Fig. 5: Community dynamics is independent of mode of delivery but there is a time shift in species dynamics.
a Prediction of a single microbe’s behavior by MTV-LMM method (see Methods section). Black line represents the actual behavior of a given microbe; red line represents predicted behavior. b Autoregressive microbes are more predictable than any other randomly selected microbes. Pearson correlation between predicted and actual community composition for autoregressive microbes compared to a random set of microbes. The random set was picked using a permutation test (npermutations = 1000) in which at each iteration, 495 microbes are picked and used as predictors for the next time point. c Illustration of the center of mass (COM) calculation and clustering. COM is the weighted average for an OTU’s relative abundance over time. \(COM = \frac{{\mathop {\sum }\nolimits_{i = 1}^n R.A_t \cdot Day_t}}{{\mathop {\sum }\nolimits_{i = 1}^n Day_t}}\) where i is the cow ID (1–45), R.An is the relative abundance of a species at time point t, Dayt is the day of life when the sample was taken (1–831). d COM is lower for the C-section-delivered autoregressive microbes. Clustering using the K-means method for the MTV-LMM microbes. Each dot represents the mean COM of autoregressive microbes in a particular cow. Only microbes found to be autoregressive in one mode of delivery, originating either from C-section (blue) or vaginal delivery (red), are presented for each cow. Stars represent the center of the cluster for each delivery mode. Each axis represents the COM values for C-section (Y-axis) and vaginal-delivery mode (X-axis). e Time shift between C-section and vaginal delivery in all autoregressive microbes, with lower COM for microbes from C-section cows. Average COM for all MTV-LMM microbes (OTU index on the X-axis, average COM on the Y-axis) displayed for either vaginal delivery (red) or C-section (blue), showing a time shift in the COM dependent on the mode of delivery for all OTUs. Each dot represents the COM for a single OTU averaged across all cows within one of the two modes of delivery. Source data is provided as a Source Data file.
