Fig. 5: Increased alpha diversity over time in the RV3-BB Malawi and Indonesia study cohorts.

a–c Alpha diversity using the Fisher’s alpha index, Simpson’s index and Observed Richness were compared between time points for the Malawi, and the Indonesia cohort (d–f), independent of vaccine response. g–i Fisher’s alpha index, Simpson’s index and Observed Richness analysis for the Malawi cohort separated by time points. j–l Fisher’s alpha index, Simpson’s index and Observed Richness analysis for the Indonesia cohort separated by time points. Data were tested for Gaussian distribution using the Anderson-Darling and Shapiro-Wilk tests. Data were not normally distributed, and therefore, the two-sided non-parametric Skillings-Mack test for incompletely matched data with Dunn’s multiple comparisons test was used for analysis. Only p-values < 0.05 are shown for this time-point analysis. For statistical analysis in (g–I), the two-tailed non-parametric Mann-Whitney test was applied. Data are presented in a box and whisker plot. The box extends from the 25th to the 75th percentile, and the line in the middle is plotted at the median. The whiskers represent the 10–90 percentiles. All data points outside the 10–90 percentile are shown. Statistical analysis and plotting were performed in Prism 10 for MacOS. The Skillings-Mack test was performed in R using the PMCMR plus package (v1.9.10). All the individual numbers used for box plot generation are presented in Table 2 and Supplementary Table 4. Abbreviations: BL = baseline; w = week; IF = infant vaccine schedule group; NE = neonatal vaccine schedule group; PB = placebo group.