Abstract 1163: Lung and salivary microbiome in electronic cigarette users, never-smokers, and smokers: A pilot cross-sectional study
Authors: Ying Kevin L. , Song Min-Ae , Weng Daniel Y. , Nickerson Quentin A. , McElory Joseph P. , Brasky Theodore M. , Whiteman Noah B. , Wewers Mark D. , Freudenheim Jo L. , Mathé Ewy A. , Shields Peter G. 
Published: September 2020

Abstract
Background: Little is known about the microbiomes of the lung and oral cavity with electronic cigarette (e-cig) use and how they compare to those of smokers and never-smokers. E-cigs have been promoted as a safe alternative to smoking cigarettes. Given the recent outbreak of E-cigarette or Vaping product use Associated Lung Injury (EVALI) there is an urgent need for understanding the biological effects of e-cig use on the lung and oral cavity, including effects on the microbiome. Previous studies have been limited to 16S-rRNA sequencing which were used to detect bacteria genera. In this study, we used metatranscriptome profiling to study differentially abundant bacteria species in the oral and lung microbiome of never-smokers, smokers, and e-cig users.
Methods: A cross-sectional study of 10 never-smokers, 8 cigarette smokers, and 10 e-cig users was conducted, with saliva and bronchoalveolar lavage (BAL) collected for each study participant. RNA was extracted from saliva and BAL samples for total transcriptome RNA-seq analysis. Sequences were aligned with bowtie2 v.2.2.8 to the human genome (hg19) and non-aligned reads were aligned and annotated using NCBI metagenomes database and Kraken v.1. Differences in the microbiome by smoking status were determined by pairwise comparisons using limma-voom with FDR q-value cutoffs &lt;0.2.
Results: The distribution of richness and evenness of bacterial communities measured by Shannon diversity in our metatranscriptome data did not significantly differ between the three smoking status groups. When comparing levels of bacteria species between groups in the saliva, 234 were differentially abundant between smokers and never-smokers, and 39 were differentially abundant between smokers and e-cig users. In the lung, 87 bacterial species were differentially abundant between smokers and never-smokers and 36 were differentially abundant between smokers and e-cig users. Notably, no bacteria species were differentially abundant when comparing e-cig users and never-smokers in both the saliva and lung samples. There are 50 bacterial species found to be differentially abundant in both the lung and saliva samples, 47 of which are decreased in smokers. These 47 bacteria species included common commensal oral microbiome species such as Haemophilus parainfluenzae, Capnocytophaga gingivalis and Neisseria species. The 3 species that were increased in smokers were Lactobacillus species.
Conclusion: Our findings suggests that smoking cigarettes may alter populations of common commensal species in both the oral and lung microbiome. The lack of differentially abundant bacterial species between electronic cigarette users and never-smokers indicates that e-cigs may alter bacterial species to a lesser extent than smoking.
Citation Format: Kevin L. Ying, Min-Ae Song, Daniel Y. Weng, Quentin A. Nickerson, Joseph P. McElory, Theodore M. Brasky, Noah B. Whiteman, Mark D. Wewers, Jo L. Freudenheim, Ewy A. Mathé, Peter G. Shields. Lung and salivary microbiome in electronic cigarette users, never-smokers, and smokers: A pilot cross-sectional study [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1163.