The lung microbiota in nontuberculous mycobacterial pulmonary disease

Bo-Guen Kim; Noeul Kang; Su-Young Kim; Dae Hun Kim; Hojoong Kim; O Jung Kwon; Hee Jae Huh; Nam Yong Lee; Byung Woo Jhun

doi:10.1371/journal.pone.0285143

The lung microbiota in nontuberculous mycobacterial pulmonary disease

PLoS One. 2023 May 26;18(5):e0285143. doi: 10.1371/journal.pone.0285143. eCollection 2023.

Authors

Bo-Guen Kim¹, Noeul Kang¹, Su-Young Kim¹, Dae Hun Kim¹, Hojoong Kim¹, O Jung Kwon¹, Hee Jae Huh², Nam Yong Lee², Byung Woo Jhun¹

Affiliations

¹ Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
² Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.

Abstract

Background: The role of bacterial microbiota in the pathogenesis of nontuberculous mycobacterial pulmonary disease (NTM-PD) is unclear. We aimed to compare the bacterial microbiome of disease-invaded lesions and non-invaded lung tissue from NTM-PD patients.

Methods: We analyzed lung tissues from 23 NTM-PD patients who underwent surgical lung resection. Lung tissues were collected in pairs from each patient, with one sample from a disease-involved site and the other from a non-involved site. Lung tissue microbiome libraries were constructed using 16S rRNA gene sequences (V3-V4 regions).

Results: Sixteen (70%) patients had Mycobacterium avium complex (MAC)-PD, and the remaining seven (30%) had Mycobacterium abscessus-PD. Compared to non-involved sites, involved sites showed greater species richness (ACE, Chao1, and Jackknife analyses, all p = 0.001); greater diversity on the Shannon index (p = 0.007); and genus-level differences (Jensen-Shannon, PERMANOVA p = 0.001). Analysis of taxonomic biomarkers using linear discriminant analysis (LDA) effect sizes (LEfSe) demonstrated that several genera, including Limnohabitans, Rahnella, Lachnospira, Flavobacterium, Megamonas, Gaiella, Subdoligranulum, Rheinheimera, Dorea, Collinsella, and Phascolarctobacterium, had significantly greater abundance in involved sites (LDA >3.00, p <0.05, and q <0.05). In contrast, Acinetobacter had significantly greater abundance at non-involved sites (LDA = 4.27, p<0.001, and q = 0.002). Several genera were differentially distributed between lung tissues from MAC-PD (n = 16) and M. abscessus-PD (n = 7), and between nodular bronchiectatic form (n = 12) and fibrocavitary form (n = 11) patients. However, there was no genus with a significant q-value.

Conclusions: We identified differential microbial distributions between disease-invaded and normal lung tissues from NTM-PD patients, and microbial diversity was significantly higher in disease-invaded tissues.

Trial registration: Clinical Trial registration number: NCT00970801.

Copyright: © 2023 Kim et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Humans
Lung
Lung Diseases* / microbiology
Microbiota* / genetics
Mycobacterium Infections, Nontuberculous* / microbiology
Mycobacterium avium Complex
Nontuberculous Mycobacteria / genetics
RNA, Ribosomal, 16S / genetics

Substances

RNA, Ribosomal, 16S

Associated data

ClinicalTrials.gov/NCT00970801

Grants and funding

This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (2020R1C1C1008038). The funders were not involved in study design, data collection and analysis, decision to publish, or manuscript preparation.