Comparative analysis of the bronchoalveolar microbiome in Portuguese patients with different chronic lung disorders

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The lung is inhabited by a diverse microbiome that originates from the oropharynx by a mechanism of micro-aspiration. Its bacterial biomass is usually low; however, this condition shifts in lung cancer (LC), chronic obstructive pulmonary disease (COPD) and interstitial lung disease (ILD). These chronic lung disorders (CLD) may coexist in the same patient as comorbidities and share common risk factors, among which the microbiome is included. We characterized the microbiome of 106 bronchoalveolar lavages. Samples were initially subdivided into cancer and non-cancer and high-throughput sequenced for the 16S rRNA gene. Additionally, we used a cohort of 25 CLD patients where crossed comorbidities were excluded. Firmicutes, Proteobacteria and Bacteroidetes were the most prevalent phyla independently of the analyzed group. Streptococcus and Prevotella were associated with LC and Haemophilus was enhanced in COPD versus ILD. Although no significant discrepancies in microbial diversity were observed between cancer and non-cancer samples, statistical tests suggested a gradient across CLD where COPD and ILD displayed the highest and lowest alpha diversities, respectively. Moreover, COPD and ILD were separated in two clusters by the unweighted UniFrac distance (P value = 0.0068). Our results support the association of Streptoccocus and Prevotella with LC and of Haemophilus with COPD, and advocate for specific CLD signatures.
This work was supported by Norte Portugal Regional Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (FEDER)—project NORTE-01-0145-FEDER-000029. This work was also financed by FEDER funds through COMPETE 2020 (Operacional Programme for Competitiveness and Internationalization— POCI) and by private funds through the Young Investigator Prize Francisco Augusto da Fonseca Dias and Maria José Melenas da Fonseca Dias to P.I.M. FCT supports P.I.M. through a post-doctoral fellowship (SFRH/BPD/120777/2016), financed by the Portuguese State Budget of the Ministry for Science, Technology and High Education and from the European Social Fund (Programa Operacional do Capital Humano—POCH). M.P-L was partially supported by FCT under the Programa Operacional Potencial Humano—Quadro de Referência Estratégico Nacional funds from the European Social Fund and Portuguese State Budget of the Ministry for Science, Technology and High Education (IF/00764/2013; RX: IF/00359/2015).