Fig. 3: Species-level differences between infection groups, stratified by country.

A Prevalence-based comparison showing phylogenetic relationships of species that were significantly more or less prevalent in at least one country. Statistical significance was determined using Fisher’s exact test with Benjamini-Hochberg false discovery rate (FDR) correction (adjusted P < 0.05). B Comparison of relative abundances between infection status groups, stratified by country. Three statistical tests were applied: Kruskal–Wallis test, LEfSe differential abundance pipeline, and MaAsLin2 (adjusted for the country variable). Only species that were statistically significant across all three tests were retained. The log2 fold-change values, generated using MaAsLin2, are displayed to represent effect sizes. Positive log2 fold-change values indicate higher abundance in uninfected individuals, while negative values indicate higher abundance in infected patients. Taxa highlighted in orange are associated with infection status in two or more settings but show opposite directions of change. Taxa highlighted in green differ in two or more settings and show a concordant direction of change. C Comparison of cumulative relative abundances of species significantly enriched or depleted in one versus two (or more) study sites. Statistical comparisons were performed using the Kruskal-Wallis test, with Bonferroni correction for P-values (adjusted P < 0.05).