Article Figures & Data
Figures
- FIG 1
The aerodigestive tract. Schematic of the flow relationship between the oral and nasal cavities and the lungs and stomach. The numbers indicate the five sites sampled in this study.
- FIG 2
(A) Intrasubject similarity indices (θYC distance [1 − θYC]) between the bacterial communities of the first return BAL fluid (BAL1) and oral wash samples, compared to the second return BAL fluid (BAL2) and oral wash samples from that same subject. Distances were based on a 3% OTU definition with subsampling of 700 sequences/sample. There was no statistically significant difference in the oral-BAL fluid sample comparison of the first and second return BAL fluid samples in terms of bacterial community composition. (B) 16S rRNA gene qPCR of DNA prepared from the samples in this study, as well as bronchoscope rinse saline and prebronchoscope saline. The number of copies of bacterial 16S rRNA genes per 5 ml of sample (saline, scope, BAL, oral, and gastric) or per (nasal) swab was measured by qPCR as described in Materials and Methods. Sample groups were compared by ANOVA and Tukey's multiple-comparison test. Data are the mean ± the standard error of the mean. *, P < 0.05 compared to saline only; other significant comparisons are shown in the graph; nd, not done (because the swab was of a different sample type). (C) Bacterial species richness of each site, as determined by calculating the number of OTUs (97% identity) per sample after subsampling of all samples to the same depth of 700 reads. Sample groups were compared by ANOVA and Tukey's multiple-comparison test.
- FIG 3
(A, B) Graphic representation of the results of an RDA of the bacterial samples isolated from each of the four sites to determine whether a significant amount of the variation can be explained by differences in sample location. (A) Comparison of nasal, oral, and lung samples in RDA1 versus RDA2. (B) Comparison of nasal, oral, and gastric samples on RDA1 versus RDA2. (C) Indices of intrasubject similarity (θYC distance [1 − θYC]) between the bacterial communities of the two source sites (mouth and nose) and two target sites (lungs and stomach) of that subject. As shown, shorter θYC distances correspond to greater similarities between the bacterial communities of the samples indicated. Distances were based on a 3% OTU definition with subsampling of 700 sequences/sample.
- FIG 4
Rank abundance plots for each of the sampling locations based on the top 50 OTUs from the overall order (greatest to smallest) taken from all of the samples combined. The bars depict the mean ± the standard error of the mean. Bars are colored according to their phyla. The family, genus, and OTU identification of the bacterial community members are displayed along the x axis of panel D.
- FIG 5
Paired analysis of Prevotella abundance distribution in the oral wash of an individual and the abundance of that same OTU in the gastric aspirate (A) and BAL fluid (B) of the same individual. Prevotella OTUs were determined as described in Materials and Methods, and all of the samples from all of the sites were subsampled to 700 reads. For this analysis, any OTU below the limit of detection was assigned an abundance of 0.07%. The solid line indicates a 1:1 ratio of abundance in the oral wash compared to the gastric aspirate (A) or BAL fluid (B), and the dotted lines are 2:1 and 1:2 ratios. Six Prevotella OTUs were detected in the analysis, and the abundance of each OTU in each of the 28 subjects is displayed on the graphs (168 data points/graph). The oral-BAL fluid sample and oral-gastric sample data sets were significantly different from each other (P = 0.003). The mean ratio within the oral-gastric sample data set was 1.18:1, while the mean ratio within the oral-BAL fluid sample data set was 2.04:1. Other abundance comparisons: 11.4% of the observations in the oral-BAL fluid sample data set were at a ratio of 64:1 or greater, and 31.0% were at 8:1 or higher, while only 2.4% of the observations in the oral-gastric sample data set were 64:1 or greater and only 14.3% were 8:1 or greater.
Tables
- TABLE 1
Statistical significances of differences between sample types
Comparison AMOVAa PERMANOVAb RDAc Overall model <0.001 0.001 0.005 BAL1 vs BAL2 0.963 0.967 BAL1 vs oral <0.001 0.001 BAL2 vs oral 0.001 0.001 BAL1 vs nasal <0.001 0.001 BAL2 vs nasal <0.001 0.001 BAL1 vs gastric 0.001 0.003 BAL2 vs gastric 0.011 0.006 BAL vs oral 0.001 0.001 BAL vs nasal <0.001 0.001 BAL vs gastric 0.002 0.013 Oral vs nasal <0.001 0.001 Oral vs gastric 0.016 0.002 Nasal vs gastric <0.001 0.001 RDA1 (1st axis) 0.005 RDA2 (2nd axis) 0.005 RDA3 (3rd axis) 0.025 - TABLE 2
Study subject demographics
Parameter Value Total no. 28.0 No. of females/males 19/9 No. (%) who never smoked 20.0 (71.4) No. (%) of current smokers 4.0 (14.3) No. (%) of former smokers 4.0 (14.3) FEV1% range (mean ± SD 59.0–120.0 (102.0 ± 17.7)
