Fig. 4

Clustering of mouse gut microbiomes. A Heatmap and dendrogram of unsupervised hierarchical clustering of metagenomic samples using relative abundance of MAGs. Rows and columns represent MAGs and samples, respectively. Black boxes highlight MAGs showed significant changes between littermates from different mother mice. Red box highlights MAGs that differentiated gut microbiome of mouse S^*. B PCA of metagenomic samples using relative abundance of MAGs. C Heatmap and dendrogram of unsupervised hierarchical clustering of metaproteomic samples using quantitative community profiles (as measured by consensus spectrum \(SI_{N}\)). Each column corresponds to a sample and each row represents \(SI_{N}\) of the consensus spectrum across samples. D PCA of metaproteomic samples using consensus spectrum \(SI_{N}\). Sample name with and without asterisk indicates littermates of mother mouse 207H and 189C, respectively. Clustering and PCA results based upon consensus spectrum \(SI_{N}\) clearly shows microbial changes of the mouse gut microbiome over time; metaproteomic samples collected at the first time point form one cluster (P1) and split into two different clades (P2 and P3) throughout the period of sampling