Fig. 5

Taxonomic distribution in procedural samples when different approaches to dealing with contamination have been applied. When negative control sample (NCS) operational taxonomic units (OTUs) are kept, the Streptococcus genus dominated the procedural samples with an average relative abundance of 31.66% in oral wash (OW) (n = 23), 27.95% in protected bronchoalveolar lavage (PBAL) (n = 23) and 22.27% in protected specimen brushes (PSB) (n = 23). With the removal of NCS OTUs, the Streptococcus genus no longer dominated the procedural samples and was present at an average relative abundance of 4.80% in OW (n = 23), 6.12% in PBAL (n = 23) and 7.60% in PSB (n = 23). With the removal of OTUs identified as contaminants in Decontam (method = “either”, threshold = 0.5), the Streptococcus genus again dominated the samples, with an average relative abundance of 32.52% in OW (n = 23), 34.40% in PBAL (n = 23) and 35.08% in PSB (n = 23). Taxonomic rank is described using prefixes (c__: class, o__: order, f__: family, g__: genus). Data unrarefied