Additional file 1. Community States are Consistent between Datasets. Deblurred data from the staging study and GBS colonization study were merged and rarified to 500 sequences per sample. Merged data was clustered by community state with Ward’s linkage of Euclidean distances (silhouette score 0.659, sklearn). Bacterial abundances are indicated by heatmap intensity corresponding to the colorbar ranging from purple to yellow

Additional file 2. Rarefaction Curves for Estrous Staging Experiment. Curves were generated with QIIME2 to calculate Observed OTUs alpha diversity for samples with contaminant, mitochondria, and chloroplast reads removed. Samples with less than 500 reads are not depicted in these images.

Additional file 3. GBS CFU is only recovered in mCST VI mice on Day 21. Tissue CFU/g on days 14 (top) and 21 (bottom) grouped according to mCST classification.

Additional file 4. Murine Study Design (a) Study 1: Estrous Cycle staging experiment, (b) Study 2: GBS Pathogen Challenge experiment. Mouse image is an open source image taken from Pixabay.