display rapid changes that cluster in time. By decomposing variability into stochastic and deterministic components, differences in carrying capacities were identified as the main factor driving community differences. A model was introduced to quantitatively predict statistical properties of variability within and between individuals, providing a unique macroecological framework for summarizing variation.