Fig. 2

a Core microbiome heatmaps showing abundance of taxa and prevalence across samples at baseline and at each time point, providing a measure of the lung microbiota dynamics in the progression of Mtb infection. Highlighted in red are some of the taxa that change significantly over the course of the infection. Letters appended before names indicate whether the taxonomic assignment was made at the phylum (p_), class (c_), order (o_), family (f_), or genus (g_) level. b Boxplots of relative abundance of significant taxa enriched in the lung airways at baseline and at month 4. Significance was determined by LefSE. Whiskers indicate the highest or lowest occurring value within 1.5*IQR (interquartile range) of the upper or lower quartile