Fig. 4

Miscarriage outcome according to vaginal microbial classification. Stacked bar chart illustrating increased representation of Lactobacillus spp. depleted vaginal microbial communities in euploid miscarriages compared to aneuploid miscarriages (P = 0.01, two tailed Fisher’s exact test a). Analysis of vaginal microbiome subgroups showed that this difference was largely driven by non-Gardnerella-dominance of the vaginal niche (P = 0.02, two-tailed Fisher’s exact test b) and increased relative abundance of Streptococcus and Prevotella species in euploid miscarriages compared to aneuploid miscarriages (c). Consistent with this, significantly higher richness (P = 0.0273, two-tailed Mann-Whitney U, d) and diversity (P = 0.0353, two-tailed Mann-Whitney U, e) was observed in euploid miscarriage compared to aneuploid miscarriage. The linear discriminant analysis (LDA) effect size (LEFse) method (f) was then used to identify differentially abundant taxa in euploid compared to aneuploid miscarriage, which were presented at differing taxonomic levels using a cladogram (g). Data represented as percentages a, b and c and mean ± standard error of mean in d and e. LEfSe analysis (f, g) depicting particular vaginal microbial taxa associated with different clinical outcomes