Differences in female gut microbiome based on supplementation. (A) Principal coordinate analysis (PCoA) of female pups’ microbiome samples was done at different time points: P21, P30, and P70. At P21, the control group microbiomes separated from Lactobacillus‐supplemented groups (p = 0.056). L. reuteri, L. johnsonii, and control groups progressively separated with aging (P30; p = 0.017 and P70; p = 0.001). By P70, L. reuteri supplemented female pups separated from L. johnsonii and control groups. (B) Comparisons of the female pups’ microbiomes were done at the genus level. The top 10 genera of microbial differences between L. reuteri, L. johnsonii, and control groups are shown at each time point. For P21, Muribaculum (p = 0.0038) and Ruminiclostridium (p = 0.0314) were the only genera with significant separation as p < 0.05. For P30, Lachnoclostridium (p = 0.0087), Muribaculum (p = 0.0131), and Tyzzerella (p = 0.0491) were significant. Finally, at P70, eight out of the top 10 genera separated significantly [Colour figure can be viewed at wileyonlinelibrary.com]