Two dynamic regimes in the human gut microbiome

Background/Question/Methods: The gut microbiome is a dynamic system that changes with host development, health, behavior, diet, and microbe-microbe interactions. Dynamics reveal crucial information about how a system functions. In this study, we developed an approach for disentangling two types of dynamics within the human gut microbiome. We investigated the four longest, densest human gut time series currently available in the literature. Prior work on gut microbial time series has largely focused on autoregressive models (e.g., Lotka-Volterra). However, we found that most of the variance in microbial time series is non-autoregressive. Abundant gut bacteria exhibited stable, mean-reverting behavior suggestive of fixed carrying capacities. This mean-reverting behavior allowed us to apply sparse vector autoregression (sVAR) - a multivariate method developed for econometrics - to separate the autoregressive and non-autoregressive components of community variance.

Results/Conclusions: We found a strong phylogenetic signal in non-autoregressive species-species co-variance from our sVAR model residuals, which suggests niche filtering. We show how day-to-day changes in diet are also non-autoregressive and that Operational Taxonomic Units (OTUs) strongly correlated with dietary variables lack any detectable autoregressive variance. Therefore, we suggest that diet is the major driver of microbial dynamics. Autoregressive variance appears to be driven by multi-day recovery from frequent blooms of facultative anaerobes and aerotolerant taxa, which may be driven by fluctuations in luminal redox, pH, and/or stool transit time. Our results - based on a limited number of individuals - paint a coherent picture of the gut ecosystem and the major forces underlying its structure and stability, with two distinct dynamical regimes: one driven by external factors (e.g., diet) and the other by internal autoregressive processes (e.g., recovery from a disturbance). Despite frequently observed disruptions to the gut ecosystem, there exists a returning force that continually pushes the gut microbiome back towards its steady-state configuration. Moving forward, we hope to identify the major factors underlying this returning force.