Fig. 3

Community types found in the lung microbiota. a Alpha diversity. p values from Wilcoxon rank sum tests are included. The alpha diversities of community types B and C were overall significantly lower (p value = 2.2e-16) than those of community types A and D. b Relative abundance of taxa over-represented in each community type. Letters appended before names indicate whether the taxonomic assignment was made at the class (c_), order (o_), family (f_), or genus (g_) level. c tSNE, colored by community types. d Community type that predominates in each monkey at each time point. Triangles represent radiographic evidence of lung pathology (i.e., a granuloma or other grossly visible disease at a resolution of 1 mm by CT) that coincide with microbiome sampling at the indicated time point. From top to bottom (arrow), monkeys were ordered, low to high, by the log transformed total [¹⁸F]-FDG activity at 4–5 months. Xs indicate samples not collected; white (blank) boxes indicate that the sequence depth was not sufficient for analysis (fewer than 1000 sequence reads) and so the sample was not included