Fig. 1: Gender-specific persistence of B. bifidum, B. longum subsp. longum, B. breve, and B. pseudocatenulatum species and the 14 genes shared between the female-associated persistent bifidobacterial species.

In panel (a), the bar chart on the top displays the species-level persistence from pre- (1–6 months) to post-weaning stages (12–24 months) of B. bifidum, B. longum subsp. longum, B. breve, and B. pseudocatenulatum in the infant population. Below, bar plots represent the 12–24-months gender-specific stability of the bifidobacterial strains, expressed as the percentage of (infant) females and males showing after-weaning persistence of the same bifidobacterial strains identified at 0–6 months. Statistically significant gender-related differences were highlighted with an asterisk on the top of the columns (Fisher test, p-value = 0.006 and p-value = 0.005). Panel (b) refers to the inspection of the whole B. longum subsp. longum strain communities in female and male infants. Each pair of bar plots shows the number of strains identified in the pre-weaning (left) and post-weaning phase (right). Different colors highlight the number of B. longum subsp. longum strains found only in pre-weaning age (light blue), only in the post-weaning phase (light green), and shared between pre- and post-weaning time-point (pink). Panel (c) depicts the statistically significant difference in an estimated relative abundance (obtained by normalizing the genome coverage on the corresponding genome length) of persistent (n = 83, light blue) and non-persistent (n = 171, orange) B. longum subsp. longum strains in the infant post-weaning time points (Mann–Whitney test, p-value = 0.001). The boxes are determined by the 25th and 75th percentiles. The whiskers are determined by 1.5 interquartile range (IQR). The line in the boxes represents the median, while the cross marker (X) represents the average. In panel (d), the Venn diagram on the left highlights the 14 genes shared by B. longum subsp. longum and B. bifidum, while bar charts on the right-side report the prevalence of each PDC in publicly available complete genomes B. longum and B. bifidum.