Two dynamic regimes in the human gut microbiome

The gut microbiome is a dynamic system that changes with host development, health, behavior, diet, and microbe-microbe interactions. Prior work on gut microbial time series has largely focused on autoregressive models (e.g. Lotka-Volterra). However, we show that most of the variance in microbial time series is non-autoregressive. In addition, we show how community state-clustering is flawed when it comes to characterizing within-host dynamics and that more continuous methods are required. Most organisms exhibited stable, mean-reverting behavior suggestive of fixed carrying capacities and abundant taxa were largely shared across individuals. This mean-reverting behavior allowed us to apply sparse vector autoregression (sVAR)—a multivariate method developed for econometrics—to model the autoregressive component of gut community dynamics. We find a strong phylogenetic signal in the non-autoregressive co-variance from our sVAR model residuals, which suggests niche filtering. We show how changes in diet are also non-autoregressive and that Operational Taxonomic Units strongly correlated with dietary variables have much less of an autoregressive component to their variance, which suggests that diet is a major driver of microbial dynamics. Autoregressive variance appears to be driven by multi-day recovery from frequent facultative anaerobe blooms, which may be driven by fluctuations in luminal redox. Overall, we identify two dynamic regimes within the human gut microbiota: one likely driven by external environmental fluctuations, and the other by internal processes.Author summary: Dynamics reveal crucial information about how a system functions. In this study, we develop an approach for disentangling two types of dynamics within the human gut microbiome. We find that autoregressive dynamics involve recovery from large deviations in community structure. These recovery processes appear to involve the blooming of facultative anaerobes and aerotolerant taxa, likely due to transient shifts in redox potential, followed by re-establishment of obligate anaerobes. Non-autoregressive dynamics carry a strong phylogenetic signal, wherein highly related taxa fluctuate coherently. These non-autoregressive dynamics appear to be driven by external, non-autoregressive variables like diet. We find that most of the community variance is driven by day-to-day fluctuations in the environment, with occasional autoregressive dynamics as the system recovers from larger shocks. 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.