Fig. 1: Vaccination against C. coli does not impact the maturation of the infant macaque gut microbiome.

The fecal microbiome was profiled using 16 S rRNA gene amplicon sequencing of samples collected longitudinally for all infants from two birth cohorts (2017 and 2018) to assess the development and maturation of their microbiome. a Longitudinal measurements of Observed Amplicon Sequencing Variants (ASV) were used to assess microbial richness and the lines are colored by vaccination cohort and year with each line indicating the average development for that group with symbols and error bars indicating the average ± SEM. Significance was assessed by a mixed effect model comparing the vaccine arms against controls across time within each cohort. In each case, there was no significant difference between these groups in both birth cohorts (P > 0.05). b Principal coordinate analysis (PcoA) Weighted unique fraction metric (UniFrac) distance, a dimensional reduction technique in which beta-diversity can be visualized in 2-dimensions with distance between points indicating dissimilarity of overall microbiome composition, are indicated by symbol (i.e., by time point) and colors indicate birth year and vaccination cohort. c A PERMANOVA result table was prepared to assess the impact of vaccination on microbiome composition at each timepoint, with split birth cohorts to account for yearly variation, and all vaccine arms considered separately. P values shown are unadjusted one-sided F test P values from each PERMANOVA test. Time points with non-significant test results indicate that the overall community composition cannot distinguish between the indicated groups. The number of microbiome samples available for analysis varied by group and by time point as follows: VDI-1/3/12 (n = 24, 23, 9, 9); VI-1/3/12 (n = 28, 25, 9, 10), 2017 Controls (n = 10, 10, 9, 9), VI-1/3/5 (n = 46, 45, 10, 42) and 2018 Controls (n = 15, 9, 9, 13) were examined at the 1, 3, 6, and 9 month time points, respectively. A single microbiome sample was obtained from VDI-1/3/12 dams (n = 25), VI-1/3/12 dams (n = 28), and 2017 Control dams (n = 8) at 1 month post-delivery. Source data are provided as a Source Data file.