Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features

Abstract

Background: The human lung tissue microbiota remains largely uncharacterized, although a number of studies based on airway samples suggest the existence of a viable human lung microbiota. Here we characterized the taxonomic and derived functional profiles of lung microbiota in 165 non-malignant lung tissue samples from cancer patients.

Results: We show that the lung microbiota is distinct from the microbial communities in oral, nasal, stool, skin, and vagina, with Proteobacteria as the dominant phylum (60 %). Microbiota taxonomic alpha diversity increases with environmental exposures, such as air particulates, residence in low to high population density areas, and pack-years of tobacco smoking and decreases in subjects with history of chronic bronchitis. Genus Thermus is more abundant in tissue from advanced stage (IIIB, IV) patients, while Legionella is higher in patients who develop metastases. Moreover, the non-malignant lung tissues have higher microbiota alpha diversity than the paired tumors.

Conclusions: Our results provide insights into the human lung microbiota composition and function and their link to human lifestyle and clinical outcomes. Studies among subjects without lung cancer are needed to confirm our findings.

Keywords: 16S rRNA; Air pollution; Tumor stage.

Fig. 1

Taxonomic and functional profiles of non-malignant lung tissue microbiota. a Phylum-level taxonomic profiles. b Genus-level taxonomic profiles. c Kyoto Encyclopedia of Genes and Genomes (KEGG) module-level functional profiles. Each vertical bar represents a unique sample. Samples were ordered by anatomical sites shown below the figure. The y-axis shows the relative abundance of each phylum/genera/module. The average relative abundance (percentage) is shown in parentheses after each taxon or module. Only the most common taxa or modules are shown

Fig. 2

Comparison of microbiotas from non-malignant lung tissue and other human body sites (HMP 16S V3–V5 phase 1 data). a, b Principal coordinates analysis (PCoA) of Euclidean distance of phylum-level taxonomic profiles (a) and KEGG module functional profiles (b). The proportion of variance explained by each principal component is denoted in the corresponding axis label. c, d Phylum-level taxonomic profiles (c) and KEGG module functional profiles (d) by body site. The dendrogram shows similarity by body site based on the Euclidean distance of phylum-level/KEGG module profiles (average by body sites). Only phyla/modules with relative abundance >1 % are shown. Branch colors show different body sites (blue, oral, lung, and stool; black, nasal and skin; purple, vagina). “H” and “L” indicate that lung is significantly higher or lower, respectively, in relative abundance of the designated phylum/module compared with all the other body sites’ samples combined (P < 0.05 by Wilcoxon test with Bonferroni correction)

Fig. 3

Non-malignant lung tissue microbiota in relation to participants’ residential areas (a), particulate matter 10 micrometers in diameter (PM₁₀) at enrollment (b) and tumor stage (c). The P values shown in a and c are based on Kruskal–Wallis tests but were also validated in an adjusted linear regression model (model with residential area, history of chronic bronchitis, and tumor stage). The P values in b are based on a linear regression model with PM₁₀, history of chronic bronchitis, and tumor stage in the model. The asterisks in a indicate areas significantly different from the overall mean. Proteobacteria for residential areas and air pollution and Thermus for tumor stage are the only taxa that showed significant association according to both an adjusted linear regression model and a Kruskal–Wallis test with Bonferroni correction

Fig. 4

Comparison of non-malignant (N) and tumor (T) tissue microbiotas. a Non-malignant and tumor tissue microbiotas significantly differ in taxonomic alpha diversity. The P value was computed by the signed rank Wilcoxon test based on paired samples and was also confirmed by the bootstrap analysis (see “Statistical methods”) of all paired and unpaired samples (P < 0.001). b Comparison of microbiota by tumor morphology in non-malignant and tumor tissues. Taxonomic alpha diversity (PD_whole_tree) is statistically significantly higher in patients with adenocarcinoma in microbiota from the tumor samples but not from non-malignant samples. P values are based on Wilcoxon tests