Pulmonary Microbiome: Analysis Of Microbial Diversity In Lung Cancer

The lungs, despite constant interaction with the environment, have classically been defined as sterile. Analysis of the microbiome, the community of organisms that live in and on us, is an emerging area of discovery. The advent of culture independent high throughput sequencing technology reveals abundant and diverse microbial communities in the lower respiratory tract. Development of cancer has been associated with genetic and environmental factors including bacterial and viral agents. However, the association between the pulmonary microbiome and tumorogenesis is not well defined. Our objective is to investigate the microbial diversity in lung neoplasms compared to pulmonary inflammation and healthy controls. Methods: Bronchoalveolar lavage (BAL) samples were acquired utilizing standard fiberoptic bronchoscopy technique. Aliquots of the BAL samples were obtained and bacterial DNA was extracted. Metagenomic data was examined utilizing culture and cloning free methods with paired-end sequencing with the Illumina MiSeq® system. Further analysis of microbial communities was performed by CLC Genomics Workbench ® and the metagenomics RAST server. Results: Microbiomes obtained from BAL samples of subjects with pulmonary malignancy (n=2) and one healthy control were compared at the phylum level. Consistent with a prior report of healthy lung bacterial communities by Erb-Downard et al. (2011), our control demonstrated abundance of Proteobacteria (20%) and Firmicutes (20%) and, to a lesser extent, Bacteriodetes (8%) and Actinobacteria (8%). Phyla richness was lower in malignancy. Phyla diversity of the communities based on Shannon-Wiener Index effective number demonstrated that the malignancies were only 55 and 65% as diverse as the healthy control. Compared to each other, the pulmonary malignancies were 84% as diverse. A trend towards increased percentage of Proteobacteria and a reduction in the amount of Firmicute communities was observed in both cancer samples. Also, the presence of fungal colonies was decreased in the healthy control (12%) compared to both malignancies (17% and 22%). Both pulmonary malignancy samples had high counts of uncultured bacterial DNA and in one it was the most frequently encountered microbial sequence. Conclusions: Our results suggest that a decreased microbial diversity with a shift favoring a predominance of Proteobacteria in the pulmonary microbiome may be associated with malignancy. Further depiction of the microbiome in lung cancer is necessary; the role of uncultured species has yet to be characterized.