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Background  The microbiota of the lower respiratory tract in patients with non-tuberculous mycobacterial pulmonary disease (NTM-PD) has not been fully evaluated. We explored the role of the lung microbiota in NTM-PD by analyzing protected specimen brushing (PSB) and bronchial washing samples from patients with NTM-PD obtained using a flexible bronchoscope.    Results  Bronchial washing and PSB samples from the NTM-PD group tended to have fewer OTUs and lower Chao1 richness values compared with those from the control group. In both bronchial washing and PSB samples, beta diversity was significantly lower in the NTM-PD group than in the control group ( P  = 2.25E-6 and  P  = 4.13E-4, respectively). Principal component analysis showed that the PSBs and bronchial washings exhibited similar patterns within each group but differed between the two groups. The volcano plots indicated differences in several phyla and genera between the two groups.    Conclusions  The lower respiratory tract of patients with NTM-PD has a unique microbiota distribution that is low in richness/diversity.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12866-021-02141-1.

The lung microbiota in Korean patients with non-tuberculous mycobacterial pulmonary disease