Two dynamic regimes in the human gut microbiome
Fig 3
Two dynamic regimes in the gut microbiome.
The top panel shows the relative abundance trace for an OTU. The second panel shows the same time series after first-differencing (i.e. taking the derivative to obtain the rate). In this data set, first-differencing ensured that each time series was stationary and appropriate for sparse vector autoregressive (sVAR) modeling. The third row of plots shows autoregressive and non-autoregressive rate dynamics, based on fitting the sVAR model. Autoregressive model coefficients (bottom left) provide information on time-lagged interactions between OTUs within the model (i.e. equivalent to partial Granger coefficients). OTU-OTU covariance (bottom right) of non-autoregressive dynamics provides information on co-fluctuating taxa.