Fig. 3

Temporal microbial community dynamics in the oral cavity. A Relative abundances over time of the 12 most abundant families in the oral cavity. B Tree-based sparse linear discriminant analysis (LDA). Coefficients of discriminating clades of ASVs on the first LDA axis, colored by taxonomic family, and plotted along the phylogenetic tree. C Trajectories of ASVs affiliated with the families Actinomycetaceae, Streptococcaceae, Prevotellaceae, and Family XI (Class Bacillales), with decreasing abundances after HSCT and recovery at late follow-up time points. The most abundant discriminating ASV for each family is indicated. Detailed taxonomic information and LDA coefficients of the displayed ASVs are listed in Additional File 1: Table S2. D PCA biplots with the top 100 predictors (ASVs) identified by PCA (left) and the top predictors (ASVs) identified by sparse LDA (right). The time points are indicated in the same color as in Fig. 1C (phase I: yellow colors; phase II: red colors; phase III: blue colors). The PCA plots with dimensions 1 and 2 are displayed here, and additional PCA plots are available from https://doi.org/10.6084/m9.figshare.14510661