Additional file 1: Table S1. of Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection

Estimates from a linear mixed model comparing taxa abundance between COPD+ and COPD− samples. Fold change estimates and basic statistics of several OTUs comparing COPD+ and COPD− samples 20 days after infection. In the linear mixed model, we accounted for individual monkey effects, days sampled, and included normalization factors. We filtered OTUs to those with at least 100 counts and declared OTUs significant if lower and upper log fold change estimates agreed in directionality. Row colors represent enrichment, green in COPD− and red in COPD+ samples. Table S2 Smoothing Spline ANOVA estimates comparing COPD+ and COPD− taxa abundances through time. Smoothing Spline ANOVA estimates of the difference in genera abundances between COPD+ and COPD− groups through time. To test for differentially abundant time intervals, we fit a smoothing spline and calculated 95 % Bayesian confidence intervals under the SSANOVA framework. The SSANOVA procedure also included time, obstruction status and their interaction. We estimate significance using a permutation procedure and calculate significance with area under the curve as our test statistic. Row colors represent enrichment, green in COPD− and red in COPD+ samples. (XLSX 52 kb)