Fig. 4: Mode of delivery drives historical contingency effects on rumen microbiome development.

a (i) Major phylum distribution differs between delivery-mode groups and shows long-term repercussions for mode of delivery. Major phylum kernel density (see Material and methods section for further elaboration of kernel density), depicting significant differences in species (OTUs) count over time, originating from the two delivery-mode groups: C-section (left (i)) and vaginal delivery (right (ii)) (P < 0.001; see Supplementary Figures and Results). b Early invasion of C-section-associated microbes. Mean ± SE for time of first arrival of delivery mode-associated species. Red line represents average day of appearance of vaginal delivery-associated species (n = 809), blue line of C-section-associated species (n = 1041), gray bars are SE. X-axis depicts the first day of appearance, Y-axis depicts the number of delivery mode-associated species arriving in each group. Microbes were ordered by time of appearance. c Mean first appearance day for each delivery mode-associated microbe cohort is significantly lower in the C-section cows (t-test, P = 2.2 × 10–15, two-sided test). d Mean maximum time of colonization, depicted as the delta between time of first appearance in any cow to time of last appearance in any cow, is higher in vaginally delivered cows. Colonization time for C-section-associated species is significantly lower (t-test, P = 2.2 × 10–15, two-sided test). In the data shown as box plots (c, d),boxes represent the interquartile range (IQR) between the first and third quartiles (25th and 75th percentiles, respectively) and the horizontal line inside the box defines the median. Whiskers represent the lowest and highest values within 1.5 times the IQR from the first and third quartiles, respectively. Source data is provided as a Source Data file.