Fig. 2

Phylogenetic assignment and relative quantification of microbiome metatranscriptome. a Clusters of microbial species obtained by determining an optimal number of clusters using fviz_nbclust from the ‘factoextra’ package with the gap statistic method and performing clustering using tsclust with shape-based distance (SBD), which makes the clustering particularly useful for time series where the shape matters more than exact numerical values. Clusters are standardized to log2 fold-change of abundance. Colors and cluster numbers are arbitrary. The actual composition of the different clusters is presented in Table 

S1. b Profiles of abundance of the periodontopathogens Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, and Fusobacterium nucleatum. c Temporal LEfSe analysis showing the distribution of taxonomic lineages within different samples at different time points as determined by linear discriminant analysis (LDA) effect size (LEfSe). Only taxons with LDA scores higher than two are shown