Bacterial lineages enriched in BAL samples identified after replicate sampling of each subject.

OTUs were identified as significant outliers after controlling for a false discovery rate (FDR) of 5%. The same OTUs were rarely identified in pairwise comparisons when controlling for an FDR of 5% (column 8). When no FDR adjustment was made, the OTUs were often identified in pairwise comparisons (p<0.05, column 9). Under these circumstances, however, several additional OTUs were identified in pairwise comparisons that did not achieve significance in the analysis of replicate sampling (column 10).