The composition of the lung microbiome differs between patients with dermatomyositis and rheumatoid arthritis associated with interstitial lung disease.

Dermatomyositis and rheumatoid arthritis are inflammatory diseases which affect the skeletal muscles and joints, respectively. A common systemic complication of these diseases is interstitial lung disease (ILD) which leads to poor prognosis and increased mortality. However, the mechanism for initiation and development of ILD in patients with dermatomyositis is currently unknown. In this study, we used 16S rRNA high-throughput sequencing to profile the bacterial community composition of bronchoalveolar lavage fluid (BALF) of patients with dermatomyositis associated with ILD (DM-ILD, shortened to DM below), rheumatoid arthritis associated with ILD (RA-ILD, shortened to RA below) and healthy controls (N) to understand the differences in their lung microbiota and to predict gene function. We found that there were more operational taxonomic units (OTUs) in the lung microbiota of both RA and DM, compared to N, but there was no significant difference in the number of OTUs between RA and DM. Similarly, the diversity in alphaproteobacteria differed between RA and DM compared to N, but not between RA and DM. The lung microbiota of RA, DM, and N was mainly comprised of five phyla: Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria and 10 dominant genera. Despite the similarity in microbiota composition, we also identified 41 OTUs of lung microbiota that differed among RA, DM, and N. Additionally, linear discriminant analysis effect size (LEfSe) and linear discriminant analysis genus scores confirmed that 31 microbial biomarkers were clearly distinguished among RA, DM, and N. The functional and metabolic alterations of the lung microbiota among RA, DM, and N were predicted using PICRUSt, and differentially abundant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified. Research on the lung microbiota of patients with DM and RA may open new opportunities to develop biomarkers to identify high-risk patients.